A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ 

A

A - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
accept(File, String) - Method in class edu.dartmouth.bglab.beam.PhiScoreDriver.SuffixFilter
Returns true if the filename is of the propert type; the directory is ignored.
accept(File) - Method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.AffinityFileFilter
 
accept(File) - Method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.SiteFileFilter
 
ACGTRY - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ACGTRY_ARRAY - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ACGTRY_BIN_ARRAY - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ACGTRY_BIN_INDICES - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ACGTRY_COMPLEMENT - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ACGTRY_EXPANSION - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ACGTRY_ID - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ACGTRY_INDICES - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ACGTRY_SUPERSETS - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
add(Motif) - Method in class edu.dartmouth.bglab.motif.MotifList
 
add(FindResults) - Method in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
add(Motif) - Method in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
add(FindResults) - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
add(Motif) - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
add(AveStatBox) - Method in class edu.dartmouth.bglab.util.AveStatBox
Merges the results of this AveStatBox and the given AveStatBox.
add(double) - Method in class edu.dartmouth.bglab.util.AveStatBox
Adds val to this running average and standard deviation.
add(StatBox) - Method in class edu.dartmouth.bglab.util.AveStatBox
Adds the value of the StatBox to this AveStatBox.
add(StatBox) - Method in class edu.dartmouth.bglab.util.FPFNStatBox
Returns a new FPFNStatBox whose variables are the sums of the variables of this stat box and the given stat box.
add(Object) - Method in class edu.dartmouth.bglab.util.Heap
Adds the object to the heap.
add(double) - Method in class edu.dartmouth.bglab.util.Histogram
Adds a new occurrence in the bin that the given value bins to.
add(StatBox) - Method in class edu.dartmouth.bglab.util.LinCorrStatBox
Adds the points from the given box to this box.
add(StatBox) - Method in interface edu.dartmouth.bglab.util.StatBox
Allows two StatBoxes to be added, whatever that means for a given StatBox.
addBase(char, boolean) - Method in class edu.dartmouth.bglab.motif.Motif
Returns a motif with a base added in the specified direction; direction should be set to Motif.LEFT or Motif.RIGHT.
addHitsUsingBestMethod(Collection<Integer>, MotifFinder, Motif, Matcher) - Static method in class edu.dartmouth.bglab.search.MotifFinder
 
addHitsUsingBothEnds(Collection<Integer>, MotifFinder, Motif, Matcher) - Static method in class edu.dartmouth.bglab.search.MotifFinder
 
addHitsUsingOneEndAndRegex(Collection<Integer>, MotifFinder, Motif, Matcher) - Static method in class edu.dartmouth.bglab.search.MotifFinder
 
addHitsUsingRegex(Collection<Integer>, MotifFinder, Motif) - Static method in class edu.dartmouth.bglab.search.MotifFinder
 
addMotif(GeneMapImageDrawer.Motif, int) - Method in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Gene
 
addMotif(ServerSocketImageWriter.Motif, int) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Gene
 
addPoint(double, double) - Method in class edu.dartmouth.bglab.util.LinCorrStatBox
Adds a the poitn (x,y) to the list of point in consideration for correlation, as long as both x and y are non-inifinite.
addScorer(Scorer) - Method in class edu.dartmouth.bglab.score.CombinedScorer
Adds the scorer to this CombinedScorer, and sets the use prior variable to false.
AFFINITY_FILE_SUFFIX - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
AffinityEvaluator - Class in edu.dartmouth.bglab.model
Methods to evaluate a CREModel on affinity data.
AffinityEvaluator() - Constructor for class edu.dartmouth.bglab.model.AffinityEvaluator
 
AffinityEvaluatorDriver - Class in edu.dartmouth.bglab.model
A driver for the AffinityEvaluator class.
AffinityEvaluatorDriver() - Constructor for class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
AffinityEvaluatorDriver.AffinityFileFilter - Class in edu.dartmouth.bglab.model
A file filter that accepts only affinity files.
AffinityEvaluatorDriver.AffinityFileFilter() - Constructor for class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.AffinityFileFilter
 
AffinityEvaluatorDriver.BackgroundEvalFunc - Class in edu.dartmouth.bglab.model
Just a special designation that this requires a background.
AffinityEvaluatorDriver.BackgroundEvalFunc() - Constructor for class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.BackgroundEvalFunc
 
AffinityEvaluatorDriver.EvaluatorFunction - Interface in edu.dartmouth.bglab.model
 
AffinityEvaluatorDriver.FPFNEvalFunc - Class in edu.dartmouth.bglab.model
 
AffinityEvaluatorDriver.FPFNEvalFunc() - Constructor for class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.FPFNEvalFunc
 
AffinityEvaluatorDriver.ROCEvalFunc - Class in edu.dartmouth.bglab.model
Only allows ProbCREModel's to be scored.
AffinityEvaluatorDriver.ROCEvalFunc() - Constructor for class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.ROCEvalFunc
 
AffinityEvaluatorDriver.SiteFileFilter - Class in edu.dartmouth.bglab.model
A file filter that accepts only site files and affinity files.
AffinityEvaluatorDriver.SiteFileFilter() - Constructor for class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.SiteFileFilter
 
AffinityEvaluatorDriver.TestModel - Class in edu.dartmouth.bglab.model
 
AffinityEvaluatorDriver.TestModel(String, CREModel) - Constructor for class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.TestModel
 
AggregatedFindResults - Class in edu.dartmouth.bglab.search
 
AggregatedFindResults(FindResults[]) - Constructor for class edu.dartmouth.bglab.search.AggregatedFindResults
 
aLetter - Static variable in class edu.dartmouth.bglab.beam.CGIDriver
 
alf - Variable in class edu.dartmouth.bglab.motif.Motif
 
ALF_ARRAY - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ALF_BIN_ARRAY - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ALF_BIN_INDICES - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ALF_COMPLEMENT - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ALF_EXPANSION - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ALF_INDICES - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
ALF_SUPERSETS - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
alfID - Variable in class edu.dartmouth.bglab.motif.Alphabet
 
algorithm - Variable in class edu.dartmouth.bglab.motif.Motif
 
allowUnforcedPrints - Static variable in class edu.dartmouth.bglab.util.Print
 
allowUnforcedPrints() - Static method in class edu.dartmouth.bglab.util.Print
Enables all of the print methods of this class except for the forcePrintln() and errln() methods.
allowUsePermanentCache - Static variable in class edu.dartmouth.bglab.search.MotifFinder.GenomeSoftValueHashMap
 
Alphabet - Class in edu.dartmouth.bglab.motif
Represents the set of bases that can be present in motifs.
Alphabet(int) - Constructor for class edu.dartmouth.bglab.motif.Alphabet
Creates an alphabet object for the specified alphabet; alphabetID should be set to one of the Alphabet.*_ID constants.
ambiguizeMotifs(Motif[], Scorer, UberProperties) - Static method in class edu.dartmouth.bglab.beam.Ambiguizer
This is the master method for Motif arrays.
Ambiguizer - Class in edu.dartmouth.bglab.beam
A general utilities class for ambiguizing motifs.
Ambiguizer() - Constructor for class edu.dartmouth.bglab.beam.Ambiguizer
 
AMBIGUIZER_NAME - Static variable in class edu.dartmouth.bglab.beam.BeamDriver
 
AmbiguizerTester - Class in edu.dartmouth.bglab.test
THIS CLASS IS DEPRICATED; IT NEEDS SOME WORK TO BE COMPILABLE AGAIN.
AmbiguizerTester() - Constructor for class edu.dartmouth.bglab.test.AmbiguizerTester
 
ambiguizerUnscoredMotif - Static variable in class edu.dartmouth.bglab.beam.Ambiguizer
 
ambiguousBaseCountOf(String, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
Returns the total number of ambiguous bases in the passed in sequence
ambiguousFactorOf(String, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
Returns the ambiguous factor of a sequence.
ambiguousMatch(char, char) - Static method in class edu.dartmouth.bglab.beam.CGIDriver
 
appendOnHamming(Motif[], int, boolean) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Performs a pairwise comparison on all the motifs and returns an array of MotifLists that are within maxHD of at least one other Motif.
appendToFile(Object, String) - Static method in class edu.dartmouth.bglab.io.FileWriters
Appends the toString() of the given object in the given file.
appendToProgressFile(Object) - Static method in class edu.dartmouth.bglab.io.FileWriters
If FileWriters.useProgressFile() is true, this will append s to the end of progressFile.
approximateExpansionSize() - Method in class edu.dartmouth.bglab.model.KMismatchModel
Returns an approximation of the number of strings of primary bases that this k-mismatch model represents.
areEquivalent(char, char) - Method in class edu.dartmouth.bglab.motif.Alphabet
Returns true if one of the chars is a subset of the other.
areOnSameGene(int, int) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns true if pos1 and pos2 are on the same gene, where pos1 <= pos2.
areProbabilities(double[]) - Static method in class edu.dartmouth.bglab.util.MoreMath
Calls MoreMath.areProbabilities(double[], double) with a default TOLERANCE of 0.
areProbabilities(double[], double) - Static method in class edu.dartmouth.bglab.util.MoreMath
Returns true iff each value in d is a probability in the range [0..1] and teh sum of the values of d are within TOLERANCE of 1.0.
argsFile - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
arr1 - Variable in class edu.dartmouth.bglab.score.MaximalMatcher
 
arr2 - Variable in class edu.dartmouth.bglab.score.MaximalMatcher
 
AssessmentDriver - Class in edu.dartmouth.bglab.beam
This driver is a simple wrapper around the basic BeamDriver; it outputs a file in the format required for the Tompa assessment.
AssessmentDriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.AssessmentDriver
Sets the file root, test ID, thread ID, properties, and scorer.
AssessmentDriver(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.AssessmentDriver
Sets the file root, test ID, thread ID, properties, and scorer; uses the specified group instead of pulling the group ID from the properties.
AUTO_TRAINING_SIZE - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
AveStatBox - Class in edu.dartmouth.bglab.util
Holds averages of other stat boxes and values.
AveStatBox() - Constructor for class edu.dartmouth.bglab.util.AveStatBox
 
avgLength() - Method in class edu.dartmouth.bglab.motif.MotifList
Returns the average length of the component motifs.

B

b - Variable in class edu.dartmouth.bglab.beam.web.StreamPipe
 
B - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
BACKGROUND - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
BackgroundDriver - Class in edu.dartmouth.bglab.beam
 
BackgroundDriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.BackgroundDriver
Sets the file root, test ID, thread ID, properties, and scorer.
BackgroundDriver(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.BackgroundDriver
Sets the file root, test ID, thread ID, properties, and scorer; uses the specified group instead of pulling the group ID from the properties.
backgroundFrequencies - Variable in class edu.dartmouth.bglab.score.ConservationICScorer
The background base frequencies in the motif finder.
BASE_KEY - Static variable in class edu.dartmouth.bglab.model.PWM
Tells which base is represented by each row in the pwm.
baseCount - Variable in class edu.dartmouth.bglab.search.MotifFinder
Number of bases in the sequence.
baseEntropy(char, Alphabet) - Static method in class edu.dartmouth.bglab.score.Scorer
 
BayesDeltaSig - Class in edu.dartmouth.bglab.beam
 
BayesDeltaSig(Motif, double, double, double, int, int, int) - Constructor for class edu.dartmouth.bglab.beam.BayesDeltaSig
 
bayesDeltaSigProbability - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
Beam - Class in edu.dartmouth.bglab.beam
Contains the beam and bipartite beam search method.
Beam() - Constructor for class edu.dartmouth.bglab.beam.Beam
 
BEAM_NAME - Static variable in class edu.dartmouth.bglab.beam.BeamDriver
 
BEAM_PACKAGE - Static variable in class edu.dartmouth.bglab.beam.BeamDriverFactory
 
BeamDriver - Class in edu.dartmouth.bglab.beam
Beam drivers are threads that can run beam, the ambiguizer, bipartite beam, and filters for a group of genes.
BeamDriver(String) - Constructor for class edu.dartmouth.bglab.beam.BeamDriver
Makes a beam driver, setting the thread ID and leaving the rest of initialization up to subclasses who want to be creative.
BeamDriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.BeamDriver
Makes a beam driver.
BeamDriver(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.BeamDriver
Makes a beam driver using the specified group instead of pulling the group ID from the properties; the group doesn't need to be sorted.
BeamDriver(String, UberProperties, MotifFinder, MotifFinder) - Constructor for class edu.dartmouth.bglab.beam.BeamDriver
 
BeamDriver(String, UberProperties, String[]) - Constructor for class edu.dartmouth.bglab.beam.BeamDriver
Makes a beam driver using the specified group instead of pulling the group ID from the properties; the group doesn't need to be sorted.
BeamDriverFactory - Class in edu.dartmouth.bglab.beam
This class builds BeamDrivers.
BeamDriverFactory() - Constructor for class edu.dartmouth.bglab.beam.BeamDriverFactory
 
beamDriverScoreDataSuffix - Static variable in class edu.dartmouth.bglab.beam.BeamDriver
 
BeamTester - Class in edu.dartmouth.bglab.test
For testing the .beam package.
BeamTester() - Constructor for class edu.dartmouth.bglab.test.BeamTester
 
beamUnscoredMotif - Static variable in class edu.dartmouth.bglab.beam.Beam
 
benchmark() - Static method in class edu.dartmouth.bglab.test.ScoreTester
 
bestChar(int[]) - Static method in class edu.dartmouth.bglab.model.PLConsensusModel
 
bestChars(int[]) - Static method in class edu.dartmouth.bglab.model.PLConsensusModel
Given a frequency vector f, returns those IUPAC chars over the FULL Alphabet that are closest to f.
bestUnionOf(char[], char[]) - Method in class edu.dartmouth.bglab.motif.Motif
Returns a sequence that is the length of seq1 and is the most unambiguous of all possible char-by-char unions between seq1 and seq2; ie.if one motif is longer than the other, a sliding window approach is used to try all possible matches.
BETA - Static variable in class edu.dartmouth.bglab.model.KRModel
 
beta - Variable in class edu.dartmouth.bglab.model.KRModel
 
bgProbs - Variable in class edu.dartmouth.bglab.model.KRModel
 
binIndexOf(int) - Method in class edu.dartmouth.bglab.motif.Alphabet
 
binItems(double[]) - Method in class edu.dartmouth.bglab.util.Histogram
Converts the values in each item into bin number.
Binnable - Interface in edu.dartmouth.bglab.util
An interface for creating histograms.
Binomial - Class in edu.dartmouth.bglab.util
A class for computing N choose K.
Binomial() - Constructor for class edu.dartmouth.bglab.util.Binomial
 
bins - Variable in class edu.dartmouth.bglab.util.Histogram
 
binValOf(char) - Method in class edu.dartmouth.bglab.motif.Alphabet
 
binWidth - Variable in class edu.dartmouth.bglab.util.Histogram
 
BiologicalBeamDriver - Class in edu.dartmouth.bglab.beam
Use this driver when you are running a biological test set and you know the motifs.
BiologicalBeamDriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.BiologicalBeamDriver
Sets the file root, test ID, thread ID, properties, and scorer.
BiologicalBeamDriver(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.BiologicalBeamDriver
Sets the file root, test ID, thread ID, properties, and scorer; uses the specified group instead of pulling the group ID from the properties.
BIPARTITE_INIT_CACHE_SIZE - Static variable in class edu.dartmouth.bglab.search.MotifFinder
When initializing bipartite cache, specifies the initial cache size.
BIPARTITE_INIT_LEN - Static variable in class edu.dartmouth.bglab.search.MotifFinder
When initializing bipartite cache, specifies the number of non N bases to initialize with.
BIPARTITE_INIT_N_COUNT_MAX - Static variable in class edu.dartmouth.bglab.search.MotifFinder
When initializing bipartite cache, specifies the max # of Ns to initialize with.
BIPARTITE_INIT_N_COUNT_MIN - Static variable in class edu.dartmouth.bglab.search.MotifFinder
When initializing bipartite cache, specifies the min # of Ns to initialize with.
BIPARTITE_NAME - Static variable in class edu.dartmouth.bglab.beam.BeamDriver
 
bipartiteLength(Motif) - Static method in class edu.dartmouth.bglab.beam.Beam
Returns the number of non-N characters in m.
bipartiteMotifPattern - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
blockUnforcedPrints() - Static method in class edu.dartmouth.bglab.util.Print
Disables all of the print methods of this class except for the forcePrintln() and errln() methods.
BOOT_STRAP - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
bootStrap(CREModel, MotifList, AffinityEvaluatorDriver.EvaluatorFunction, int, int) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
Likst crossValidate, only trainig sets are randomly chosen each time, independent of the last iteration.
boundedAverage(Binnable[]) - Static method in class edu.dartmouth.bglab.util.Histogram
Returns the mean and standard error of values.
bpScorer - Variable in class edu.dartmouth.bglab.beam.BeamDriver
 
buildBeamDriver(String, UberProperties) - Static method in class edu.dartmouth.bglab.beam.BeamDriverFactory
Creates a new BeamDriver of the specified type using the two argument constructor; the package name is automatically prepended to the beamDriverClassName, so don't include that!
buildBeamDriver(String, UberProperties, int[]) - Static method in class edu.dartmouth.bglab.beam.BeamDriverFactory
Builds the specified driver using the three-argument constructor; the package name is automatically prepended to the beamDriverClassName, so don't include that!
buildBeamDrivers(UberProperties, String) - Static method in class edu.dartmouth.bglab.beam.BeamDriverFactory
Builds a set of BeamDrivers, one for each group in the file groupsToUse, which must be in the GlobalParams GENE_LIST_FILE; the thread name of each group will be the key used to create the group.
buildCRE(CREModel, MotifList) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
Builds a CREModel form the given MotifList using CREModel.newInstanceOf(MotifList).
buildGroupMFFromFile(String, String, String, int, int[]) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Returns a motif finder with runtime type mfClassName that has discardOverlaps set to false and wildcard optimization turned off.
buildGroupScorer(String, MotifFinder, MotifFinder, boolean) - Static method in class edu.dartmouth.bglab.score.ScorerFactory
Builds the specified scorer using the specified MotifFinders.
buildGroupScorer(String, String, String, String, int, int[], boolean) - Static method in class edu.dartmouth.bglab.score.ScorerFactory
Builds the specified scorer using the specified MotifFinder class for both the group MotifFinder and the genome MotifFinder; only the class names should be specified, as the package name is added automatically; the group array doesn't need to be sorted.
buildGroupScorer(String, String, String, String, int, String, String, boolean) - Static method in class edu.dartmouth.bglab.score.ScorerFactory
Reads the given group file, which can be either a .txt file or a .raw file, and builds the specified scorer using the specified MotifFinder class for both the group MotifFinder and the genome MotifFinder; only the class names should be specified, as the package name is added automatically.
buildGroupSequence(String, int, int[]) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Returns a sequence that contains the specified group genes in the order given in the array, which doesn't need to be sorted.
buildMF(String, String, int, String) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Returns a motif finder with runtime type mfClassName that has discardOverlaps set to false and wildcard optimization turned off.
buildMFFromFasta(String, Scanner, String) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Makes a motif finder from a fasta file pointed at by filename.
buildMFFromFasta(String, Scanner, String, int) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
 
buildMFFromFasta(String, String, String) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Makes a motif finder from a fasta string.
buildMFFromFastaFile(String, String, String) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Makes a motif finder from a fasta file pointed at by filename.
buildMFFromFile(String, String, String) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Returns a motif finder with runtime type mfClassName that has discardOverlaps set to false and wildcard optimization turned off.
buildMFFromFile(String, String, String, int) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Returns a motif finder with runtime type mfClassName that has discardOverlaps set to false and wildcard optimization turned off.
buildSequenceFromFile(String, boolean, int, int[]) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Returns a sequence with the contents of filePath.

C

C - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
cacheRetrievalCountForCount - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
cacheRetrievalCountForFind - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
cacheStorageCountForCount - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
cacheStorageCountForFind - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
calcMotifSpecificity(Motif) - Static method in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
calcProb() - Method in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.CombinedScorer
Returns the some of the scores from s1 and s2, minus the prior.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.CombinedScorer
Returns the some of the scores from s1 and s2, minus the prior.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.ConservationICScorer
The conservation of this motif as measured by the relative entropy of the PWM of this motif and it's neighbors around the given hamming space against the background base distribution of the PWM.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.ConservationICScorer
This method has not been implemented.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.ConservationRatioScorer
The conservation of this motif as measured by the ratio of the number of occurrences of m to the the number of occurrences of m and all it's ConservationRatioScorer.HD neighbors.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.ConservationRatioScorer
This method has not been implemented.
calculateScore(int, int, double) - Method in class edu.dartmouth.bglab.score.CoverageScorer
Computes the score based on the groupCount, total count and a prior to use.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.CoverageScorer
Returns the score of m.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.CoverageScorer
Calculates the score of ml using the sum of the group counts and total counts of all motifs in ml and using the average prior and motif length.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.KSGroupScorer
 
calculateScore(MotifFinder, FindResults, MotifFinder, FindResults, double, double) - Method in class edu.dartmouth.bglab.score.KSGroupScorer
Returns the -log likelihood that hits came from the CDF given in the constructor.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.KSGroupScorer
Returns the -log probability that this motif is drawn from the CDF supplied in the constructor.
calculateScore(FindResults, double, double) - Method in class edu.dartmouth.bglab.score.KSScorer
 
calculateScore(int[], double, double) - Method in class edu.dartmouth.bglab.score.KSScorer
Returns the -log likelihood that hits came from the CDF given in the constructor.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.KSScorer
Returns the -log probability that this motif is drawn from the CDF supplied in the constructor.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.KSScorer
Returns the -log probability that this motif is drawn from the CDF supplied in the constructor.
calculateScore(double, double, double, int) - Method in class edu.dartmouth.bglab.score.LogOccurrenceScorer
Computes the score based on the groupCount, total count, a prior to use, and a motif length for calculating the probability that any given motif is this motif.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.LogOccurrenceScorer
Returns the score of m.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.LogOccurrenceScorer
Calculates the score of ml using the sum of the group counts and total counts of all motifs in ml and using the average prior and motif length.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.MarkovMaxOrderScorer
 
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.MarkovMaxOrderScorer
Not implemented.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.OccurrenceKSScorer
Returns the some of the scores from s1 and s2, minus the prior.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.OccurrenceKSScorer
Returns the some of the scores from s1 and s2, minus the prior.
calculateScore(int, int, double, int) - Method in class edu.dartmouth.bglab.score.OccurrenceScorer
Computes the score based on the groupCount, total count, a prior to use, and a motif length for calculating the probability that any given motif is this motif.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.OccurrenceScorer
Returns the score of m.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.OccurrenceScorer
Calculates the score of ml using the sum of the group counts and total counts of all motifs in ml and using the average prior and motif length.
calculateScore(int, int, double, int) - Method in class edu.dartmouth.bglab.score.RatioScorer
This is only used if calculateScore(MotifList) is caled -- computes the score based on the groupCount and total count as the log_2 ratio of groupCount / totalCount.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.RatioScorer
 
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.RelativeEntropyScorer
The conservation of this motif as measured by the relative entropy of the PWM of this motif and it's neighbors in the test motif finder versus in the reference motif finder.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.RelativeEntropyScorer
This method has not been implemented.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.Scorer
Returns the score of m and increments the lookupCount.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.Scorer
Returns the score of ml and increments the lookupCount.
calculateScore(Motif) - Method in class edu.dartmouth.bglab.score.ZScoreScorer
Calculates the Z-score of this motif by sampling numTrials (as specified in constructor) motifs from the regions where m is found.
calculateScore(MotifList) - Method in class edu.dartmouth.bglab.score.ZScoreScorer
This has not been implemented.
capacity() - Method in class edu.dartmouth.bglab.util.Heap
Returns the size of this heap's array, and so how many elements it can hold before it will be expanded.
caseInsensitiveStringComparator - Static variable in class edu.dartmouth.bglab.util.MiscUtils
 
cdf - Variable in class edu.dartmouth.bglab.score.KSScorer
 
CDF - Interface in edu.dartmouth.bglab.util
Provides a common interface for cumulative density functions.
CGIDriver - Class in edu.dartmouth.bglab.beam
 
CGIDriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.CGIDriver
 
CGIDriver.MotifGeneListSummary - Class in edu.dartmouth.bglab.beam
 
CGIDriver.MotifGeneListSummary(Motif, MotifFinder, GroupScorer) - Constructor for class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
CGIDriver.MotifGeneSummary - Class in edu.dartmouth.bglab.beam
 
CGIDriver.MotifGeneSummary(int, int, double) - Constructor for class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
CGIScope - Class in edu.dartmouth.bglab.beam
 
CGIScope() - Constructor for class edu.dartmouth.bglab.beam.CGIScope
 
CharlieTester - Class in edu.dartmouth.bglab.test
For running tests and doing things that Arijit tells me to do.
CharlieTester() - Constructor for class edu.dartmouth.bglab.test.CharlieTester
 
charToDist(char, int[]) - Static method in class edu.dartmouth.bglab.model.PLConsensusModel
Converts a character b over the FULL alphabet to an array of frequencies that most closely matches the given array of frequencies.
checkData(char[], int[]) - Static method in class edu.dartmouth.bglab.util.SuffixArray
Compares the array to the string to make sure they match.
checkMotifFinderResults - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
ChildProcessProblem - Class in edu.dartmouth.bglab.beam.web
Used to reconstruct a throwable object thrown by a child process so that ChildProcessProblem.toString(), ChildProcessProblem.getReconstructedStackTrace(), and getCause() behave as they would have in the original object that was caught in the child process.
ChildProcessProblem(String[]) - Constructor for class edu.dartmouth.bglab.beam.web.ChildProcessProblem
Converts a string[] form of an exception and it's cause chain into a ChildProcessProblem.
ChildProcessProblem(String[], int) - Constructor for class edu.dartmouth.bglab.beam.web.ChildProcessProblem
Same as above, but starts reading the array at the ith entry.
choose - Static variable in class edu.dartmouth.bglab.util.Binomial
 
choose(int, int) - Static method in class edu.dartmouth.bglab.util.Binomial
 
chromosomes - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
chromosomeSequences - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
classpath() - Static method in class edu.dartmouth.bglab.GlobalParams
classpath, with absolute paths
cleanMotifArray(Motif[], Motif, MotifComparator, int, int) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
 
cleanMotifArray(Motif[], MotifComparator) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns an array of unique motifs, where the highest scoring of two equivalent motifs is kept.
clear() - Method in class edu.dartmouth.bglab.search.MarkovModel
Clears all the stored lookups from this model.
clear() - Method in class edu.dartmouth.bglab.util.Heap
Empties the heap and returns the capacity to the max capacity, if specified, or the INIT_CAPACITY.
clear() - Method in class edu.dartmouth.bglab.util.Histogram
Clears the values of this histogram.
clear() - Method in class edu.dartmouth.bglab.util.SoftValueHashMap
 
clHash - Static variable in class edu.dartmouth.bglab.beam.CGIScope
 
clHash - Static variable in class edu.dartmouth.bglab.beam.Scope
 
clHash - Static variable in class edu.dartmouth.bglab.beam.WebScope
 
clone() - Method in class edu.dartmouth.bglab.beam.RankedMotifPair
Performs a deep copy of this object, cloning each of the motifs.
clone() - Method in class edu.dartmouth.bglab.motif.Motif
Returns a shallow copy of this motif, which is the same as a deep copy since all member data is primitive or immutable objects.
clone() - Method in class edu.dartmouth.bglab.motif.MotifList
Returns a deep copy of this motif list.
clone() - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
Returns a deep copy of this suffix array motif finder, with the exception that the new suffix array uses the same array and string, which never get changed.
clone() - Method in class edu.dartmouth.bglab.search.MarkovModel
Returns a deep copy of this markov model.
clone() - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns a copy of this motif finder.
clone() - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
Returns a deep copy of this suffix array motif finder, with the exception that the new suffix array uses the same array and string, which never get changed.
close() - Method in class edu.dartmouth.bglab.io.Scanner
Closes this scanner.
COLLAPSE_DEGEN_GEN_NEIGHBORS_RECON_METHOD - Static variable in class edu.dartmouth.bglab.beam.Ambiguizer
 
COLLAPSE_DEGEN_RECON_METHOD - Static variable in class edu.dartmouth.bglab.beam.Ambiguizer
 
color - Variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Motif
 
color - Variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Motif
 
COLOR_PROGRESSION - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
COLOR_PROGRESSION - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
CombinedScorer - Class in edu.dartmouth.bglab.score
Given two Scorers whose results are presumed to be independent and based on log probabilities, returns the probability of seeing both scores (ie, the intersection of the probabilities.
CombinedScorer(Scorer) - Constructor for class edu.dartmouth.bglab.score.CombinedScorer
Sets the scores, and takes the motif finders from s1.
combineHitsToBipartiteHits(int[], int[], int) - Method in class edu.dartmouth.bglab.search.MotifFinder
Combines sorted arrays of hits for the first and second submotifs of a bipartite motif, returning a sorted array of the bipartite motifs where the distance between the starts of the first and second submotifs equals sm2Pos, and they are located in the same biological gene.
combineOnHamming(Motif[], int, boolean) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Performs a pairwise comparison on all the motifs and returns an array of motifs that are the union of two motifs within maxHD of each other.
comp - Variable in class edu.dartmouth.bglab.util.Heap
 
ComparatorMotifFinder - Class in edu.dartmouth.bglab.search
Uses a SuffixArray as its internal representation of a biological sequence, allowing access to the number of occurrences of a given motif and the indices of these occurrences in the sequence.
ComparatorMotifFinder(String, int) - Constructor for class edu.dartmouth.bglab.search.ComparatorMotifFinder
ComparatorMotifFinder(String, String, int) - Constructor for class edu.dartmouth.bglab.search.ComparatorMotifFinder
compare(RankedMotifPair, RankedMotifPair) - Method in class edu.dartmouth.bglab.beam.RankedMotifPair.FoundMotifComparator
Both o1 and o2 must be RankedMotifPairPairs; the comparison is the natural ordering of Motifs, comparing the motif instance variables (the found motif).
compare(Motif, Motif) - Method in class edu.dartmouth.bglab.motif.MotifComparator
Compares m1 to m2.
compare(Motif, Motif) - Method in class edu.dartmouth.bglab.motif.ReverseScoreComparator
 
compare(Motif, Motif) - Method in class edu.dartmouth.bglab.motif.ScoreComparator
 
compare(Motif, Motif) - Method in class edu.dartmouth.bglab.motif.SequenceComparator
 
compare(String, String) - Method in class edu.dartmouth.bglab.search.MarkovModel.KeyComparator
 
compare(Object, Object) - Method in class edu.dartmouth.bglab.util.Heap
Functions like the comparator's compare method.
compare(char[], int, int) - Static method in class edu.dartmouth.bglab.util.SuffixArray
Compares the suffix starting at i to the suffix starting at j.
compareTo(CGIDriver.MotifGeneSummary) - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
compareTo(RankedMotifPair) - Method in class edu.dartmouth.bglab.beam.RankedMotifPair
Orders by rank.
compareTo(FileReaders.NameAndID) - Method in class edu.dartmouth.bglab.io.FileReaders.NameAndID
 
compareTo(KRModel) - Method in class edu.dartmouth.bglab.model.KRModel
Allows Arrays.sort() to sort pwm's by score in descending order; not consistent with KRModel.equals(Object).
compareTo(PWM) - Method in class edu.dartmouth.bglab.model.PWM
Allows Arrays.sort() to sort pwm's by score in descending order; not consistent with PWM.equals(Object).
compareTo(Motif) - Method in class edu.dartmouth.bglab.motif.Motif
Allows Arrays.sort() to sort Motifs by score in descending order; not consistent with Motif.equals(Object).
compareTo(Motif.ScoreData) - Method in class edu.dartmouth.bglab.motif.Motif.ScoreData
 
compareTo(MotifInstance) - Method in class edu.dartmouth.bglab.motif.MotifInstance
Allows Arrays.sort() to sort MotifInstances by gene name in alphabetical order; not consistent with Object.equals(Object).
compareTo(MotifList) - Method in class edu.dartmouth.bglab.motif.MotifList
Allows Arrays.sort() to sort MotifList objects by score in descending order.
compareTo(SuffixArrayMotifFinder.SuffixArrayFindResults) - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
compareTo(Range) - Method in class edu.dartmouth.bglab.util.Range
Orders in ascending order by left, right.
complementOf(char) - Method in class edu.dartmouth.bglab.motif.Alphabet
 
CompositeMotifFinder - Class in edu.dartmouth.bglab.search
Uses a SuffixArray as its internal representation of a biological sequence, allowing access to the number of occurrences of a given motif and the indices of these occurrences in the sequence.
CompositeMotifFinder(List<MotifFinder>) - Constructor for class edu.dartmouth.bglab.search.CompositeMotifFinder
CompositeMotifFinder(MotifFinder, MotifFinder) - Constructor for class edu.dartmouth.bglab.search.CompositeMotifFinder
 
CompositeMotifFinder.CompositeFindResults - Class in edu.dartmouth.bglab.search
 
CompositeMotifFinder.CompositeFindResults(List<MotifFinder>, FindResults[], int[]) - Constructor for class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
compressToChar(String) - Method in class edu.dartmouth.bglab.motif.Alphabet
Returns the char that represents the given string of primary bases; the inverse of Alphabet.expansionOf(char).
computeCDF(double) - Method in interface edu.dartmouth.bglab.util.CDF
Must return the percentage of datapoints that lie strictly to the left of x.
computeCorrelation() - Method in class edu.dartmouth.bglab.util.LinCorrStatBox
Computes the linear correlation between the points (r^2 value).
computeEntropy() - Method in class edu.dartmouth.bglab.model.PWM
Returns the average entropy for each position in the pwm.
computeEntropy(int) - Method in class edu.dartmouth.bglab.model.PWM
Returns the entropy at the given position.
computeEntropy() - Method in class edu.dartmouth.bglab.search.MarkovModel
 
computeEntropy(int) - Method in class edu.dartmouth.bglab.search.MarkovModel
Computes the entropy of the given order, as H = -SUM[p lg p] where p = probability of the given motif.
computeMean(Binnable[]) - Static method in class edu.dartmouth.bglab.util.Histogram
Computes the mean of the given set.
computeMean(double[]) - Static method in class edu.dartmouth.bglab.util.Histogram
Computes the mean of the given set.
computeOneSampleKS(int[], CDF) - Static method in class edu.dartmouth.bglab.util.KS
Computes the Kuiper's statistic on own data set given a CDF distribution (see Numerical Recipes in C); assumes the dataset is sorted.
computePhi(Motif, Motif) - Method in class edu.dartmouth.bglab.score.GroupScorer
Calculates a phi score for a pair of motifs.
computePhi(Motif, MotifList) - Method in class edu.dartmouth.bglab.score.GroupScorer
Calculates a phi score for a pair of motifs.
computePhi(MotifList, MotifList) - Method in class edu.dartmouth.bglab.score.GroupScorer
Calculates a phi score for a pair of motifs.
computePhi(MotifList, MotifList, MotifFinder) - Static method in class edu.dartmouth.bglab.score.MaximalMatcher
Computes a phi score for the given motifs lists as their occurrences are described by the Motif Finder.
computePhi() - Method in class edu.dartmouth.bglab.score.MaximalMatcher
Computes a phi score for the given motifs as their occurrences are described by the Motif Finder.
computePhi(Motif, Motif) - Method in class edu.dartmouth.bglab.score.Scorer
Calculates a phi score for a pair of motifs.
computePhi(Motif, MotifList) - Method in class edu.dartmouth.bglab.score.Scorer
 
computePhi(MotifList, MotifList) - Method in class edu.dartmouth.bglab.score.Scorer
Calculates a phi score for a pair of motifs.
computePrior(Motif) - Method in class edu.dartmouth.bglab.score.Scorer
Returns the natural log of a Bayesian prior derived from a Bonferoni correction.
computePrior(MotifList) - Method in class edu.dartmouth.bglab.score.Scorer
Returns the average prior of all the motifs in ml; no checks are made for duplicate motifs.
computeRelativeEntropy(int, int[]) - Method in class edu.dartmouth.bglab.model.PWM
Returns the relative entropy at the given position; the array of reference weights should correspond to the base ordering defined in PWM.BASE_KEY.
computeRelativeEntropy(int, PWM) - Method in class edu.dartmouth.bglab.model.PWM
Returns the relative entropy at the given position.
computeRelativeEntropy(int[]) - Method in class edu.dartmouth.bglab.model.PWM
Returns the average relative entropy for each position in the pwm; the array of reference weights should correspond to the base ordering defined in PWM.BASE_KEY.
computeRelativeEntropy(PWM) - Method in class edu.dartmouth.bglab.model.PWM
Returns the average relative entropy for each position in the pwm.
computeROC(CREModel, MotifList, MotifList, boolean, String) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
 
computeScalingFactor(Motif) - Static method in class edu.dartmouth.bglab.score.Scorer
Returns the number of possible motif sequences with the same length as m.
computeSD(Binnable[]) - Static method in class edu.dartmouth.bglab.util.Histogram
Computes the standard deviation of the given set.
computeSD(double[]) - Static method in class edu.dartmouth.bglab.util.Histogram
Computes the standard deviation of the given set.
computeSensSpec(MotifList, MotifList, int) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
Returns a FPFNStatBox that includes the TP FP FN and FP rates when matches is compared against the truePositives.
computeSum(double[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Computes the sum of the elements of d.
computeSum(int[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Computes the sum of the elements of d.
computeTwoSampleKS(int[], int[]) - Static method in class edu.dartmouth.bglab.util.KS
Computes the Kuiper's statistic on the two data sets (see Numerical Recipes in C); assumes the datasets are sorted.
CONS_CRE - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
consensus - Variable in class edu.dartmouth.bglab.model.KRModel
 
ConsensusSequence - Class in edu.dartmouth.bglab.model
Implementation of the consensus sequence model that keeps track of reverse complement status.
ConsensusSequence(Motif) - Constructor for class edu.dartmouth.bglab.model.ConsensusSequence
Creates a consensus sequence from the given sequence with the reverse complement flag set to m's reverse compliment.
ConsensusSequence(String) - Constructor for class edu.dartmouth.bglab.model.ConsensusSequence
Creates a consensus sequence from the given sequence with the reverse complement flag set to CREModel.DEFAULT_RC.
ConsensusSequence(String, boolean) - Constructor for class edu.dartmouth.bglab.model.ConsensusSequence
Creates a consensus sequence from the given sequence with the given reverse complemnt flag.
ConservationICScorer - Class in edu.dartmouth.bglab.score
Measures the conservation of a motif m as the information content of m, as defined by Stormo in all his papers.
ConservationICScorer(MotifFinder, boolean, int) - Constructor for class edu.dartmouth.bglab.score.ConservationICScorer
Sets the motif finder and discardOverlaps parameters of the motif finder appropriately; hammingDistance determines the space into which we will expand each motif.
ConservationICScorer(MotifFinder, MotifFinder, boolean) - Constructor for class edu.dartmouth.bglab.score.ConservationICScorer
For compatability with other Group Scorers; simply uses the groupFinder and the default ConservationICScorer.DEFAULT_HD.
ConservationRatioScorer - Class in edu.dartmouth.bglab.score
Measures the conservation of a motif m as the percentage of approximate instances of m that are exact matches to m.
ConservationRatioScorer(MotifFinder, boolean, int) - Constructor for class edu.dartmouth.bglab.score.ConservationRatioScorer
Sets the motif finder and discardOverlaps parameters of the motif finder appropriately; hammingDistance determines the space into which we will expand each motif.
consProbs - Variable in class edu.dartmouth.bglab.model.KRModel
 
convertNamesToIDs(String[], String) - Static method in class edu.dartmouth.bglab.io.FileReaders
Given the name of a file that contains gene name to gene ID mappings, and an array of gene names, will return a sorted array of database IDs with duplicates removed, and modify names so that its elements correspond to those of the returned array, with trailing empty slots in names set to null.
corrPts - Variable in class edu.dartmouth.bglab.util.LinCorrStatBox
 
CorruptionDriver - Class in edu.dartmouth.bglab.beam
 
CorruptionDriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.CorruptionDriver
Sets the file root, test ID, thread ID, properties, and scorer.
CorruptionDriver(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.CorruptionDriver
Sets the file root, test ID, thread ID, properties, and scorer; uses the specified group instead of pulling the group ID from the properties.
count(Motif, int) - Method in class edu.dartmouth.bglab.search.ComparatorMotifFinder
Returns the number of times that any motif with a hamming distance from m of up to k occurs in the sequence; not implemented.
count(String) - Method in class edu.dartmouth.bglab.search.ComparatorMotifFinder
Returns the number of times that pattern occurs in the sequence.
count(Motif) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
Returns the number of times that pattern occurs in the sequence.
count(Motif, int) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
Returns the number of times that any motif with a hamming distance from m of up to k occurs in the sequence; not implemented.
count(String) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
Returns the number of times that pattern occurs in the sequence.
count(Motif) - Method in class edu.dartmouth.bglab.search.MarkovModel
The expected number of occurences of the motif.
count(Motif, int) - Method in class edu.dartmouth.bglab.search.MarkovModel
 
count(String) - Method in class edu.dartmouth.bglab.search.MarkovModel
Computes the expected number of occurences in the given sequence.
count(Motif) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the number of times that m occurs in the sequence.
count(Motif, int) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the number of times that any motif with a hamming distance from m of up to k occurs in the sequence.
count(MotifList) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the sum of the counts of all motif in ml; no checks are made of the presence of duplicate motifs.
count(String) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the number of times that pattern occurs in the sequence.
count - Variable in class edu.dartmouth.bglab.util.AveStatBox
 
count(String) - Method in class edu.dartmouth.bglab.util.SuffixArray
Returns the number of times that x occurs in the sequence.
countBins(double[]) - Method in class edu.dartmouth.bglab.util.Histogram
Initializes the state variables bins and minVal.
countCache - Variable in class edu.dartmouth.bglab.search.MotifFinder
To speed up lookups in MotifFinder.count(Motif) when caching is turned on.
countCallCount - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
countCallNegativeCount - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
countCallPositiveCount - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
countGenes(Motif) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the number of genes m is in.
counts - Variable in class edu.dartmouth.bglab.search.MarkovModel
 
CoverageScorer - Class in edu.dartmouth.bglab.score
 
CoverageScorer(MotifFinder, MotifFinder, boolean) - Constructor for class edu.dartmouth.bglab.score.CoverageScorer
Sets the motif finder and group motif finder and tells them whether or not to discard overlaps.
cre - Variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.TestModel
 
createFindResults(MotifFinder, Motif, Matcher, boolean) - Static method in class edu.dartmouth.bglab.search.MotifFinder
 
createFindResults(Motif) - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
 
createFindResultsUsingRegex(MotifFinder, Motif) - Static method in class edu.dartmouth.bglab.search.MotifFinder
 
createMotifListAndGeneListSummary(Motif[]) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
createNewInstance(String, String, int) - Method in class edu.dartmouth.bglab.search.ComparatorMotifFinder
createNewInstance(String, String, int) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
createNewInstance(String, String, int) - Method in class edu.dartmouth.bglab.search.MarkovModel
createNewInstance(String, int) - Method in class edu.dartmouth.bglab.search.MotifFinder
createNewInstance(String, String, int) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns a new motif finder with the same runtime type, MotifFinder.discardOverlaps status, and MotifFinder.wildcardOptimizationCutoff as the calling instance.
createNewInstance(String, String, int) - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
CREModel - Interface in edu.dartmouth.bglab.model
Interface for defining different ways of modeling cis-regulatory elements.
crossEntropy(MarkovModel) - Method in class edu.dartmouth.bglab.search.MarkovModel
Computes the cross entropy (KL Distance) between the highest shared order of this model vs the given model.
crossEntropy(MarkovModel, Motif[], int, int) - Method in class edu.dartmouth.bglab.search.MarkovModel
Computes the cross entropy (KL Distance) between the highest shared order of this model vs the given model, using only the specified motifs, in the range [start,stop).
crossEntropy(Motif[]) - Method in class edu.dartmouth.bglab.search.MarkovModel
Computes the cross entropy of the motifs versus the background model.
crossEntropy(String[]) - Method in class edu.dartmouth.bglab.search.MarkovModel
Computes the cross entropy of the motifs versus the background model.
crossValidate(CREModel, MotifList, AffinityEvaluatorDriver.EvaluatorFunction, int, int) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
cumProb(int, int, double) - Static method in class edu.dartmouth.bglab.util.Binomial
Returns the cumulative probability as the sum of i=k to N prob(N, i, p).
cumProb(int, double) - Static method in class edu.dartmouth.bglab.util.Poisson
Uses the default MIN_COUNT.
cumProb(int, double, int) - Static method in class edu.dartmouth.bglab.util.Poisson
Computes the probability of AT LEAST k observations given N trials with a probabiligy p of success on each trial.
cumProb(int, int, double) - Static method in class edu.dartmouth.bglab.util.Poisson
Uses the default MIN_COUNT.
cumProb(int, int, double, int) - Static method in class edu.dartmouth.bglab.util.Poisson
Computes the probability of AT LEAST k kobservations given the lambda (which is N*p).
cumulativeDeltaHybridSearchMinusSimpleFind - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 

D

d - Variable in class edu.dartmouth.bglab.model.PWM.StringDoublePair
 
D - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
DARK_COLOR - Static variable in class edu.dartmouth.bglab.beam.web.WebDriver
Dark color for web pages.
dbCacheConnection - Variable in class edu.dartmouth.bglab.search.MotifFinder.GenomeSoftValueHashMap
 
DBRESULT_INVALIDFASTA - Static variable in class edu.dartmouth.bglab.beam.CGIScope
 
DBRESULT_MISSINGGENES - Static variable in class edu.dartmouth.bglab.beam.CGIScope
 
DBRESULT_SUCCESS - Static variable in class edu.dartmouth.bglab.beam.CGIScope
 
DBRESULT_UNSPECIFIEDERROR - Static variable in class edu.dartmouth.bglab.beam.CGIScope
 
dbUrl - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
debug - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
debug - Static variable in class edu.dartmouth.bglab.score.KSGroupScorer
 
DEBUGGING - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluator
 
DEFAULT - Static variable in class edu.dartmouth.bglab.motif.Alphabet
The default full alphabet.
DEFAULT_BACKGROUND_COLOR - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
DEFAULT_BACKGROUND_COLOR - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
DEFAULT_HD - Static variable in class edu.dartmouth.bglab.score.ConservationICScorer
 
DEFAULT_MAX_HASH_LENGTH - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
DEFAULT_PARAM_FILE - Static variable in class edu.dartmouth.bglab.GlobalParams
 
DEFAULT_PRIMARY - Static variable in class edu.dartmouth.bglab.motif.Alphabet
The default primary alphabet-- useful if we ever wanted to use RNA or nucleic acid alphabets.
DEFAULT_PROPERTIES - Static variable in class edu.dartmouth.bglab.util.UberProperties
Loads "GlobalParams.paramFileRoot() + GlobalParams.DEFAULT_PARAM_FILE"; also loads "GlobalParams.paramFileRoot() + GlobalParams.ABSOLUTE_PATHS_PARAM_FILE" if GlobalParams.RELATIVE_PATHS is set to false.
DEFAULT_RC - Static variable in interface edu.dartmouth.bglab.model.CREModel
 
DEFAULT_STRINGENCY - Static variable in class edu.dartmouth.bglab.model.KRModel
Default upper bound for sum of -log(base_probability) for the bases in a sequence in order for that sequence to get output by KRModel.expandAsStrings() and KRModel.expandAsMotifList();
DEFAULT_STRINGENCY - Static variable in class edu.dartmouth.bglab.model.PWM
Default upper bound for sum of -log(base_probability) for the bases in a sequence in order for that sequence to get output by PWM.expandAsStrings() and PWM.expandAsMotifList();
defaultScoreData - Static variable in class edu.dartmouth.bglab.motif.Motif
 
DELIMITER - Static variable in class edu.dartmouth.bglab.io.Scanner
 
deltaSig - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
deltaSigMedianRatio - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
deltaSigMedProb - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
deltaSigProb - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
denominatorMM - Variable in class edu.dartmouth.bglab.score.RatioScorer
 
destn - Variable in class edu.dartmouth.bglab.beam.PRISM
 
DF - Static variable in class edu.dartmouth.bglab.util.NiceFormatter
 
DFE - Static variable in class edu.dartmouth.bglab.util.NiceFormatter
 
DIR - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
DISCARD_OVERLAPS - Static variable in class edu.dartmouth.bglab.beam.MLDriver
 
discardOverlaps - Variable in class edu.dartmouth.bglab.search.MotifFinder
True if overlapping motifs are not to be included by count() and find() methods.
distance(int[], int[]) - Static method in class edu.dartmouth.bglab.model.PLConsensusModel
Returns the minimum number of changes needed to turn a into b (or vice versa).
doingFindBipartiteHitsComparisonTiming - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
doPersisting - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
doubleLengthOf(int[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Returns an array twice the length of a, with a copied into the first half of the new array.
doubleLengthOf(Object[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Returns an array twice the length of a with the same runtime type, with a copied into the first half of the new array.
draw(Graphics2D, int, double) - Method in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Gene
 
draw(Graphics2D, int, double) - Method in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.MotifInstance
 
draw(Graphics2D, int, double) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Gene
 
draw(Graphics2D, int, double) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.MotifInstance
 
drawGenes(int, int, List<GeneMapImageDrawer.Gene>) - Static method in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
drawGenes(HashMap<String, String>, HashMap<String, ServerSocketImageWriter.Gene>) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
drawGenes(String, BufferedOutputStream) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
Draws the genes with the annotated motifs as a gif on the given output stream.
drawImage(BufferedOutputStream, BufferedImage) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
drawScale(Graphics2D, int, double) - Static method in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
drawScale(Graphics2D, int, double) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
drawSeqLogo(BufferedOutputStream, HashMap<String, String>) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
Draws a sequence logo to the output stream.
drawString(String) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
driver - Variable in class edu.dartmouth.bglab.beam.PRISM
 
driverError(Throwable, boolean) - Static method in class edu.dartmouth.bglab.beam.Scope
 

E

edu.dartmouth.bglab - package edu.dartmouth.bglab
Provides a class to hold global constants.
edu.dartmouth.bglab.beam - package edu.dartmouth.bglab.beam
Provides the top level of the algorithms for BEAM, PRISM, and SPACER, along with the command-line version of SCOPE.
edu.dartmouth.bglab.beam.web - package edu.dartmouth.bglab.beam.web
Provides WebDriver and its associated classes as a simple API to a multi-process version of SCOPE designed for use by a web front end.
edu.dartmouth.bglab.dataImportPreparation - package edu.dartmouth.bglab.dataImportPreparation
 
edu.dartmouth.bglab.io - package edu.dartmouth.bglab.io
Provides static classes for reading and writing common objects to and from file, along with a main class for loading new organisms into SCOPE.
edu.dartmouth.bglab.model - package edu.dartmouth.bglab.model
Provides implementations of several different models for representing cis-regulatory elements, along with command-line programs for testing the accuracy of these models.
edu.dartmouth.bglab.motif - package edu.dartmouth.bglab.motif
Provides classes for representing, manipulating, and comparing motifs.
edu.dartmouth.bglab.score - package edu.dartmouth.bglab.score
Provides objective functions for scoring motifs.
edu.dartmouth.bglab.search - package edu.dartmouth.bglab.search
Provides classes for finding the occurrences of motifs in biological sequences.
edu.dartmouth.bglab.test - package edu.dartmouth.bglab.test
Provides test code for the other packages, and a few other odds and ends.
edu.dartmouth.bglab.util - package edu.dartmouth.bglab.util
Provides an assortment of data structures and other utilities classes; the classes in this package perform general functions which are not directly related to biology, whereas all other packages are motif-centric.
emailAddress - Variable in class edu.dartmouth.bglab.beam.web.WebDriver
 
encodeQueryString(String) - Static method in class edu.dartmouth.bglab.beam.web.WebDriver
Encodes a String to make it safe to send to the ServerSocketImageWriter by replacing special strings.
endOfStringNumber - Static variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
entrySet() - Method in class edu.dartmouth.bglab.util.SoftValueHashMap
Returns a copy of the key/values in the map at the point of calling.
enumerateMotifs(Alphabet, Alphabet, int, boolean) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns an alphabetically sorted array of all of the unique "primary alphabet" motifs of a given length.
enumerateMotifs(Alphabet, Alphabet, int, boolean, int, int) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns an alphabetically sorted array of all of the bipartite versions (that have from minNCount to maxNCount N's in the middle) of each of the unique "primary alphabet" motifs of a given length.
enumerateMotifs(int, boolean) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Calls MotifUtils.enumerateMotifs(Alphabet, Alphabet, int, boolean) using Alphabet.DEFAULT and Alphabet.DEFAULT_PRIMARY as default alphabets.
enumerateMotifs(int, boolean, int, int) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Calls MotifUtils.enumerateMotifs(Alphabet, Alphabet, int, boolean, int, int) using Alphabet.DEFAULT and Alphabet.DEFAULT_PRIMARY as default alphabets.
EOF - Static variable in class edu.dartmouth.bglab.io.Scanner
 
equals(Object) - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
equals(Object) - Method in class edu.dartmouth.bglab.beam.RankedMotifPair
Returns true if and only if Comparable.compareTo(Object) returns 0.
equals(Object) - Method in class edu.dartmouth.bglab.io.FileReaders.NameAndID
 
equals(Object) - Method in class edu.dartmouth.bglab.model.KRModel
Not implemented yet.
equals(Object) - Method in class edu.dartmouth.bglab.model.PWM
Not implemented yet.
equals(Motif, Motif) - Method in class edu.dartmouth.bglab.motif.EquivalenceComparator
 
equals(Object) - Method in class edu.dartmouth.bglab.motif.Motif
Returns true if this motif has the same sequence, and reverse complement status as o; score is NOT taken into account, nor is alphabet.
equals(Motif, Motif) - Method in class edu.dartmouth.bglab.motif.MotifComparator
Returns compare(m1, m2) == 0.
equals(Object) - Method in class edu.dartmouth.bglab.motif.MotifList
Returns true if and only if the to motif lists are the same size and each motif in order is equal to the motif in the same position in the other motif list, as determined by the motif equals method; score is NOT taken into account.
equals(Motif, Motif) - Method in class edu.dartmouth.bglab.motif.OverlapComparator
 
equals(Motif, Motif) - Method in class edu.dartmouth.bglab.motif.ScoreComparator
 
equals(Motif, Motif) - Method in class edu.dartmouth.bglab.score.PhiComparator
 
equals(Object) - Method in class edu.dartmouth.bglab.search.AggregatedFindResults
 
equals(Object) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
equals(Object) - Method in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
equals(Object) - Method in class edu.dartmouth.bglab.search.MotifFinder.UncompressedFindResults
 
equals(Object) - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
EquivalenceComparator - Class in edu.dartmouth.bglab.motif
A comparator for assessing motif equivalence.
EquivalenceComparator() - Constructor for class edu.dartmouth.bglab.motif.EquivalenceComparator
 
EquivalenceComparator(double) - Constructor for class edu.dartmouth.bglab.motif.EquivalenceComparator
 
equivalentTo(Motif) - Method in class edu.dartmouth.bglab.motif.Motif
Returns true if this motif is equivalent to the given motif, with the minimum coverage set to Motif.MIN_COVERAGE.
equivalentTo(Motif, double) - Method in class edu.dartmouth.bglab.motif.Motif
Assesses the equivalence of this motif to the given motif.
errln(Object) - Static method in class edu.dartmouth.bglab.util.Print
 
error - Variable in class edu.dartmouth.bglab.beam.BeamDriver
 
ERROR_STRING_HEIGHT - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
evaluate(CREModel, MotifList) - Method in interface edu.dartmouth.bglab.model.AffinityEvaluatorDriver.EvaluatorFunction
 
evaluate(CREModel, MotifList) - Method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.FPFNEvalFunc
 
evaluate(CREModel, MotifList) - Method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.ROCEvalFunc
 
evaluateGene(Integer, MotifFinder) - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
exchange(int, int) - Method in class edu.dartmouth.bglab.util.Heap
Simply exchanges the objects at indeces i and j.
execute() - Method in class edu.dartmouth.bglab.beam.PRISM
 
expand(double[][], int, MotifFinder) - Method in class edu.dartmouth.bglab.model.PWM
Returns a vector of the strings and -log probabilities for the strings that pass the stringency test in the first length positions.
expand() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the unsorted set of unambiguous motifs that this motif represents.
expandAsMotifList() - Method in class edu.dartmouth.bglab.model.ConsensusSequence
Returns a MotifList containing the unambiguous Motifs that this consensu sequence represents.
expandAsMotifList() - Method in interface edu.dartmouth.bglab.model.CREModel
Returns a MotifList containing the unambiguous Motifs that this cre represents.
expandAsMotifList() - Method in class edu.dartmouth.bglab.model.KMismatchModel
Returns a MotifList containing the unambiguous Motifs that this k-mismatch model represents.
expandAsMotifList() - Method in class edu.dartmouth.bglab.model.KRModel
This method has not been implemented.
expandAsMotifList(MotifFinder) - Method in class edu.dartmouth.bglab.model.KRModel
This method has not been implemented.
expandAsMotifList() - Method in class edu.dartmouth.bglab.model.PWM
Returns a MotifList containing the unambiguous Motifs that this pwm represents; each motif's score is set to its -log (average base probability) (it's stringency).
expandAsMotifList(MotifFinder) - Method in class edu.dartmouth.bglab.model.PWM
Returns a MotifList containing the unambiguous Motifs that this pwm represents; each motif's score is set to its -log (average base probability) (it's stringency).
expandAsStrings() - Method in class edu.dartmouth.bglab.model.ConsensusSequence
Returns an array of the strings of primary bases that this consensus sequence represents.
expandAsStrings() - Method in interface edu.dartmouth.bglab.model.CREModel
Returns an array of the strings of primary bases that this cre represents.
expandAsStrings() - Method in class edu.dartmouth.bglab.model.KMismatchModel
Returns an array of the strings of primary bases that this k-mismatch model represents.
expandAsStrings() - Method in class edu.dartmouth.bglab.model.KRModel
This method has not been implemented.
expandAsStrings(MotifFinder) - Method in class edu.dartmouth.bglab.model.KRModel
This method has not been implemented.
expandAsStrings() - Method in class edu.dartmouth.bglab.model.PWM
Returns an array of the strings of primary bases that this pwm represents.
expandAsStrings(MotifFinder) - Method in class edu.dartmouth.bglab.model.PWM
Returns an array of the strings of primary bases that this pwm represents.
expandAsStrings() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the unsorted set of unambiguous sequences that this motif represents, without any duplicates.
expandNeighbors() - Method in class edu.dartmouth.bglab.motif.Motif
Returns an array of all of the unambiguous motifs that are within a hamming distance of 1 from this motif, without any duplicates.
expandNeighbors(int) - Method in class edu.dartmouth.bglab.motif.Motif
Returns an array of all of the unambiguous motifs that are within a hamming distance of hd from this motif, without any duplicates.
expansion - Variable in class edu.dartmouth.bglab.motif.Motif.LastExpansion
 
expansionCountOf(String, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
Returns the number of unambiguous sequences that seq represents.
expansionCountOf() - Method in class edu.dartmouth.bglab.motif.Motif
 
expansionCountOf(String) - Method in class edu.dartmouth.bglab.motif.Motif
Returns the number of unambiguous sequences that seq represents.
expansionOf(char) - Method in class edu.dartmouth.bglab.motif.Alphabet
Returns the set of primary bases in c.
expansionOf(String) - Method in class edu.dartmouth.bglab.motif.Motif
Returns the unsorted set of unambiguous sequences that this sequence represents.
ExpansionTooLargeException - Exception in edu.dartmouth.bglab.model
An exception for specifying the a pwm, kmm, or consensus expands to too many bases to be computable.
ExpansionTooLargeException() - Constructor for exception edu.dartmouth.bglab.model.ExpansionTooLargeException
 
ExpansionTooLargeException(String) - Constructor for exception edu.dartmouth.bglab.model.ExpansionTooLargeException
 
ExpansionTooLargeException(String, Throwable) - Constructor for exception edu.dartmouth.bglab.model.ExpansionTooLargeException
 
ExpansionTooLargeException(Throwable) - Constructor for exception edu.dartmouth.bglab.model.ExpansionTooLargeException
 
expungeStaleEntries() - Method in class edu.dartmouth.bglab.util.SoftValueHashMap
 
extractMotifs(String, Alphabet) - Static method in class edu.dartmouth.bglab.io.FileReaders
Reads motifs from anywhere in the file.
extractTop() - Method in class edu.dartmouth.bglab.util.Heap
Removes the top object off the heap and returns it.
ExtraGeneMotifFinderIdentifier - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
extraGeneSoftCache - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 

F

factory(List<MotifFinder>, int[], Motif) - Static method in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
FASTAdriver - Class in edu.dartmouth.bglab.beam
This is a simple BeamDriver that will generate FASTA files of the group genes, where the geneIDs are the unique integer IDs.
FASTAdriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.FASTAdriver
Sets the file root, test ID, thread ID, properties, and scorer.
FASTAdriver(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.FASTAdriver
Sets the file root, test ID, thread ID, properties, and scorer; uses the specified group instead of pulling the group ID from the properties.
FIELD_DELIMITER - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
FIELD_SEPARATOR - Static variable in class edu.dartmouth.bglab.GlobalParams
 
fileName - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
FileReaders - Class in edu.dartmouth.bglab.io
Contains static methods for reading motifs from file, converting gene names to integer IDs, and reading motifs and genes from files by matching a given key.
FileReaders() - Constructor for class edu.dartmouth.bglab.io.FileReaders
 
FileReaders.NameAndID - Class in edu.dartmouth.bglab.io
 
FileReaders.NameAndID(String, int) - Constructor for class edu.dartmouth.bglab.io.FileReaders.NameAndID
 
fileRoot - Variable in class edu.dartmouth.bglab.beam.BeamDriver
 
FileWriters - Class in edu.dartmouth.bglab.io
Contains static methods that for creating buffered files and printing arrays and other objects to file.
FileWriters() - Constructor for class edu.dartmouth.bglab.io.FileWriters
 
FILLER - Static variable in class edu.dartmouth.bglab.motif.Alphabet
For filling space in biological sequences so that breaks come at regular intervals in the string.
fillTriangle(double[][]) - Static method in class edu.dartmouth.bglab.util.Binomial
Creates Pascal's Triangle for the size of choose.
filterByKey(String[], String) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Assumes that the input string array has at least two fields that are tab-delimited, and returns all fields beyond the 1st, where the 1st field matches the given key.
filterByScore(Motif[], double) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns only those motifs that have a score over the given cutoff.
FILTERED - Static variable in class edu.dartmouth.bglab.beam.BiologicalBeamDriver
 
filterOnAffinity(MotifList, double) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
filterOnStringency(MotifList, double, boolean) - Static method in class edu.dartmouth.bglab.model.ModelEvaluator
 
finalize() - Method in class edu.dartmouth.bglab.search.MotifFinder.GenomeSoftValueHashMap
 
find(Motif, int) - Method in class edu.dartmouth.bglab.search.ComparatorMotifFinder
Returns the indices of where any motif with a hamming distance from m of up to k occurs in the sequence; not implemented.
find(String) - Method in class edu.dartmouth.bglab.search.ComparatorMotifFinder
Returns an unsorted array of the indices of where pattern occurs in the sequence.
find(Motif) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
Returns the number of times that pattern occurs in the sequence.
find(Motif, int) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
Returns the indices of where any motif with a hamming distance from m of up to k occurs in the sequence; not implemented.
find(String) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
Returns an unsorted array of the indices of where pattern occurs in the sequence.
find(Motif, int) - Method in class edu.dartmouth.bglab.search.MarkovModel
 
find(String) - Method in class edu.dartmouth.bglab.search.MarkovModel
Returns the result of the finder's find call.
find(Motif) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns a SORTED array of the indices of where m occurs in the sequence.
find(Motif, int) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns a sorted array of the indices of where any motif with a hamming distance from m of up to k occurs in the sequence.
find(MotifList) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the SORTED result of calling MotifFinder.find(Motif) on all the motifs of the given MotifList; no checks are made for duplicate motifs.
find(String) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns an array of the indices of where pattern occurs in the sequence.
find(String) - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
Returns an unsorted array of the indices of where pattern occurs in the sequence.
find(String) - Method in class edu.dartmouth.bglab.util.SuffixArray
Returns an unsorted array of the indices of where x occurs in the sequence.
findBegin(String) - Method in class edu.dartmouth.bglab.util.SuffixArray
Returns the array index for the alphabetically first instance of x.
findCallCount - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
findCallNegativeCount - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
findCallPositiveCount - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
findEnd(String) - Method in class edu.dartmouth.bglab.util.SuffixArray
Returns the array index one past the alphabetically last instance of x.
finder - Variable in class edu.dartmouth.bglab.search.MarkovModel
 
findMaxList(Motif[], Scorer, int, int) - Static method in class edu.dartmouth.bglab.beam.Ambiguizer
Creates that subset of the given list of motifs that forms the highest scoring MotifList.
findName(String[], String) - Static method in class edu.dartmouth.bglab.io.FileReaders
Identifies the equivalent name in names, ignoring case.
findResults(String) - Method in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
findResults(Motif) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
 
findResults(String) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
 
FindResults - Interface in edu.dartmouth.bglab.search
 
findResults(String) - Method in class edu.dartmouth.bglab.search.MarkovModel
 
findResults(Motif) - Method in class edu.dartmouth.bglab.search.MotifFinder
 
findResults(MotifList) - Method in class edu.dartmouth.bglab.search.MotifFinder
 
findResults(String) - Method in class edu.dartmouth.bglab.search.MotifFinder
 
findResults(String) - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
 
findResultsArray - Variable in class edu.dartmouth.bglab.search.AggregatedFindResults
 
findResultsArray - Variable in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
findResultsStartOffsets - Variable in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
first() - Method in class edu.dartmouth.bglab.search.AggregatedFindResults
 
first() - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
first() - Method in interface edu.dartmouth.bglab.search.FindResults
 
first() - Method in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
first() - Method in class edu.dartmouth.bglab.search.MotifFinder.UncompressedFindResults
 
first() - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
fixedGeneLengthGrabber - Static variable in class edu.dartmouth.bglab.io.OrganismLoader
 
flaggedSequence - Variable in class edu.dartmouth.bglab.motif.Motif
 
flaggedSequence - Variable in class edu.dartmouth.bglab.motif.Motif.LastExpansion
 
flaggedSequence - Variable in class edu.dartmouth.bglab.search.MotifFinder.UncompressedFindResults
 
FN - Variable in class edu.dartmouth.bglab.util.FPFNStatBox
 
FN_AVE - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
FOLD - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
FONT_COLOR - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
FONT_COLOR - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
FONTNAME - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
FONTNAME - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
FONTSIZE - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
FONTSIZE - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
forcePrintln() - Static method in class edu.dartmouth.bglab.util.Print
 
forcePrintln(Object) - Static method in class edu.dartmouth.bglab.util.Print
 
format(double) - Static method in class edu.dartmouth.bglab.util.NiceFormatter
Formats a double to display three decimal places.
found - Variable in class edu.dartmouth.bglab.beam.RankedMotifPair
Intended to be used to flag whether the rank is high enough, but can be any boolean.
foundResult - Variable in class edu.dartmouth.bglab.score.MaximalMatcher
 
FP - Variable in class edu.dartmouth.bglab.util.FPFNStatBox
 
FP_AVE - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
FPFNStatBox - Class in edu.dartmouth.bglab.util
Holds standard statistics, like FP, FN, TP, TN, etc.
FPFNStatBox() - Constructor for class edu.dartmouth.bglab.util.FPFNStatBox
 
FULL - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
FULL_ARRAY - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
FULL_BIN_ARRAY - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
FULL_BIN_INDICES - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
FULL_COMPLEMENT - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
FULL_EXPANSION - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
FULL_ID - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
FULL_INDICES - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
FULL_STRINGENCIES - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
FULL_SUPERSETS - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 

G

G - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
Gaussian - Class in edu.dartmouth.bglab.util
 
Gaussian() - Constructor for class edu.dartmouth.bglab.util.Gaussian
 
GEN_NEIGHBORS_RECON_METHOD - Static variable in class edu.dartmouth.bglab.beam.Ambiguizer
 
GENE_COLOR - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
GENE_COLOR - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
GENE_NAME_SEPARATOR - Static variable in class edu.dartmouth.bglab.io.FileReaders
Used to separate gene names in UnkownGeneException.
GENE_THICKNESS - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
GENE_THICKNESS - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
geneFileRoot() - Static method in class edu.dartmouth.bglab.GlobalParams
 
geneID - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
geneIDs - Variable in class edu.dartmouth.bglab.beam.CGIDriver
 
geneIds - Variable in class edu.dartmouth.bglab.io.OrganismLoader.FastaRecord
 
geneLength - Variable in class edu.dartmouth.bglab.beam.CGIDriver
 
geneLength - Variable in class edu.dartmouth.bglab.score.KSScorer
 
geneLength - Variable in class edu.dartmouth.bglab.search.MotifFinder
The distance between break characters in the biological sequence; set to MotifFinder.UNEQUAL_GENE_LENGTHS if the breaks are not evenly spaced.
GeneMapImageDrawer - Class in edu.dartmouth.bglab.beam.web
 
GeneMapImageDrawer() - Constructor for class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
GeneMapImageDrawer.Gene - Class in edu.dartmouth.bglab.beam.web
 
GeneMapImageDrawer.Gene(String, int) - Constructor for class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Gene
 
GeneMapImageDrawer.Motif - Class in edu.dartmouth.bglab.beam.web
 
GeneMapImageDrawer.Motif(String, int, Color) - Constructor for class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Motif
 
GeneMapImageDrawer.MotifInstance - Class in edu.dartmouth.bglab.beam.web
 
GeneMapImageDrawer.MotifInstance(GeneMapImageDrawer.Motif, int) - Constructor for class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.MotifInstance
 
geneName - Variable in class edu.dartmouth.bglab.motif.MotifInstance
 
geneNameKey - Variable in class edu.dartmouth.bglab.beam.web.WebDriver
Contains the gene names in the order that they are listed in groupMF.
geneNames - Variable in class edu.dartmouth.bglab.beam.CGIDriver
 
geneNumberSynonymsMap - Variable in class edu.dartmouth.bglab.beam.CGIDriver
 
generateIslands() - Method in class edu.dartmouth.bglab.score.MaximalMatcher
Sets foundResult and knownResult to the results of running generateIslands(arr) on arr1 and arr2.
generateIslands(List<Range>) - Method in class edu.dartmouth.bglab.score.MaximalMatcher
Returns a list of islands from arr.
generateModel(int) - Method in class edu.dartmouth.bglab.search.MarkovModel
Generates a new markov model of the given order.
generates(String) - Method in class edu.dartmouth.bglab.motif.Motif
Returns true if and only if seq is an instantiation of this motif.
generateSpecialStats(Motif[], Motif, Stopwatch, String, Scorer) - Static method in class edu.dartmouth.bglab.beam.ResultsEvaluator
A special stat generative function for testing ambiguizers.
generatesString(String) - Method in class edu.dartmouth.bglab.model.ConsensusSequence
Returns true if this string is generated by this model.
generatesString(String) - Method in interface edu.dartmouth.bglab.model.CREModel
Returns true if this model generates the given string at the current stringency, which can be specified by CREModel.setStringency(double).
generatesString(String) - Method in class edu.dartmouth.bglab.model.KMismatchModel
Returns true if this string is generated by this KMM model.
generatesString(String) - Method in class edu.dartmouth.bglab.model.KRModel
Returns true if this string would be generated by this PWM at the current stringency and for the current scoringTable.
generatesString(String) - Method in class edu.dartmouth.bglab.model.PWM
Returns true if this string would be generated by this PWM at the current stringency and for the current scoringTable.
generateStats(MotifComparator, Motif[], Motif[], Stopwatch, String, Scorer, String) - Static method in class edu.dartmouth.bglab.beam.ResultsEvaluator
The core stats generating function; this produces the sum files we've been using, which include a summary of all the known motifs and which found motifs match (if any) FP/FN counts, restricted FP/FN counts, etc.
genes - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
GENES_WITH_MOTIF_WHICH_DO_NOT_IMPROVE_SCORE - Static variable in class edu.dartmouth.bglab.beam.CGIDriver
 
GENES_WITH_MOTIF_WHICH_IMPROVE_SCORE - Static variable in class edu.dartmouth.bglab.beam.CGIDriver
 
genesRatio - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
genesRatioProb - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
geneStarts - Variable in class edu.dartmouth.bglab.search.MotifFinder
Indices in sequence of gene starts.
genesWithoutMotif - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
genomeComment - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
genomeDate - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
genomeSoftCache - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
genus - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
get(int) - Method in class edu.dartmouth.bglab.motif.MotifList
 
get(Object) - Method in class edu.dartmouth.bglab.score.Scorer.ScoreSoftValueHashMap
 
get(int) - Method in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
get(String, boolean) - Method in class edu.dartmouth.bglab.search.MotifFinder.FindResultsSoftValueHashMap
 
get(String, boolean) - Method in class edu.dartmouth.bglab.search.MotifFinder.GenomeSoftValueHashMap
 
get(Object) - Method in class edu.dartmouth.bglab.util.SoftValueHashMap
 
get(int) - Method in class edu.dartmouth.bglab.util.SuffixArray
 
getAlgorithm() - Method in class edu.dartmouth.bglab.motif.Motif
 
getAlignedInstances(Motif, MotifFinder) - Static method in class edu.dartmouth.bglab.search.SearchUtils
Returns all the instances of motif in mf as "little r", but such that the motifs will align properly.
getAlphabet() - Method in class edu.dartmouth.bglab.motif.Motif
 
getAlphabeticallyFirstSequence(Motif) - Method in class edu.dartmouth.bglab.motif.SequenceComparator
Returns a motif's sequence if it doesn't use rev comp, or the alphabetically first of the motif's sequence and rev comp sequence if it does use it.
getAmbiguousBaseCount() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the total number of ambiguous bases in this motif's sequence.
getAmbiguousFactor() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the ambiguous factor of a sequence.
getArray() - Method in class edu.dartmouth.bglab.util.SuffixArray
 
getAveragePercentageLengthVariation() - Method in class edu.dartmouth.bglab.search.MotifFinder
 
getAvgGeneLength() - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the avg gene length, not including Alphabet.FILLER characters or Alphabet.SEQUENCE_BREAK characters.
getBackgroundProbs() - Method in class edu.dartmouth.bglab.model.KRModel
Returns the background probabilities that the scoring table is based on.
getBaseCount() - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
Returns the number of bases in the sequence.
getBaseCount() - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the number of bases in the sequence.
getBayesProbability() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
getBin(double) - Method in class edu.dartmouth.bglab.util.Histogram
Returns the bin that this value would be binned to.
getBooleanProperty(String) - Method in class edu.dartmouth.bglab.util.UberProperties
Returns the property with the specified key in this property list.
getCharacters() - Method in class edu.dartmouth.bglab.motif.Alphabet
 
getChars() - Method in class edu.dartmouth.bglab.motif.Alphabet
 
getComparator() - Method in class edu.dartmouth.bglab.model.ConsensusSequence
Comparator sorts arrays from greatest to least by the ConsensusSequence.scoreString(String) method.
getComparator() - Method in interface edu.dartmouth.bglab.model.CREModel
Returns a comparator that sorts arrays from greatest to least.
getComparator() - Method in class edu.dartmouth.bglab.model.KMismatchModel
Comparator sorts arrays from least to greatest by the KMismatchModel.scoreString(String) method.
getComparator() - Method in class edu.dartmouth.bglab.model.KRModel
Comparator sorts arrays from greatest to least by the KRModel.scoreString(String) method.
getComparator() - Method in class edu.dartmouth.bglab.model.PWM
Comparator sorts arrays from greatest to least by the PWM.scoreString(String) method.
getCorrelation() - Method in class edu.dartmouth.bglab.util.LinCorrStatBox
Computes the linear correlation between the points (r^2 value).
getCount() - Method in class edu.dartmouth.bglab.model.PWM
Returns the number of motifs that went into making this pwm.
getCount(char, int) - Method in class edu.dartmouth.bglab.model.PWM
 
getCount(int, int) - Method in class edu.dartmouth.bglab.model.PWM
 
getCount() - Method in class edu.dartmouth.bglab.util.Histogram
Returns the total number of items in the histogram.
getCount(double) - Method in class edu.dartmouth.bglab.util.Histogram
Returns the number of items in the bin that this would be in.
getCountCacheSize() - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the number of elements currently in the cache.
getCounts(int) - Method in class edu.dartmouth.bglab.model.PWM
Returns the base counts in this position.
getCoverageCount(MotifInstance[]) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
getD() - Method in class edu.dartmouth.bglab.model.PWM.StringDoublePair
 
getDefaultScreenDevice() - Method in class edu.dartmouth.bglab.beam.web.GraphicsEnvironment
 
getDiscardOverlaps() - Method in class edu.dartmouth.bglab.score.Scorer
 
getDiscardOverlaps() - Method in class edu.dartmouth.bglab.search.MotifFinder
Gets the value of MotifFinder.discardOverlaps.
getDoubleProperty(String) - Method in class edu.dartmouth.bglab.util.UberProperties
Returns the property with the specified key in this property list.
getDrivers(UberProperties) - Static method in class edu.dartmouth.bglab.beam.Scope
Creates the appropriate sets of driver(s) as defined by the properties.
getElapsedTime() - Method in class edu.dartmouth.bglab.util.Stopwatch
Get's the total elapsed time in the format H:mm:ss.SSS
getElapsedTimeMillis() - Method in class edu.dartmouth.bglab.util.Stopwatch
Gets the total elapsed time in milliseconds.
getEndIndexOf(int) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the index in the sequence of the break character at the end of the specified gene-- gene ID's start at 1.
getExpansion() - Method in class edu.dartmouth.bglab.motif.Motif.LastExpansion
 
getExtensionsOf(Alphabet, Motif[], boolean) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns an array of all of the motifs formed from adding a primary base to the specified side of a motif in seed; side should be set to Motif.LEFT or Motif.RIGHT; if seed is empty, then an empty array is returned.
getFileFilter() - Method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.BackgroundEvalFunc
 
getFileFilter() - Method in interface edu.dartmouth.bglab.model.AffinityEvaluatorDriver.EvaluatorFunction
 
getFindCacheSize() - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the number of elements currently in the cache.
getFindResults(MotifFinder, Motif) - Static method in class edu.dartmouth.bglab.search.MotifFinder
 
getFirstHalf() - Method in class edu.dartmouth.bglab.motif.Motif
Returns a new motif whose sequence is the first half of this motif's sequence.
getFlaggedSequence() - Method in class edu.dartmouth.bglab.motif.Motif
Returns a string representation of this motif as sequence,R/r; this can be turned back into a motif using Motif.parseMotif(String, Alphabet); reverse complement-able motifs are always returned using the alphabetically last sequence.
getFlaggedSequence() - Method in class edu.dartmouth.bglab.motif.Motif.LastExpansion
 
getFlankingSequences(int, Motif, int, MotifFinder) - Static method in class edu.dartmouth.bglab.search.SearchUtils
Returns an array of all the instances of motif in finder, flanked by prefixLength bases upstream of the motif and suffixLength bases downstream of the motif.
getFN() - Method in class edu.dartmouth.bglab.score.MaximalMatcher
Caclulates the false negative rate, defined as 1 - intersection / total number of known bases.
getFN() - Method in class edu.dartmouth.bglab.util.FPFNStatBox
 
getFP() - Method in class edu.dartmouth.bglab.score.MaximalMatcher
Caclulates the false negative rate, defined as 1 - intersection / total number of found bases.
getFP() - Method in class edu.dartmouth.bglab.util.FPFNStatBox
 
getFPFNStats(CREModel, MotifList, MotifList, int) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
 
getFrequencyTable() - Method in class edu.dartmouth.bglab.model.PWM
 
getGene(int, MotifFinder) - Static method in class edu.dartmouth.bglab.search.SearchUtils
Returns the sequence of the gene where the hit is; assumes hit is in a valid sequence range.
getGeneCount() - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
 
getGeneCount() - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the number of genes in the sequence.
getGeneGroupSequenceInFastaFormat() - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
getGeneID() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
getGeneIDOf(int) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
 
getGeneIDOf(int) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the ID of the gene on which the given index in the sequence is located-- these ID's start at 1.
getGeneName() - Method in class edu.dartmouth.bglab.motif.MotifInstance
 
getGeneNamesQuery() - Method in class edu.dartmouth.bglab.beam.web.WebDriver
Returns a query string of the names and lengths of each gene.
getGeneSequence(int) - Method in class edu.dartmouth.bglab.search.MotifFinder
 
getGenesWithoutMotifCount() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
getGenomicMotifFinder() - Method in class edu.dartmouth.bglab.score.GroupScorer
Returns the genomic MotifFinder.
getGoodGenes() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
getGoodGenesCount() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
getGoodGenesDeltaSigMedian() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
getGroupCount(Motif) - Method in class edu.dartmouth.bglab.score.GroupScorer
Changed 6/10/04: Now returns the number of distinct genes m occurs in the group.
getGroupSize() - Method in class edu.dartmouth.bglab.score.GroupScorer
Returns the number of genes in the group
getHardCodedProperties() - Static method in class edu.dartmouth.bglab.util.UberProperties
Hard coded version of default params.
getHeader() - Static method in class edu.dartmouth.bglab.beam.RankedMotifPair
A string that represents the order that things will be printed by the toString method.
getHeader() - Method in class edu.dartmouth.bglab.score.MotifFilter
Returns a tab-delimited string representation of the scorer key.
getHighestOrder() - Method in class edu.dartmouth.bglab.search.MarkovModel
Returns the highest order model we have.
getHistogram() - Method in class edu.dartmouth.bglab.util.Histogram
Returns the array of bins.
getHits(String) - Method in class edu.dartmouth.bglab.model.ConsensusSequence
Returns a MotifList of all Motifs in seq that match this model.
getHits(String) - Method in interface edu.dartmouth.bglab.model.CREModel
Returns those sequences in sequence that match this pwm according to CREModel.generatesString(String) as a MotifList.
getHits(String) - Method in class edu.dartmouth.bglab.model.KMismatchModel
Returns a MotifList of all Motifs (r) in seq that match this model.
getHits(String) - Method in class edu.dartmouth.bglab.model.KRModel
Returns those sequences in sequence that match this pwm according to KRModel.generatesString(String) as a MotifList.
getHits(String) - Method in class edu.dartmouth.bglab.model.PWM
Returns those sequences in sequence that match this pwm according to PWM.generatesString(String) as a MotifList.
getHits(int, int) - Method in class edu.dartmouth.bglab.util.SuffixArray
 
getId() - Method in class edu.dartmouth.bglab.io.FileReaders.NameAndID
 
getInstances(Motif, MotifFinder) - Static method in class edu.dartmouth.bglab.search.SearchUtils
Returns all the instances of of m in mf as motifs with "little r".
getInternalGeneLength() - Method in class edu.dartmouth.bglab.search.MotifFinder
For use in creating new MotifFinders; returns the internal geneLength.
getInternalNCount() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the number of internal Ns in this sequence.
getIntProperty(String) - Method in class edu.dartmouth.bglab.util.UberProperties
Returns the property with the specified key in this property list.
getK() - Method in class edu.dartmouth.bglab.model.KMismatchModel
 
getLeft() - Method in class edu.dartmouth.bglab.util.Range
 
getLength() - Method in class edu.dartmouth.bglab.util.Range
 
getLinCorStats(CREModel, MotifList) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
 
getLocalDirName(Class<UberProperties>) - Static method in class edu.dartmouth.bglab.util.UberProperties
 
getLocation() - Method in class edu.dartmouth.bglab.motif.MotifInstance
 
getLookupCount() - Method in class edu.dartmouth.bglab.score.Scorer
Returns the number of times calculateScore has been called.
getMaxHammingDistance(Motif, String[]) - Static method in class edu.dartmouth.bglab.model.KMismatchModel
Returns the max hamming distance between m and any string in the array.
getMaxLikelihoodMotif() - Method in class edu.dartmouth.bglab.model.PWM
Returns the most probable instantiation of this pwm.
getMean() - Method in class edu.dartmouth.bglab.util.Histogram
Computes the mean of the histogram.
getMemorySummary() - Static method in class edu.dartmouth.bglab.util.MiscUtils
 
getMiddle() - Method in class edu.dartmouth.bglab.util.Range
 
getModel() - Method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.TestModel
 
getMotif() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
getMotifCount() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
getMotifFinder() - Method in class edu.dartmouth.bglab.score.GroupScorer
Overrides Scorer's method to return the groupMF instead of the genomic MF.
getMotifFinder() - Method in class edu.dartmouth.bglab.score.Scorer
 
getMotifFinderIndex(int) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
 
getMotifInstances(Motif) - Method in class edu.dartmouth.bglab.beam.CGIDriver
Returns an array of MotifInstances that represent the locations in the group of the given motif.
getMotifInstances(Motif) - Method in class edu.dartmouth.bglab.beam.web.WebDriver
Returns an array of MotifInstances that represent the locations in the group of the given motif.
getMotifInstances(Motif, MotifFinder) - Static method in class edu.dartmouth.bglab.search.SearchUtils
Same as getInstances, but returns the array of , which includes gene, position and sequence information.
getMotifInstancesQuery(Motif) - Method in class edu.dartmouth.bglab.beam.web.WebDriver
Generates a the motif location part of the query string that gets sent as a URL to ServerSocketImageWriter, wherever that may be.
getName() - Method in class edu.dartmouth.bglab.io.FileReaders.NameAndID
 
getName() - Method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.TestModel
 
getName() - Method in class edu.dartmouth.bglab.model.ConsensusSequence
 
getName() - Method in interface edu.dartmouth.bglab.model.CREModel
Return a name that will be uniq to this type of model.
getName() - Method in class edu.dartmouth.bglab.model.KMismatchModel
 
getName() - Method in class edu.dartmouth.bglab.model.KRModel
Returns KR if beta is greater than 0; EXEMPLAR otherwise.
getName() - Method in class edu.dartmouth.bglab.model.PLConsensusModel
 
getName() - Method in class edu.dartmouth.bglab.model.PWM
 
getNCount(String) - Static method in class edu.dartmouth.bglab.motif.Motif
Returns the total number of Alphabet.N's in the given string.
getNCount() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the number of Ns in this sequence.
getNegativePredictiveValue() - Method in class edu.dartmouth.bglab.util.FPFNStatBox
 
getNoSuchElementException() - Method in class edu.dartmouth.bglab.io.Scanner
 
getOccurringInstantiations(Motif, MotifFinder) - Static method in class edu.dartmouth.bglab.search.SearchUtils
Returns all of the non-degenerate, "little r" instantiations of m that actually occur in mf.
getOkayGenes() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
getOkayGenesCount() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
getOverlap(CREModel, MotifList, MotifList) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
Essentially computes the phi score between the scores of the truePositives and teh true negatives.
getOverlap(Range) - Method in class edu.dartmouth.bglab.util.Range
 
getOverlapStats(CREModel, MotifList, MotifList) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
 
getPhiCoefCorr() - Method in class edu.dartmouth.bglab.util.FPFNStatBox
The Pearson product-moment coefficient of correlation, aka phi coefficient of correlation".
getPositionInGene(int) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
 
getPositionInGene(int) - Method in class edu.dartmouth.bglab.search.MotifFinder
 
getPositivePredictiveValue() - Method in class edu.dartmouth.bglab.util.FPFNStatBox
 
getPrefix(int) - Method in class edu.dartmouth.bglab.motif.Motif
Returns a new motif whose sequence is the first i characters of this motif's sequence.
getProbabilities() - Method in class edu.dartmouth.bglab.model.PWM
Makes a matrix of probabilities instead of counts.
getProbabilities(double) - Method in class edu.dartmouth.bglab.model.PWM
Makes a matrix of probabilities instead of counts.
getProbablityOfMatch(String, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
 
getProperty(String) - Method in class edu.dartmouth.bglab.util.UberProperties
Returns the String of the given property, with leading and trailing spaces trimmed off.
getPWMFor(Motif) - Method in class edu.dartmouth.bglab.beam.web.WebDriver
Returns an HTML-formatted position-weight matrix for the given motif.
getQueryColor() - Method in class edu.dartmouth.bglab.beam.web.WebDriver
Reformats LIGHT_COLOR so it can fit in a query string.
getQueryString(String) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
getRandomBase() - Method in class edu.dartmouth.bglab.search.MarkovModel
Returns a random base from a 0th order MM.
getRandomBase(String) - Method in class edu.dartmouth.bglab.search.MarkovModel
Returns a base drawn randomly given the history.
getRandomChar() - Method in class edu.dartmouth.bglab.motif.Alphabet
 
getRandomChar(double) - Method in class edu.dartmouth.bglab.motif.Alphabet
Returns a random char from the alphabet, where p is the probability that one of the standard 4 bases will be returned.
getRandomInstantiation() - Method in class edu.dartmouth.bglab.motif.Motif
Returns a random instantiation of this motif; the instantiation will have the same alphabet and reverse compliment flag.
getRandomInstantiations(int) - Method in class edu.dartmouth.bglab.motif.Motif
Returns count random instantiations.
getRandomNeighbors(int, Motif, MotifFinder) - Static method in class edu.dartmouth.bglab.search.SearchUtils
Pulls a specified number of random neighbors from this motif, where a neighbor is a random motif of the same length and ambiguity of m that is found in one of the genes that m is found in.
getRankLinCorStats(CREModel, MotifList) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
 
getReconstructedStackTrace() - Method in class edu.dartmouth.bglab.beam.web.ChildProcessProblem
Returns the reconstructed stack trace elements.
getRegExSearchPattern() - Method in class edu.dartmouth.bglab.motif.Motif
 
getResults(String) - Method in class edu.dartmouth.bglab.beam.web.WebDriver
Returns the results of the given stage of the run, or null if the given stage was not run; stepName should be set to BeamDriver.BEAM_NAME, BeamDriver.AMBIGUIZER_NAME, BeamDriver.BIPARTITE_NAME, or BeamDriver.MERGED_NAME.
getRevComp() - Method in class edu.dartmouth.bglab.motif.Motif
Returns a motif whose sequence is the reverse compliment of this sequence, with the same revComp flag and alphabet as this sequence.
getRevCompSequence() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the reverse complement sequence, or null if the reverse complement isn't used.
getRight() - Method in class edu.dartmouth.bglab.util.Range
 
getS() - Method in class edu.dartmouth.bglab.model.PWM.StringDoublePair
 
getScore() - Method in class edu.dartmouth.bglab.model.KRModel
 
getScore() - Method in class edu.dartmouth.bglab.model.PWM
Scans s and returns a MotifList of those motifs that pass the stringency test.
getScore() - Method in class edu.dartmouth.bglab.motif.Motif
 
getScore() - Method in class edu.dartmouth.bglab.motif.MotifList
 
getScoreDelta() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
getScorer() - Method in class edu.dartmouth.bglab.beam.BeamDriver
 
getScorerInfo() - Method in class edu.dartmouth.bglab.motif.Motif
 
getScores(Motif) - Method in class edu.dartmouth.bglab.score.MotifFilter
Calculates the score of m by all the scorers in the order of scorer key and returns a tab-delimited string of the result.
getScoringTable() - Method in class edu.dartmouth.bglab.model.PWM
 
getScrambled(Motif) - Method in class edu.dartmouth.bglab.score.ZScoreScorer
 
getScreenDevices() - Method in class edu.dartmouth.bglab.beam.web.GraphicsEnvironment
 
getSD() - Method in class edu.dartmouth.bglab.util.Histogram
Computes the sample standard deviation.
getSearchedPatternLength() - Method in class edu.dartmouth.bglab.motif.Motif
 
getSensitivity() - Method in class edu.dartmouth.bglab.util.FPFNStatBox
Sen = TP / (TP+FN).
getSequence() - Method in class edu.dartmouth.bglab.model.ConsensusSequence
Returns the sequence.
getSequence(Alphabet) - Method in class edu.dartmouth.bglab.model.PWM
 
getSequence() - Method in class edu.dartmouth.bglab.motif.Motif
 
getSequence() - Method in class edu.dartmouth.bglab.motif.MotifInstance
 
getSequence() - Method in class edu.dartmouth.bglab.motif.MotifList
Returns the getFlaggedSequence() versions of the motifs in this list, separated by MotifList.MOTIF_DELIMITER.
getSequence() - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the biological sequence.
getSequence() - Method in class edu.dartmouth.bglab.util.SuffixArray
 
getSequenceLength() - Method in class edu.dartmouth.bglab.search.MotifFinder
 
getSoftCache(MotifFinder) - Static method in class edu.dartmouth.bglab.search.MotifFinder
 
getSoftCachedFindResults(MotifFinder, String, boolean) - Static method in class edu.dartmouth.bglab.search.MotifFinder
 
getSpecificity() - Method in class edu.dartmouth.bglab.util.FPFNStatBox
Spec = TN / (TN+FP).
getStackTrace(Throwable) - Static method in class edu.dartmouth.bglab.beam.CGIScope
 
getStrand() - Method in class edu.dartmouth.bglab.motif.MotifInstance
 
getStreamContents(InputStream) - Static method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
Makes the contents of an input stream into a string.
getStringency() - Method in class edu.dartmouth.bglab.model.KRModel
 
getStringency() - Method in class edu.dartmouth.bglab.model.PWM
 
getStrippedRevCompSequence() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the reverse complement sequence stripped of leading and trailing N's, or null if the reverse complement isn't used.
getStrippedSequence() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the sequence stripped of leading and trailing N's.
getSubset(Motif[], int, int) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
Gets a continuous subset of length length from marr starting at start and wrapping when the end of the array is reached.
getTextMotifGeneSummary(CGIDriver.MotifGeneSummary) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
getTN() - Method in class edu.dartmouth.bglab.util.FPFNStatBox
 
getTop() - Method in class edu.dartmouth.bglab.util.Heap
Returns the top of the heap.
getTP() - Method in class edu.dartmouth.bglab.util.FPFNStatBox
 
getUniformCDF(double, double) - Static method in class edu.dartmouth.bglab.util.KS
Returns a uniform CDF.
getUpstreamOffset() - Method in class edu.dartmouth.bglab.motif.MotifInstance
 
getUsedMemory() - Static method in class edu.dartmouth.bglab.util.MoreMath
 
getUsedMemoryInMb() - Static method in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
getUsedMemoryInMb() - Static method in class edu.dartmouth.bglab.search.CompositeMotifFinder
 
getUsedMemoryInMb() - Static method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
 
getUsePrior() - Method in class edu.dartmouth.bglab.score.Scorer
 
getValue() - Method in class edu.dartmouth.bglab.model.KRModel
Same as getScore().
getValue() - Method in class edu.dartmouth.bglab.model.PWM
Same as getScore().
getValue() - Method in class edu.dartmouth.bglab.motif.Motif
Same as getScore().
getValue() - Method in class edu.dartmouth.bglab.motif.MotifList
Same as getScore().
getValue() - Method in class edu.dartmouth.bglab.util.AveStatBox
Returns the average of all points seen thus far.
getValue() - Method in interface edu.dartmouth.bglab.util.Binnable
Returns the value by which the item will be binned.
getValue() - Method in class edu.dartmouth.bglab.util.FPFNStatBox
Returns the coefficient of correlation.
getValue(int) - Method in class edu.dartmouth.bglab.util.Histogram
Converts a bin into the lowest value that would be placed in that bin.
getValue() - Method in class edu.dartmouth.bglab.util.LinCorrStatBox
Returns the linear correlation.
getWellBehavedInstantiations(Motif, MotifFinder) - Static method in class edu.dartmouth.bglab.search.SearchUtils
Returns all the non-degenerate instantiations of m that actually occur in mf, and forces them to be in the same orientiation; the motifs returned will have the same flag as the given motif, will be sorted in alphabetical order, and will contain no duplicates.
getWildcardOptimizationCutoff() - Method in class edu.dartmouth.bglab.search.MotifFinder
GffToSql - Class in edu.dartmouth.bglab.dataImportPreparation
 
GffToSql(String[]) - Constructor for class edu.dartmouth.bglab.dataImportPreparation.GffToSql
Creates a new instance of GffToSql
GlobalParams - Class in edu.dartmouth.bglab
Contains global constants for the bglab sub-packages.
GlobalParams() - Constructor for class edu.dartmouth.bglab.GlobalParams
 
globalTimer - Static variable in class edu.dartmouth.bglab.beam.CGIScope
 
globalTimer - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
goodGenes - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
GR(Motif, Scorer, int, int, int, int) - Static method in class edu.dartmouth.bglab.beam.Ambiguizer
Given a Motif, generates all the 1HD neighbors using expandNeighbors(), then reconstructs a new motif from those neighbors using reconstructFromList().
GR(Motif[], Scorer, UberProperties) - Static method in class edu.dartmouth.bglab.beam.Ambiguizer
Calls GR on all the Motifs.
GraphicsEnvironment - Class in edu.dartmouth.bglab.beam.web
 
GraphicsEnvironment(GraphicsEnvironment) - Constructor for class edu.dartmouth.bglab.beam.web.GraphicsEnvironment
 
group - Variable in class edu.dartmouth.bglab.beam.web.WebDriver
 
GROUP_SIZES - Static variable in class edu.dartmouth.bglab.beam.BackgroundDriver
 
groupLength - Variable in class edu.dartmouth.bglab.beam.CGIDriver
 
groupMF - Variable in class edu.dartmouth.bglab.beam.web.WebDriver
 
groupMF - Variable in class edu.dartmouth.bglab.score.GroupScorer
 
groupScorer - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
GroupScorer - Class in edu.dartmouth.bglab.score
Used to calculate sig scores for motifs or motif lists using two motif finders, one to represent the entire relevant biological sequence, and another to represent the group of subsequences of specific importance.
GroupScorer(MotifFinder, MotifFinder, boolean, int) - Constructor for class edu.dartmouth.bglab.score.GroupScorer
Sets the motif finder and group motif finder and tells them whether or not to discard overlaps and what wildcard optimization cutoff to use.
groupSoftCache - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 

H

H - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
hammingDistance(Motif, Motif, boolean) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Computes the hamming distance between two motifs.
hammingDistance(String, String, boolean) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Computes the hamming distance between two strings.
hammingFilter(Motif[], int, boolean) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Performs a pairwise comparison on all the motifs and returns an array of motifs that are within maxHD of at least one other Motif.
hash - Variable in class edu.dartmouth.bglab.util.SoftValueHashMap
The internal HashMap that will hold the SoftReference.
hashCode() - Method in class edu.dartmouth.bglab.motif.Motif
Simply returns the hashCode value of the Motif.getFlaggedSequence() representation.
hashCode() - Method in class edu.dartmouth.bglab.motif.MotifList
Simply returns the hashCode value of the MotifList.getSequence() representation.
hasNext() - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if this scanner has another token in its input.
hasNextBigDecimal() - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a BigDecimal using the nextBigDecimal() method.
hasNextBigInteger() - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a BigInteger in the default radix using the nextBigInteger() method.
hasNextBigInteger(int) - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a BigInteger in the specified radix using the nextBigInteger() method.
hasNextBoolean() - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a boolean value.
hasNextByte() - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a byte value in the default radix using the nextByte() method.
hasNextByte(int) - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a byte value in the specified radix using the nextByte() method.
hasNextChar() - Method in class edu.dartmouth.bglab.io.Scanner
 
hasNextDouble() - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a double value using the nextDouble() method.
hasNextFloat() - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a float value using the nextFloat() method.
hasNextInt() - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as an int value in the default radix using the nextInt() method.
hasNextInt(int) - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as an int value in the specified radix using the nextInt() method.
hasNextLine() - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if there is another line in the input of this scanner.
hasNextLong() - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a long value in the default radix using the nextLong() method.
hasNextLong(int) - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a long value in the specified radix using the nextLong() method.
hasNextShort() - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a short value in the default radix using the nextShort() method.
hasNextShort(int) - Method in class edu.dartmouth.bglab.io.Scanner
Returns true if the next token in this scanner's input can be interpreted as a short value in the specified radix using the nextShort() method.
hasRepetitiveInstantiation(Motif) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns true if this motif has an instantiation that is all one base.
hasRunningProcesses(String) - Static method in class edu.dartmouth.bglab.beam.web.WebDriver
Returns true if this user has processes running.
hasUniformGeneLengths() - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns true if the genes are all the same length.
HD - Variable in class edu.dartmouth.bglab.score.ConservationICScorer
The hamming space around which to expand each motif.
HD - Variable in class edu.dartmouth.bglab.score.ConservationRatioScorer
The hamming space around which to expand each motif.
HD - Static variable in class edu.dartmouth.bglab.score.MotifFilter
 
HD - Variable in class edu.dartmouth.bglab.score.RelativeEntropyScorer
The hamming space around which to expand each motif.
Heap - Class in edu.dartmouth.bglab.util
A partial impelentation of the Collection interface as a heap.
Heap() - Constructor for class edu.dartmouth.bglab.util.Heap
Creates a new Heap of type MAX_HEAP and initial capacity of INIT_CAPACITY.
Heap(Comparator<? super Object>) - Constructor for class edu.dartmouth.bglab.util.Heap
Creates a new Heap of type MAX_HEAP and initial capacity of INIT_CAPACITY.
Heap(Comparator<? super Object>, int) - Constructor for class edu.dartmouth.bglab.util.Heap
Creates a new Heap of type MAX_HEAP and the specified initial capacity.
Heap(Comparator<? super Object>, int, int) - Constructor for class edu.dartmouth.bglab.util.Heap
Creates a new Heap of type MAX_HEAP and the specified initial capacity.
Heap(int) - Constructor for class edu.dartmouth.bglab.util.Heap
Creates a new Heap of the specified type and initial capacity of INIT_CAPACITY.
Heap(int, int) - Constructor for class edu.dartmouth.bglab.util.Heap
Creates a new Heap of type MAX_HEAP and the specified initial capacity.
heapify(int) - Method in class edu.dartmouth.bglab.util.Heap
Given a node i, assumes that left(i) and right(i) are roots of proper heaps, but that the heap rooted at i may not be.
heapSize - Variable in class edu.dartmouth.bglab.util.Heap
 
Histogram - Class in edu.dartmouth.bglab.util
For generating histograms of Binnable objects.
Histogram(Binnable[], int) - Constructor for class edu.dartmouth.bglab.util.Histogram
The most often used constructor.
Histogram(Binnable[], int, int) - Constructor for class edu.dartmouth.bglab.util.Histogram
Specifying the minValue allows you to normalize different Histograms around the same min value.
Histogram(int, int, int) - Constructor for class edu.dartmouth.bglab.util.Histogram
Sets up the variables such that single values can be added to the Histogram.
hits - Variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Gene
 
hits - Variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Gene
 
hits - Variable in class edu.dartmouth.bglab.search.MotifFinder.UncompressedFindResults
 

I

id - Variable in class edu.dartmouth.bglab.io.FileReaders.NameAndID
 
idMappingMetaTable - Static variable in class edu.dartmouth.bglab.io.FileReaders
A hashtable of hashtables; contains a hashtable for each gene ID file.
IllegalFastaFileException - Exception in edu.dartmouth.bglab.io
An exception used to notify a caller that what was expected to be in Fasta format was not.
IllegalFastaFileException() - Constructor for exception edu.dartmouth.bglab.io.IllegalFastaFileException
 
IllegalFastaFileException(String) - Constructor for exception edu.dartmouth.bglab.io.IllegalFastaFileException
 
IllegalFastaFileException(String, Throwable) - Constructor for exception edu.dartmouth.bglab.io.IllegalFastaFileException
 
IllegalFastaFileException(Throwable) - Constructor for exception edu.dartmouth.bglab.io.IllegalFastaFileException
 
in - Variable in class edu.dartmouth.bglab.beam.web.StreamPipe
 
incrementSuccessfulGetCtr() - Method in class edu.dartmouth.bglab.score.Scorer.ScoreSoftValueHashMap
 
incrementUnsuccessfulGetCtr() - Method in class edu.dartmouth.bglab.score.Scorer.ScoreSoftValueHashMap
 
indexOf(char) - Method in class edu.dartmouth.bglab.motif.Alphabet
Returns the index of c in the array returned by Alphabet.getChars().
INIT_CAPACITY - Static variable in class edu.dartmouth.bglab.util.Heap
 
INIT_SIZE - Static variable in class edu.dartmouth.bglab.score.MaximalMatcher
 
initialize() - Method in class edu.dartmouth.bglab.motif.Motif
 
initialize(String, String, int) - Method in class edu.dartmouth.bglab.search.MotifFinder
initializeBipartiteCaches() - Method in class edu.dartmouth.bglab.search.MotifFinder
Turns on caching, then computes count and find to initialize the caching appropriately for bipartite searching.
initializeDataStructure() - Method in class edu.dartmouth.bglab.search.ComparatorMotifFinder
Initializes the internal suffix array.
initializeDataStructure() - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
Initializes the internal suffix array.
initializeDataStructure() - Method in class edu.dartmouth.bglab.search.MarkovModel
Initializes the model and counts array.
initializeDataStructure() - Method in class edu.dartmouth.bglab.search.MotifFinder
Subclasses should implement to initialize any data structures used to perform searches; this method is called automatically by the MotifFinder constructor.
initializeDataStructure() - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
Initializes the internal suffix array.
initiateMFvars(MotifFinder, boolean) - Static method in class edu.dartmouth.bglab.model.ModelEvaluator
 
INSTANCE_DELIMITER - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
intArrayToString(int[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Returns a string version of an int array with the ints separated by commas.
integersToInts(Integer[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Converts the Integers to ints.
intersectionOf(char, char) - Method in class edu.dartmouth.bglab.motif.Alphabet
Returns the char representing the set of bases that is the intersection of c1 and c2.
intersectionOf(char[], char[]) - Method in class edu.dartmouth.bglab.motif.Motif
Returns the intersection of two sequences, which must be the same length, although that is not checked here.
intersectionOf(String, String) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns the degenerate intersection of two sequences of the same length.
intersectionWith(Motif) - Method in class edu.dartmouth.bglab.motif.Motif
Returns the intersection of this motif and m, which must be the same length; if either motif uses the reverse complement, the motif returned is the most unambiguous of the two possible char-by-char intersections between this and m.
INTRON_MARKER - Static variable in class edu.dartmouth.bglab.beam.CGIDriver
 
InvalidGeneListException - Exception in edu.dartmouth.bglab.beam.web
A RuntimeException that is thrown if the gene list contains some error in it.
InvalidGeneListException() - Constructor for exception edu.dartmouth.bglab.beam.web.InvalidGeneListException
 
InvalidGeneListException(String) - Constructor for exception edu.dartmouth.bglab.beam.web.InvalidGeneListException
 
InvalidGeneListException(String, Throwable) - Constructor for exception edu.dartmouth.bglab.beam.web.InvalidGeneListException
 
InvalidGeneListException(Throwable) - Constructor for exception edu.dartmouth.bglab.beam.web.InvalidGeneListException
 
inverseOf(char) - Method in class edu.dartmouth.bglab.motif.Alphabet
Returns the char that represents the bases that aren't in c.
ioException() - Method in class edu.dartmouth.bglab.io.Scanner
Returns the IOException last thrown by this Scanner.
IOTester - Class in edu.dartmouth.bglab.test
For testing the .io package.
IOTester() - Constructor for class edu.dartmouth.bglab.test.IOTester
 
isAmbiguous(char) - Method in class edu.dartmouth.bglab.motif.Alphabet
 
isCachingOn() - Method in class edu.dartmouth.bglab.search.MotifFinder
 
isDegenerateRepetitive(String, int) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns true if this degenerate motif is repetitive up to the given maxPeriodicity, where the maxPeriodicity is the maximum length of a repeat.
isDegenerateRepetitivePeriod(String, int) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns true if this degenerate motif is repetitive at the given period, where the period is the length of a repeat.
isDone() - Method in class edu.dartmouth.bglab.beam.web.WebDriver
Returns true if the run finished successfully; throws an exception if the run crashed.
isEmpty() - Method in class edu.dartmouth.bglab.motif.MotifList
 
isEmpty() - Method in class edu.dartmouth.bglab.util.Heap
Returns true if there are no elements in the heap.
isFasta - Variable in class edu.dartmouth.bglab.beam.CGIDriver
 
isMotifBackwards(Motif) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
isN(char) - Static method in class edu.dartmouth.bglab.motif.Alphabet
Returns true if c is the Alphabet.N character.
isProbability(double) - Static method in class edu.dartmouth.bglab.util.MoreMath
Calls MoreMath.areProbabilities(double[], double) with a default TOLERANCE of 0.
isProbability(double, double) - Static method in class edu.dartmouth.bglab.util.MoreMath
Returns true iff d is in the range [0..1] allowing for the given TOLERANCE.
isRepetitive(Motif) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
isRepetitive(String) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
isRepetitive(String, int) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns true if this motif is repetitive up to the given maxPeriodicity, where the maxPeriodicity is the maximum length of a repeat.
isRepetitive(String, int, int) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns true if any substring of seq of length minRepStretchLength evaluates to true when run on MotifUtils.isRepetitive(String, int).
isTerminalChar(char) - Static method in class edu.dartmouth.bglab.util.SuffixArray
 
isWhitespace(int) - Method in class edu.dartmouth.bglab.io.Scanner
 
iterator(MotifFinder) - Method in class edu.dartmouth.bglab.search.AggregatedFindResults
 
iterator(MotifFinder) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
iterator(MotifFinder) - Method in interface edu.dartmouth.bglab.search.FindResults
 
iterator(MotifFinder) - Method in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
iterator(MotifFinder) - Method in class edu.dartmouth.bglab.search.MotifFinder.UncompressedFindResults
 
iterator(MotifFinder) - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
Note this does not return the hits in order

J

jobIDRegEx - Static variable in class edu.dartmouth.bglab.beam.CGIScope
 
join(String, Collection<String>) - Static method in class edu.dartmouth.bglab.GlobalParams
join items in a collection into a delimited String
join(String, String[]) - Static method in class edu.dartmouth.bglab.util.MiscUtils
join items in a collection into a delimited String

K

k - Variable in class edu.dartmouth.bglab.model.KMismatchModel
 
K - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
key - Variable in class edu.dartmouth.bglab.score.MotifFilter
 
killRunningProcesses(String) - Static method in class edu.dartmouth.bglab.beam.web.WebDriver
Kills all of this user's processes running.
KMismatchModel - Class in edu.dartmouth.bglab.model
Implementation of the k-mismatch model that keeps track of reverse complement status.
KMismatchModel(Motif, int) - Constructor for class edu.dartmouth.bglab.model.KMismatchModel
Creates a new k-mismatch model using the given Motif as the model and k as the number of allowable mismatches.
KMismatchModel(String, boolean, String[]) - Constructor for class edu.dartmouth.bglab.model.KMismatchModel
Creates a new k-mismatch model from a consensus sequence and the array of actual binding site sequences, setting k to the max hamming distance of any of the binding sites from the consensus; uses the given reverse complement flag.
KMismatchModel(String, int) - Constructor for class edu.dartmouth.bglab.model.KMismatchModel
Creates a new k-mismatch model.
KMismatchModel(String, String[]) - Constructor for class edu.dartmouth.bglab.model.KMismatchModel
Creates a new k-mismatch model from a consensus sequence and the array of actual binding site sequences, setting k to the max hamming distance of any of the binding sites from the consensus; reverse complement flag is set to true if this results in a smaller k than does false, but otherwise it is set to false.
KMM_CRE - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
knownMotif - Variable in class edu.dartmouth.bglab.beam.RankedMotifPair
Intended to be the known motif, but can be any motif.
knownMotifs - Variable in class edu.dartmouth.bglab.beam.BeamDriver
 
knownResult - Variable in class edu.dartmouth.bglab.score.MaximalMatcher
 
KR_CRE - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
KRModel - Class in edu.dartmouth.bglab.model
An implementation of the non-parametric model described by King and Roth.
KRModel() - Constructor for class edu.dartmouth.bglab.model.KRModel
This creates an empty PWM--most methods will cause unchecked exceptions to be thrown.
KRModel(double) - Constructor for class edu.dartmouth.bglab.model.KRModel
This creates an empty PWM with a specific beta--most methods will cause unchecked exceptions to be thrown.
KRModel(Motif, MotifFinder) - Constructor for class edu.dartmouth.bglab.model.KRModel
Converts a consensus motif into a position-weight matrix.
KRModel(Motif[], MotifFinder) - Constructor for class edu.dartmouth.bglab.model.KRModel
Converts an array of unambiguous motifs of the same length and same reverse complement status into a KRModel.
KRModel(MotifList) - Constructor for class edu.dartmouth.bglab.model.KRModel
Converts a whitespace-delimited table into a position-weight matrix with the given reverse complement flag, and with stringency set to KRModel.DEFAULT_STRINGENCY.
KRModel(String[]) - Constructor for class edu.dartmouth.bglab.model.KRModel
Converts a whitespace-delimited table into a position-weight matrix with the reverse complement flagset to CREModel.DEFAULT_RC, and with stringency set to KRModel.DEFAULT_STRINGENCY.
KRModel(String[], boolean) - Constructor for class edu.dartmouth.bglab.model.KRModel
Converts a whitespace-delimited table into a position-weight matrix with the given reverse complement flag, and with stringency set to KRModel.DEFAULT_STRINGENCY.
KS - Class in edu.dartmouth.bglab.util
The Kolmogorov-Smirnov statistic and probability methods.
KS() - Constructor for class edu.dartmouth.bglab.util.KS
 
KSGroupScorer - Class in edu.dartmouth.bglab.score
A scorer based on the probability that a motif (or motif list) is distributed genomically according to some given CDF.
KSGroupScorer(MotifFinder, MotifFinder, boolean) - Constructor for class edu.dartmouth.bglab.score.KSGroupScorer
Sets the motif finder and discardOverlaps parameters of the motif finder appropriately and defaults the cdf for the uniform cdf with a range [0..averageGeneLength] (if finder has uniform gene lengths) or [0..sequenceLength] (if finder has variable length genes).
KSScorer - Class in edu.dartmouth.bglab.score
A scorer based on the probability that a motif (or motif list) is distributed genomically according to some given CDF.
KSScorer(MotifFinder, boolean) - Constructor for class edu.dartmouth.bglab.score.KSScorer
Sets the motif finder and discardOverlaps parameters of the motif finder appropriately and defaults the cdf for the uniform cdf with a range [0..averageGeneLength] (if finder has uniform gene lengths) or [0..sequenceLength] (if finder has variable length genes).
KSScorer(MotifFinder, boolean, CDF) - Constructor for class edu.dartmouth.bglab.score.KSScorer
Sets the motif finder and discardOverlaps parameters of the motif finder appropriately and sets the cdf to the given cdf.

L

LAPLACE - Static variable in class edu.dartmouth.bglab.model.PWM
Used in relative entropy calculations.
LAPLACE - Static variable in class edu.dartmouth.bglab.score.MarkovMaxOrderScorer
The a pseuodo count that is added to all counts in the ratio calculations.
LAPLACE - Static variable in class edu.dartmouth.bglab.score.RatioScorer
The a pseuodo count that is added to all counts in the ratio calculations.
LAPLACE - Static variable in class edu.dartmouth.bglab.search.MarkovModel
 
last() - Method in class edu.dartmouth.bglab.search.AggregatedFindResults
 
last() - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
last() - Method in interface edu.dartmouth.bglab.search.FindResults
 
last() - Method in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
last() - Method in class edu.dartmouth.bglab.search.MotifFinder.UncompressedFindResults
 
last() - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
lastExpansion - Static variable in class edu.dartmouth.bglab.motif.Motif
 
LEFT - Static variable in class edu.dartmouth.bglab.motif.Motif
Defines the left (5') side of a motif.
left(int) - Method in class edu.dartmouth.bglab.util.Heap
 
left - Variable in class edu.dartmouth.bglab.util.Range
 
LEFT_PADDING - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
LEFT_PADDING - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
length - Variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Gene
 
length - Variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Motif
 
length - Variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Gene
 
length - Variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Motif
 
length() - Method in class edu.dartmouth.bglab.model.KRModel
 
length() - Method in class edu.dartmouth.bglab.model.PWM
 
length() - Method in class edu.dartmouth.bglab.motif.Motif
 
LIGHT_COLOR - Static variable in class edu.dartmouth.bglab.beam.web.WebDriver
Light color for web pages.
linCorr - Variable in class edu.dartmouth.bglab.util.LinCorrStatBox
 
LinCorrStatBox - Class in edu.dartmouth.bglab.util
A StatBox for computing Linear Correlation (r^2).
LinCorrStatBox() - Constructor for class edu.dartmouth.bglab.util.LinCorrStatBox
 
LinCorrStatBox(boolean) - Constructor for class edu.dartmouth.bglab.util.LinCorrStatBox
 
LinCorrStatBox.Point - Class in edu.dartmouth.bglab.util
 
LinCorrStatBox.Point(double, double) - Constructor for class edu.dartmouth.bglab.util.LinCorrStatBox.Point
 
LinearityTesterDriver - Class in edu.dartmouth.bglab.beam
This is a general utility driver for testing things involved in the Linearity proof paper.
LinearityTesterDriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.LinearityTesterDriver
Sets the file root, test ID, thread ID, properties, and scorer.
LinearityTesterDriver(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.LinearityTesterDriver
Sets the file root, test ID, thread ID, properties, and scorer; uses the specified group instead of pulling the group ID from the properties.
linearlyOptimize(Motif[], Scorer, UberProperties) - Static method in class edu.dartmouth.bglab.beam.Ambiguizer
The mutational ambiguizer method.
list - Variable in class edu.dartmouth.bglab.motif.MotifList
 
LIST_STRINGENCIES - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
loadBipartiteCaches() - Method in class edu.dartmouth.bglab.search.MotifFinder
Turns on caching, fills the find cache with all of the 2-mers and 3-mers, and fills the count cache with bipartite versions, containing from MotifFinder.BIPARTITE_INIT_N_COUNT_MIN to MotifFinder.BIPARTITE_INIT_N_COUNT_MAX N's in the middle, of all of the MotifFinder.BIPARTITE_INIT_LEN-mers.
loadPropertiesFile(String) - Static method in class edu.dartmouth.bglab.util.UberProperties
 
log4jProps() - Static method in class edu.dartmouth.bglab.GlobalParams
 
LOG_2 - Static variable in class edu.dartmouth.bglab.util.MoreMath
Precomputed ln(2).
LOG_DIR - Static variable in class edu.dartmouth.bglab.beam.web.WebDriver
Directory for storing various log files.
LOG_ODDS - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
logCount(MotifFinder, Motif) - Method in class edu.dartmouth.bglab.score.LogOccurrenceScorer
Returns sum_i [ln(f_im + 1)] where f_im is the number of occurrences of motif m in gene i.
logCount(MotifFinder, MotifList) - Method in class edu.dartmouth.bglab.score.LogOccurrenceScorer
Returns sum_i [ln(f_im + 1)] where f_im is the number of occurrences of MotifList m in gene i.
logFactorial(int) - Static method in class edu.dartmouth.bglab.util.MoreMath
Computes and returns ln(n!).
logFileRoot() - Static method in class edu.dartmouth.bglab.GlobalParams
 
logger - Static variable in class edu.dartmouth.bglab.beam.Scope
 
logger - Static variable in class edu.dartmouth.bglab.beam.web.WebDriver
 
logger - Static variable in class edu.dartmouth.bglab.beam.web.WebDriverJr
 
logger - Static variable in class edu.dartmouth.bglab.beam.WebScope
 
logger - Static variable in class edu.dartmouth.bglab.util.UberProperties
 
logInit() - Method in class edu.dartmouth.bglab.util.UberProperties
initialize log4j logging
logLikelihood(double, double) - Static method in class edu.dartmouth.bglab.util.MoreMath
Returns the log likelihood ratio, definied as log_2[observed / average].
LogOccurrenceScorer - Class in edu.dartmouth.bglab.score
An occurrence scorer is a group scorer that scores motifs based on the number of times they occur in the sequence and in the group.
LogOccurrenceScorer(MotifFinder, MotifFinder, boolean) - Constructor for class edu.dartmouth.bglab.score.LogOccurrenceScorer
Sets the motif finder and group motif finder and tells them whether or not to discard overlaps.
logProbabilityOf(Motif) - Method in class edu.dartmouth.bglab.search.MarkovModel
The probability of any substring of this motif's length actually being an instance of this motif; returns in Natural log space.
logProbabilityOf(String) - Method in class edu.dartmouth.bglab.search.MarkovModel
Computes the probability of seq given the highest order model we have.
logUser(String, String, String, String) - Static method in class edu.dartmouth.bglab.beam.web.WebDriver
Write's information about a user to a log file named after the current year found in WebDriver.LOG_DIR.
lookupCount - Variable in class edu.dartmouth.bglab.score.Scorer
 

M

m - Variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.MotifInstance
 
m - Variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.MotifInstance
 
m - Variable in class edu.dartmouth.bglab.model.ConsensusSequence
 
m - Variable in class edu.dartmouth.bglab.model.KMismatchModel
 
M - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
M - Static variable in class edu.dartmouth.bglab.test.SearchTester
 
m_closed - Variable in class edu.dartmouth.bglab.io.Scanner
 
m_ioException - Variable in class edu.dartmouth.bglab.io.Scanner
 
m_lnReader - Variable in class edu.dartmouth.bglab.io.Scanner
 
m_previousNextBuffer - Variable in class edu.dartmouth.bglab.io.Scanner
 
m_radix - Variable in class edu.dartmouth.bglab.io.Scanner
 
m_reader - Variable in class edu.dartmouth.bglab.io.Scanner
 
madeGoodGeneBayesDeltaSig - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
main(String[]) - Static method in class edu.dartmouth.bglab.beam.CGIScope
 
main(String[]) - Static method in class edu.dartmouth.bglab.beam.PRISM
 
main(String[]) - Static method in class edu.dartmouth.bglab.beam.Scope
 
main(String[]) - Static method in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
main(String[]) - Static method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
main(String[]) - Static method in class edu.dartmouth.bglab.beam.web.WebDriverJr
Allows WebDriver to do its dirty work in a child process.
main(String[]) - Static method in class edu.dartmouth.bglab.beam.WebScope
 
main(String[]) - Static method in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
main(String[]) - Static method in class edu.dartmouth.bglab.io.OrganismLoader
 
main(String[]) - Static method in class edu.dartmouth.bglab.io.SynonymChecker
 
main(String[]) - Static method in class edu.dartmouth.bglab.io.SynonymLoader
 
main(String[]) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
Runs the current evaluation and returns the results in a StatBox.
main(String[]) - Static method in class edu.dartmouth.bglab.model.ModelEvaluator
 
main(String[]) - Static method in class edu.dartmouth.bglab.model.PWMEvaluator
 
main(String[]) - Static method in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
main(String[]) - Static method in class edu.dartmouth.bglab.search.CompositeMotifFinder
 
main(String[]) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Saves a motif finder and its bipartite caches to file so that they can be loaded in quickly in the future.
main(String[]) - Static method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
 
main(String[]) - Static method in class edu.dartmouth.bglab.test.BeamTester
 
main(String[]) - Static method in class edu.dartmouth.bglab.test.CharlieTester
 
main(String[]) - Static method in class edu.dartmouth.bglab.test.IOTester
 
main(String[]) - Static method in class edu.dartmouth.bglab.test.ModelTester
 
main(String[]) - Static method in class edu.dartmouth.bglab.test.MotifTester
 
main(String[]) - Static method in class edu.dartmouth.bglab.test.ScoreTester
 
main(String[]) - Static method in class edu.dartmouth.bglab.test.SearchTester
 
main(String[]) - Static method in class edu.dartmouth.bglab.test.UtilTester
 
main(String[]) - Static method in class edu.dartmouth.bglab.util.SuffixArray
 
makeBipartite(int) - Method in class edu.dartmouth.bglab.motif.Motif
Returns a copy of this motif with nCount N's stuck in its middle.
makeMarkovModel(Motif[]) - Static method in class edu.dartmouth.bglab.search.MarkovModel
Constructs a suffix array for a markov model using the given String[]; motifs with R have both orientations added, unless the motif is palindromic.
makeMarkovModel(String[]) - Static method in class edu.dartmouth.bglab.search.MarkovModel
Constructs a suffix array for a markov model using the given String[].
makeNeighborhoodPWM(Motif, MotifFinder) - Static method in class edu.dartmouth.bglab.model.PWM
Makes a PWM of the 1 hamming distance neighborhood of m in the motif finder mf.
makePrettySequence(String) - Method in class edu.dartmouth.bglab.motif.Motif
Returns a sequence with primary bases in caps and ambiguous bases as lowercase slash-separated lists of the base expansion
makeRandomMotif(int, boolean, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
Returns a random motif whose length is between Motif.MIN_RANDOM_LENGTH and maxLength, inclusive.
makeRandomMotif(int, int, boolean, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
Returns a random motif whose length is between minLength and maxLength, inclusive.
makeRandomMotif(int, int, double, double, boolean, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
Returns a random motif whose length is between minLength and mazLength and whose ambiguous factor is between minAmb and maxAmb.
makeRandoms(MotifList, int) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
makeRandomSequence(int, int) - Method in class edu.dartmouth.bglab.search.MarkovModel
Generates a random string from the given order markov model.
MarkovMaxOrderScorer - Class in edu.dartmouth.bglab.score
A ratio scorer that returns the log_2 ratio of the observed count over the expected count.
MarkovMaxOrderScorer(MotifFinder, boolean) - Constructor for class edu.dartmouth.bglab.score.MarkovMaxOrderScorer
Sets the motif finder to be hte denominatorFinder and the group motif finder to be the numeratorFinder and tells them whether or not to discard overlaps.
MarkovModel - Class in edu.dartmouth.bglab.search
A MarkovModel implementation of MotifFinder.
MarkovModel(MotifFinder) - Constructor for class edu.dartmouth.bglab.search.MarkovModel
Creates a new MarkovModel using the finder as the basis.
MarkovModel(String, int) - Constructor for class edu.dartmouth.bglab.search.MarkovModel
MarkovModel(String, String, int) - Constructor for class edu.dartmouth.bglab.search.MarkovModel
MarkovModel.KeyComparator - Class in edu.dartmouth.bglab.search
Implements an ordering on markov keys.
MarkovModel.KeyComparator() - Constructor for class edu.dartmouth.bglab.search.MarkovModel.KeyComparator
 
matchAmbiguity(Motif) - Method in class edu.dartmouth.bglab.motif.Motif
Returns a new motif that has the same sequence as this motif, but with ambiguous bases in the same places as the mold motif.
MAX_AMB - Static variable in class edu.dartmouth.bglab.beam.Ambiguizer
The maximum ambiguity we will allow a motif to have.
MAX_EXPANSION - Static variable in class edu.dartmouth.bglab.model.PWM
 
MAX_HEAP - Static variable in class edu.dartmouth.bglab.util.Heap
 
MAX_K - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
MAX_KMM_EXPANSION_SIZE - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
MAX_KMM_EXPANSION_SIZE - Static variable in class edu.dartmouth.bglab.model.PWMEvaluator
 
MAX_N - Static variable in class edu.dartmouth.bglab.util.Binomial
 
MAX_NAME_WIDTH - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
MAX_NAME_WIDTH - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
MAX_PERIODICITY - Static variable in class edu.dartmouth.bglab.motif.MotifUtils
The maximum periodicity that is used in MotifUtils.isRepetitive(String, int, int).
maxBase(int) - Method in class edu.dartmouth.bglab.model.PWM
Returns the most probable base at the given index.
maxCapacity() - Method in class edu.dartmouth.bglab.util.Heap
The maximum allowable size for this Heap.
maxHashLength - Variable in class edu.dartmouth.bglab.search.MotifFinder
Maximum size for caches.
MaximalMatcher - Class in edu.dartmouth.bglab.score
This class is designed primarily for phi scoring, but in general it deals with int[]'s and how they overlap each other.
MaximalMatcher(Motif, Motif, MotifFinder) - Constructor for class edu.dartmouth.bglab.score.MaximalMatcher
Wraps the motifs in two Motif Lists and sends them on to MaximalMatcher.MaximalMatcher(MotifList, MotifList, MotifFinder).
MaximalMatcher(Motif, MotifList, MotifFinder) - Constructor for class edu.dartmouth.bglab.score.MaximalMatcher
Wraps the motifs in two Motif Lists and sends them on to MaximalMatcher.MaximalMatcher(MotifList, MotifList, MotifFinder).
MaximalMatcher(MotifList, MotifList, MotifFinder) - Constructor for class edu.dartmouth.bglab.score.MaximalMatcher
Creates two sets of overlapping islands from the instances of m1 and m2 as given by mf.
maxSize - Variable in class edu.dartmouth.bglab.util.Heap
 
maxVal - Variable in class edu.dartmouth.bglab.util.Histogram
 
med3(int[], int, int, int) - Static method in class edu.dartmouth.bglab.util.SuffixArray
Returns the index of the median of the three indexed integers.
merge(Object[], T[], T[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Merges src1 and src2 into destn, without any duplicates.
MERGED_NAME - Static variable in class edu.dartmouth.bglab.beam.BeamDriver
 
mergeRanges(List<Range>, Range) - Static method in class edu.dartmouth.bglab.score.MaximalMatcher
Returns a range that represents the full range of the given partition.
mergeResults(Motif[][]) - Static method in class edu.dartmouth.bglab.beam.BiologicalBeamDriver
Merges all the given results, and returns an array without duplicates, null values or motifs containing repetitive instantiations.
mergeSortedArrays(int[], int[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Returns a sorted array of the elements in a1 and a2, without any duplicates; a1 and a2 must both be sorted arrays.
mf - Variable in class edu.dartmouth.bglab.score.Scorer
 
MF_PACKAGE_NAME - Static variable in class edu.dartmouth.bglab.search.MotifFinderFactory
 
mfCache - Static variable in class edu.dartmouth.bglab.search.MotifFinderFactory
 
MIN_AFFINITY - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
MIN_COUNT - Static variable in class edu.dartmouth.bglab.util.Poisson
 
MIN_COVERAGE - Static variable in class edu.dartmouth.bglab.motif.Motif
For use in determining equivalence.
MIN_HEAP - Static variable in class edu.dartmouth.bglab.util.Heap
 
MIN_MOTIF_WIDTH - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
MIN_MOTIF_WIDTH - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
MIN_OVERLAP - Static variable in class edu.dartmouth.bglab.motif.OverlapComparator
 
MIN_RANDOM_LENGTH - Static variable in class edu.dartmouth.bglab.motif.Motif
The default minimum length of randomly generated motifs.
MIN_REPETITIVE_STRETCH_LENGTH - Static variable in class edu.dartmouth.bglab.motif.MotifUtils
The length of a repetitive substring in MotifUtils.isRepetitive(String, int, int).
MIN_SCORE - Static variable in class edu.dartmouth.bglab.beam.AssessmentDriver
 
MIN_SUM_DELTA - Static variable in class edu.dartmouth.bglab.util.KS
The minimum fraction of the sum that a term can be before we'll say the sum has converged.
MIN_TERM_DELTA - Static variable in class edu.dartmouth.bglab.util.KS
The minimum fraction of the previous term a term can be before we'll say the sum has converged.
minCoverage - Variable in class edu.dartmouth.bglab.motif.EquivalenceComparator
 
minOverlap - Variable in class edu.dartmouth.bglab.motif.OverlapComparator
 
minPhi - Variable in class edu.dartmouth.bglab.score.PhiComparator
 
minVal - Variable in class edu.dartmouth.bglab.util.Histogram
 
MiscUtils - Class in edu.dartmouth.bglab.util
 
MiscUtils() - Constructor for class edu.dartmouth.bglab.util.MiscUtils
 
MLDriver - Class in edu.dartmouth.bglab.beam
This is an exploratory class; parts of this class will move to other classes when we figure out what we're really doing.
MLDriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.MLDriver
Sets the file root, test ID, thread ID, properties, and scorer.
MLDriver(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.MLDriver
Sets the file root, test ID, thread ID, properties, and scorer; uses the specified group instead of pulling the group ID from the properties.
model - Variable in class edu.dartmouth.bglab.search.MarkovModel
 
ModelEvaluator - Class in edu.dartmouth.bglab.model
Command-line program for evaluating different CRE models.
ModelEvaluator() - Constructor for class edu.dartmouth.bglab.model.ModelEvaluator
 
modelProbability(String) - Method in class edu.dartmouth.bglab.search.MarkovModel
The simple probability of the given sequence.
ModelTester - Class in edu.dartmouth.bglab.test
For testing the .motif package and aiding in the creation of new Alphabets.
ModelTester() - Constructor for class edu.dartmouth.bglab.test.ModelTester
 
modifiedMFWithBlank_count - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
modifiedMFWithBlank_score - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
moduleResults - Variable in class edu.dartmouth.bglab.beam.BiologicalBeamDriver
 
MoreArrays - Class in edu.dartmouth.bglab.util
Contains useful static array-manipulation methods not contained in the java.util.Arrays class.
MoreArrays() - Constructor for class edu.dartmouth.bglab.util.MoreArrays
 
MoreMath - Class in edu.dartmouth.bglab.util
Contains useful static math methods not contained in the java.lang.Math class.
MoreMath() - Constructor for class edu.dartmouth.bglab.util.MoreMath
 
motif - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
motif - Variable in class edu.dartmouth.bglab.beam.RankedMotifPair
Intended to be the found motif, but can be any motif.
Motif - Class in edu.dartmouth.bglab.motif
Represents a biological motif as a consensus sequence and a sig score.
Motif(String, boolean, Alphabet) - Constructor for class edu.dartmouth.bglab.motif.Motif
Creates a motif with sequence seq; rc specifies whether the reverse complement is used.
Motif.LastExpansion - Class in edu.dartmouth.bglab.motif
 
Motif.LastExpansion() - Constructor for class edu.dartmouth.bglab.motif.Motif.LastExpansion
 
Motif.ScoreData - Class in edu.dartmouth.bglab.motif
 
Motif.ScoreData(double, String) - Constructor for class edu.dartmouth.bglab.motif.Motif.ScoreData
 
MOTIF_DELIMITER - Static variable in class edu.dartmouth.bglab.motif.MotifList
 
MOTIF_LIST_SUFFIX - Static variable in class edu.dartmouth.bglab.beam.PhiScoreDriver
The suffix that files containing MotifLists must have to be interpretted properly.
MOTIF_SEPARATOR - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
MOTIF_SUFFIX - Static variable in class edu.dartmouth.bglab.beam.PhiScoreDriver
The suffix that files containing motifs must have to be interpretted properly.
MOTIF_THICKNESS - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
MOTIF_THICKNESS - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
MotifComparator - Class in edu.dartmouth.bglab.motif
A general contract for comparing motifs.
MotifComparator() - Constructor for class edu.dartmouth.bglab.motif.MotifComparator
 
motifCount - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
motifFileRoot() - Static method in class edu.dartmouth.bglab.GlobalParams
 
MotifFilter - Class in edu.dartmouth.bglab.score
This is an early rendition of a MotifFilter that will have a bunch of Scorers and will score a motif by all the scorers and come up with some composite score.
MotifFilter(UberProperties, boolean) - Constructor for class edu.dartmouth.bglab.score.MotifFilter
Calls the other constructor, but with groupFinder set to null.
MotifFilter(UberProperties, MotifFinder, boolean) - Constructor for class edu.dartmouth.bglab.score.MotifFilter
Initializes all of the various scorers.
MotifFinder - Class in edu.dartmouth.bglab.search
A motif finder contains an internal representation of a biological sequence and allows access to the number of occurrences of a given motif and the indices of these occurrences in the sequence.
MotifFinder() - Constructor for class edu.dartmouth.bglab.search.MotifFinder
 
MotifFinder(String, int) - Constructor for class edu.dartmouth.bglab.search.MotifFinder
MotifFinder(String, String, int) - Constructor for class edu.dartmouth.bglab.search.MotifFinder
MotifFinder.EmptyFindResults - Class in edu.dartmouth.bglab.search
 
MotifFinder.EmptyFindResults() - Constructor for class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
MotifFinder.FindResultsSoftValueHashMap - Class in edu.dartmouth.bglab.search
 
MotifFinder.FindResultsSoftValueHashMap() - Constructor for class edu.dartmouth.bglab.search.MotifFinder.FindResultsSoftValueHashMap
 
MotifFinder.GenomeSoftValueHashMap - Class in edu.dartmouth.bglab.search
 
MotifFinder.GenomeSoftValueHashMap(MotifFinder) - Constructor for class edu.dartmouth.bglab.search.MotifFinder.GenomeSoftValueHashMap
 
MotifFinder.UncompressedFindResults - Class in edu.dartmouth.bglab.search
 
MotifFinder.UncompressedFindResults(int[], Motif, boolean) - Constructor for class edu.dartmouth.bglab.search.MotifFinder.UncompressedFindResults
 
motifFinderClassNames - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
MotifFinderFactory - Class in edu.dartmouth.bglab.search
Contains static methods to create motif finders and aid in the creation of motif finders, along with a main method that saves a motif finder and its bipartite caches to file.
MotifFinderFactory() - Constructor for class edu.dartmouth.bglab.search.MotifFinderFactory
 
motifFinderKey - Variable in class edu.dartmouth.bglab.search.MotifFinder.GenomeSoftValueHashMap
 
motifFinders - Variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
motifFinders - Variable in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
motifFinders - Variable in class edu.dartmouth.bglab.search.CompositeMotifFinder
 
motifGeneSummaries - Variable in class edu.dartmouth.bglab.beam.CGIDriver
 
motifify(String[]) - Method in class edu.dartmouth.bglab.motif.Motif
Turns an array of sequences into an array of motifs with the same reverse complement status and alphabet as this.
MotifInstance - Class in edu.dartmouth.bglab.motif
Used to represent the location on a gene of a particular instance of a motif.
MotifInstance(String, String, int, String) - Constructor for class edu.dartmouth.bglab.motif.MotifInstance
 
MotifList - Class in edu.dartmouth.bglab.motif
A motif list consists of a list of motifs and a sig score.
MotifList() - Constructor for class edu.dartmouth.bglab.motif.MotifList
Creates a new empty motif list.
MotifList(int) - Constructor for class edu.dartmouth.bglab.motif.MotifList
Creates a new empty motif list with initial capacity set to n.
MotifList(Motif) - Constructor for class edu.dartmouth.bglab.motif.MotifList
Initializes this motif list to contain m; the score is initialized to the score of m.
MotifList(Motif[]) - Constructor for class edu.dartmouth.bglab.motif.MotifList
Creates a new motif list filled with the given array of motifs.
motifListToHashSet(MotifList) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
Creates a new HashSet consisting of each motif in ml.
motifListToString(MotifList) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
Returns a string of the form m1#m2#...mN#, where mi is the sequence of the ith motif in the given MotifList.
motifMatchesProb - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
motifOccurProb - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
motifOccurrences - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
motifScoreCache2 - Variable in class edu.dartmouth.bglab.score.Scorer
 
motifSig - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
motifSigProb - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
motifSpecificity - Variable in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
motifStatsCache - Variable in class edu.dartmouth.bglab.beam.CGIDriver
 
motifStatsCache - Variable in class edu.dartmouth.bglab.beam.web.WebDriver
Used to cache a MotifInstance[] for each motif in results.
MotifTester - Class in edu.dartmouth.bglab.test
For testing the .motif package and aiding in the creation of new Alphabets.
MotifTester() - Constructor for class edu.dartmouth.bglab.test.MotifTester
 
MotifUtils - Class in edu.dartmouth.bglab.motif
Contains static methods for creating sets of motifs and performing various other motif-related tasks.
MotifUtils() - Constructor for class edu.dartmouth.bglab.motif.MotifUtils
 
mutate(Motif, int, Scorer, int) - Static method in class edu.dartmouth.bglab.beam.Ambiguizer
Tests all the possible expansions of motif at position i and returns the best result.
mutate(Motif, Scorer, int) - Static method in class edu.dartmouth.bglab.beam.Ambiguizer
Mutates each base in the Motif.
MUTATION_METHOD - Static variable in class edu.dartmouth.bglab.beam.Ambiguizer
 

N

N - Static variable in class edu.dartmouth.bglab.motif.Alphabet
For representing unknown bases.
N_STRING - Static variable in class edu.dartmouth.bglab.motif.Alphabet
N_STRING[i] is a string of i Alphabet.N's.
name - Variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Gene
 
name - Variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Motif
 
name - Variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Gene
 
name - Variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Motif
 
name - Variable in class edu.dartmouth.bglab.io.FileReaders.NameAndID
 
name - Variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.TestModel
 
NAME_OFFSET - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
NAME_OFFSET - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
NEGATIVE_STRAND - Static variable in class edu.dartmouth.bglab.motif.MotifInstance
 
negatives - Variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.BackgroundEvalFunc
 
newInstanceOf(MotifList) - Method in class edu.dartmouth.bglab.model.ConsensusSequence
Creates a new ConsensusSequence as the union of all the motifs in ml, as specified by MotifList.uniteMotifs().
newInstanceOf(MotifList) - Method in interface edu.dartmouth.bglab.model.CREModel
Must generate a new instance of the given CREModel based of the given MotifList.
newInstanceOf(MotifList) - Method in class edu.dartmouth.bglab.model.KMismatchModel
Creates a new KMM where the motif and k value represent that motif from the MotifList ml that has the lowest k with respect to all the other motifs in ml.
newInstanceOf(MotifList) - Method in class edu.dartmouth.bglab.model.KRModel
Creates a new PWM as specified by the CREModel interface.
newInstanceOf(MotifList) - Method in class edu.dartmouth.bglab.model.PLConsensusModel
Creates a new PLConsensusModel as the union of all the motifs in ml, as specified by MotifList.uniteMotifs().
newInstanceOf(MotifList) - Method in class edu.dartmouth.bglab.model.PWM
Creates a new PWM as specified by the CREModel interface.
next() - Method in class edu.dartmouth.bglab.io.Scanner
Finds and returns the next complete token from this scanner.
nextBigDecimal() - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as a BigDecimal.
nextBigInteger() - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as a BigInteger.
nextBigInteger(int) - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as a BigInteger.
nextBoolean() - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input into a boolean value and returns that value.
nextByte() - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as a byte.
nextByte(int) - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as a byte.
nextChar() - Method in class edu.dartmouth.bglab.io.Scanner
 
nextDouble() - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as a double.
nextFloat() - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as a float.
nextInt() - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as an int.
nextInt(int) - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as an int.
nextLine() - Method in class edu.dartmouth.bglab.io.Scanner
Advances this scanner past the current line and returns the input that was skipped.
nextLong() - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as a long.
nextLong(int) - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as a long.
nextShort() - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as a short.
nextShort(int) - Method in class edu.dartmouth.bglab.io.Scanner
Scans the next token of the input as a short.
nextToken() - Method in class edu.dartmouth.bglab.io.Scanner
 
NiceFormatter - Class in edu.dartmouth.bglab.util
Provides methods for formating output in a standard way.
NiceFormatter() - Constructor for class edu.dartmouth.bglab.util.NiceFormatter
 
NO_VALID_BASE - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
NO_WILDCARD_OPTIMIZATION - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
normalizeLength(String, int) - Static method in class edu.dartmouth.bglab.util.NiceFormatter
Adds spaces to the end of a string to make it length long; useful for making columns in plaintext tables line up.
NUM_DECIMALS - Static variable in class edu.dartmouth.bglab.util.NiceFormatter
 
NUM_RAND - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
NUM_REPS - Static variable in class edu.dartmouth.bglab.beam.BackgroundDriver
 
NUM_REPS - Static variable in class edu.dartmouth.bglab.beam.CorruptionDriver
 
numBases(List<Range>) - Method in class edu.dartmouth.bglab.score.MaximalMatcher
Returns the number of bases in non-overlapping motifs.
numeratorMM - Variable in class edu.dartmouth.bglab.score.RatioScorer
 
numMotifs(int) - Method in class edu.dartmouth.bglab.search.MarkovModel
Computes the total number of motifs of the given length in the finder.
numTrials - Variable in class edu.dartmouth.bglab.score.ZScoreScorer
 

O

OBJ_FILE_EXT - Static variable in class edu.dartmouth.bglab.search.MotifFinderFactory
 
objFileRoot() - Static method in class edu.dartmouth.bglab.GlobalParams
 
OccurrenceKSScorer - Class in edu.dartmouth.bglab.score
Combines Occurrence and KS
OccurrenceKSScorer(MotifFinder, MotifFinder, boolean) - Constructor for class edu.dartmouth.bglab.score.OccurrenceKSScorer
Sets the scores, and takes the motif finders from s1.
OccurrenceScorer - Class in edu.dartmouth.bglab.score
An occurrence scorer is a group scorer that scores motifs based on the number of times they occur in the sequence and in the group.
OccurrenceScorer(MotifFinder, MotifFinder, boolean) - Constructor for class edu.dartmouth.bglab.score.OccurrenceScorer
Sets the motif finder and group motif finder and tells them whether or not to discard overlaps.
ODDS_STRINGENCIES - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
okayGenes - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
oldEvaluator(String[]) - Static method in class edu.dartmouth.bglab.model.PWMEvaluator
 
onlyForcedMotifs - Variable in class edu.dartmouth.bglab.beam.CGIDriver
 
OrganismLoader - Class in edu.dartmouth.bglab.io
Command-line program for loading new organisms into SCOPE.
OrganismLoader() - Constructor for class edu.dartmouth.bglab.io.OrganismLoader
 
OrganismLoader.FastaRecord - Class in edu.dartmouth.bglab.io
 
OrganismLoader.FastaRecord(List<String>, String) - Constructor for class edu.dartmouth.bglab.io.OrganismLoader.FastaRecord
 
out - Variable in class edu.dartmouth.bglab.beam.web.StreamPipe
 
output - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneListSummary
 
outputResultsAsText(OutputStream) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
outputResultsAsXML(OutputStream) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
OverlapComparator - Class in edu.dartmouth.bglab.motif
A comparator for assessing partial motif equivalence.
OverlapComparator() - Constructor for class edu.dartmouth.bglab.motif.OverlapComparator
 
OverlapComparator(double) - Constructor for class edu.dartmouth.bglab.motif.OverlapComparator
 
overriddenParameters - Static variable in class edu.dartmouth.bglab.beam.CGIScope
 
overrideDefaultParams(String) - Static method in class edu.dartmouth.bglab.beam.CGIScope
 
owningObject - Variable in class edu.dartmouth.bglab.score.Scorer.ScoreSoftValueHashMap
 

P

paramFileRoot() - Static method in class edu.dartmouth.bglab.GlobalParams
 
parent(int) - Method in class edu.dartmouth.bglab.util.Heap
 
parse(String[]) - Method in class edu.dartmouth.bglab.beam.PRISM
 
parse() - Method in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
parseCommands(String[]) - Static method in class edu.dartmouth.bglab.beam.CGIScope
 
parseCommands(String[]) - Static method in class edu.dartmouth.bglab.beam.Scope
Parses command line flags and sets properties accordingly.
parseCommands(String[]) - Static method in class edu.dartmouth.bglab.beam.WebScope
Parses command line flags and sets properties accordingly.
parseGenbankFile() - Static method in class edu.dartmouth.bglab.test.CharlieTester
Parses a genbank file-- I don't remember exactly what this does.
parseGenes(HashMap<String, String>) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
parseHexColor(String) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
parseMapFile(Reader) - Static method in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
parseMotif(String, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
Generates a motif from the string of the form [sequence]SEPARATOR[r/R].
parseMotif(String, Alphabet, boolean) - Static method in class edu.dartmouth.bglab.motif.Motif
 
parsePWM(String[]) - Static method in class edu.dartmouth.bglab.model.PWM
Converts a whitespace-delimited table into a position-weight matrix with the reverse complement flagset to CREModel.DEFAULT_RC, and with stringency set to PWM.DEFAULT_STRINGENCY.
parsePWM(String[], boolean) - Static method in class edu.dartmouth.bglab.model.PWM
Converts a whitespace-delimited table into a position-weight matrix with the given reverse complement flag, and with stringency set to PWM.DEFAULT_STRINGENCY.
parseQueryString(String) - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
partition() - Method in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
partition(List<Range>, int) - Static method in class edu.dartmouth.bglab.score.MaximalMatcher
Returns a pointer q to the end of the island in list beginning at start.
partOfGene - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
password - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
patLocation - Static variable in class edu.dartmouth.bglab.beam.CGIDriver
 
pattern - Variable in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
peek() - Method in class edu.dartmouth.bglab.io.Scanner
 
persistMF(String, MotifFinder) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Serializes mf and stores it in a file called GlobalParams.objFileRoot() + mfObjFileName.
PHI_AVE - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
PhiComparator - Class in edu.dartmouth.bglab.score
A SequenceComparator that uses phi scores to determine equivalence.
PhiComparator(Scorer, double) - Constructor for class edu.dartmouth.bglab.score.PhiComparator
 
PhiScoreDriver - Class in edu.dartmouth.bglab.beam
This driver facilitates computing the phi scores for entire directories of files.
PhiScoreDriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.PhiScoreDriver
Sets the file root, test ID, thread ID, properties, and scorer.
PhiScoreDriver(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.PhiScoreDriver
Sets the file root, test ID, thread ID, properties, and scorer; uses the specified group instead of pulling the group ID from the properties.
PhiScoreDriver.SuffixFilter - Class in edu.dartmouth.bglab.beam
A FilenameFilter that makes sure the file has either the MOTIF_SUFFIX or MOTIF_LIST_SUFFIX and that the name contains at least two words seperated by _.
PhiScoreDriver.SuffixFilter() - Constructor for class edu.dartmouth.bglab.beam.PhiScoreDriver.SuffixFilter
 
PL_CONS_CRE - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
PLConsensusModel - Class in edu.dartmouth.bglab.model
Variation on the ConsensusSequence that defines the consensus based on a notion of minimum distance from the median.
PLConsensusModel(Motif) - Constructor for class edu.dartmouth.bglab.model.PLConsensusModel
Creates a consensus sequence from the given sequence with the reverse complement flag set to m's reverse compliment.
PLConsensusModel(String) - Constructor for class edu.dartmouth.bglab.model.PLConsensusModel
Creates a consensus sequence from the given sequence with the reverse complement flag set to CREModel.DEFAULT_RC.
PLConsensusModel(String, boolean) - Constructor for class edu.dartmouth.bglab.model.PLConsensusModel
Creates a consensus sequence from the given sequence with the given reverse complemnt flag.
PLOT_ROC - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
plotROC(CREModel, Motif[], Motif[], String) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
 
pointProb(double, double, double) - Static method in class edu.dartmouth.bglab.util.Gaussian
 
pointProb(int, double) - Static method in class edu.dartmouth.bglab.util.Poisson
Computes the probability of exactly k kobservations given the lambda (which is N*p).
pointProb(int, int, double) - Static method in class edu.dartmouth.bglab.util.Poisson
Computes the probability of exactly k observations given N trials with a probabiligy p of success on each trial.
Poisson - Class in edu.dartmouth.bglab.util
Contains static methods for computing Poisson probabilities.
Poisson() - Constructor for class edu.dartmouth.bglab.util.Poisson
 
PORTNUM - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
POSITIVE_STRAND - Static variable in class edu.dartmouth.bglab.motif.MotifInstance
 
postMail(String, String, String, String, List<File>, List<String>) - Static method in class edu.dartmouth.bglab.beam.CGIScope
 
PrematureDeathException - Exception in edu.dartmouth.bglab.beam.web
A RuntimeException that is thrown when the child process appears to have been killed from some outside process.
PrematureDeathException() - Constructor for exception edu.dartmouth.bglab.beam.web.PrematureDeathException
 
PrematureDeathException(String) - Constructor for exception edu.dartmouth.bglab.beam.web.PrematureDeathException
 
PrematureDeathException(String, Throwable) - Constructor for exception edu.dartmouth.bglab.beam.web.PrematureDeathException
 
PrematureDeathException(Throwable) - Constructor for exception edu.dartmouth.bglab.beam.web.PrematureDeathException
 
PRIMARY - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
PRIMARY_ARRAY - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
PRIMARY_BASE_PROBABILITY - Static variable in class edu.dartmouth.bglab.motif.Motif
The probability of choosing A, C, G, or T when generating a base for a random motif.
PRIMARY_BIN_ARRAY - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
PRIMARY_BIN_INDICES - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
PRIMARY_COMPLEMENT - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
PRIMARY_EXPANSION - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
PRIMARY_ID - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
PRIMARY_INDICES - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
PRIMARY_SUPERSETS - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
PRINT - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
Print - Class in edu.dartmouth.bglab.util
Assorted static methods for printing text.
Print() - Constructor for class edu.dartmouth.bglab.util.Print
 
print(Object) - Static method in class edu.dartmouth.bglab.util.Print
 
PRINT_REV_COMP_ALPH_LAST - Static variable in class edu.dartmouth.bglab.motif.Motif
If true, motif that use the reverse compliment will have they're string printed in the alphabetically last order.
printArray(char[]) - Static method in class edu.dartmouth.bglab.util.Print
 
printArray(double[]) - Static method in class edu.dartmouth.bglab.util.Print
 
printArray(int[]) - Static method in class edu.dartmouth.bglab.util.Print
 
printArray(Object[]) - Static method in class edu.dartmouth.bglab.util.Print
 
printBestMotif(Motif) - Method in class edu.dartmouth.bglab.beam.BeamDriver
 
printBestMotif(Motif) - Method in class edu.dartmouth.bglab.beam.CGIDriver
Need to override this to do nothing so that files don't get written.
printBestMotif(Motif) - Method in class edu.dartmouth.bglab.beam.web.WebDriverJr
Need to override this to do nothing so that files don't get written.
printHelp() - Static method in class edu.dartmouth.bglab.beam.CGIScope
 
printHelp() - Static method in class edu.dartmouth.bglab.beam.Scope
 
printHelp() - Static method in class edu.dartmouth.bglab.beam.WebScope
 
println() - Static method in class edu.dartmouth.bglab.util.Print
 
println(boolean) - Static method in class edu.dartmouth.bglab.util.Print
 
println(double) - Static method in class edu.dartmouth.bglab.util.Print
 
println(int) - Static method in class edu.dartmouth.bglab.util.Print
 
println(Object) - Static method in class edu.dartmouth.bglab.util.Print
 
printPoints(PrintStream) - Method in class edu.dartmouth.bglab.util.LinCorrStatBox
 
printProgress(int, PrintStream) - Static method in class edu.dartmouth.bglab.beam.BackgroundDriver
 
printResults(Object[]) - Method in class edu.dartmouth.bglab.beam.PRISM
 
printResults(Motif[], String) - Method in class edu.dartmouth.bglab.beam.web.WebDriverJr
Uses Print.forcePrintln() to print the results for a stage to stdio.
printStatus() - Method in class edu.dartmouth.bglab.score.Scorer.ScoreSoftValueHashMap
 
printUsage() - Method in class edu.dartmouth.bglab.beam.PRISM
 
PRISM - Class in edu.dartmouth.bglab.beam
This is a simple commandline driver for PRISM.
PRISM(String[]) - Constructor for class edu.dartmouth.bglab.beam.PRISM
 
prismISMB_table2(MotifList) - Method in class edu.dartmouth.bglab.beam.LinearityTesterDriver
Generates a table of Regulon, regSize, average sig of binding sites, max delta sig, average staring phi, and max delta phi.
prob(int, int, double) - Static method in class edu.dartmouth.bglab.util.Binomial
Computets the probability that something that occurs with probability p will occur EXACTLY k times, given N chances.
probabilityOf(String) - Method in class edu.dartmouth.bglab.model.KRModel
Returns the probability that this String is generated by this model; returns in log_2 space.
probabilityOf(String, double[][], boolean) - Static method in class edu.dartmouth.bglab.model.PWM
Computes the log_2 probability of s coming from probabilities.
probabilityOf(String) - Method in class edu.dartmouth.bglab.model.PWM
Uses getProbabilities and revComp.
probabilityOf(String, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
 
probabilityOf(char, String) - Method in class edu.dartmouth.bglab.search.MarkovModel
Computes the probability of x given the sequence.
probabilityOf(Motif) - Method in class edu.dartmouth.bglab.search.MarkovModel
Converts the log probability into real space.
probabilityOf(String) - Method in class edu.dartmouth.bglab.search.MarkovModel
Converts the log probability into real space.
probAtLeastOnce(int, double) - Static method in class edu.dartmouth.bglab.util.Binomial
 
ProbCREModel - Interface in edu.dartmouth.bglab.model
Interface that extends CREModel to include methods specific to probabilistic models.
probKS(double) - Static method in class edu.dartmouth.bglab.util.KS
Computes the probability of seeing lambda given the asymptotic distribution of distribution of the V statistic.
progressFile - Static variable in class edu.dartmouth.bglab.io.FileWriters
Specifies the progress file we'll use.
properties - Variable in class edu.dartmouth.bglab.beam.BeamDriver
 
properties - Static variable in class edu.dartmouth.bglab.beam.CGIScope
 
PSEUDO - Static variable in class edu.dartmouth.bglab.model.KRModel
The pseudo count is added to every count when calculating the probabilities.
PSEUDO - Static variable in class edu.dartmouth.bglab.model.PWM
The pseudo count is added to every count when calculating the probabilities.
PUSHBACK_BUFFER_SIZE - Static variable in class edu.dartmouth.bglab.io.Scanner
 
put(Motif, Double) - Method in class edu.dartmouth.bglab.score.Scorer.ScoreSoftValueHashMap
 
put(String, FindResults, boolean) - Method in class edu.dartmouth.bglab.search.MotifFinder.FindResultsSoftValueHashMap
 
put(String, FindResults, boolean) - Method in class edu.dartmouth.bglab.search.MotifFinder.GenomeSoftValueHashMap
 
put(K, V) - Method in class edu.dartmouth.bglab.util.SoftValueHashMap
 
putCtr - Variable in class edu.dartmouth.bglab.score.Scorer.ScoreSoftValueHashMap
 
PWM - Class in edu.dartmouth.bglab.model
Implementation of the position-weight matrix model as a 2D array of the counts for each base at each position; keeps track of reverse complement status.
PWM() - Constructor for class edu.dartmouth.bglab.model.PWM
This creates an empty PWM--most methods will cause unchecked exceptions to be thrown.
PWM(Motif, MotifFinder) - Constructor for class edu.dartmouth.bglab.model.PWM
Converts a consensus motif into a position-weight matrix.
PWM(Motif[], MotifFinder) - Constructor for class edu.dartmouth.bglab.model.PWM
Converts an array of unambiguous motifs of the same length and same reverse complement status into a position-weight matrix.
PWM(MotifList) - Constructor for class edu.dartmouth.bglab.model.PWM
Same as {#PWM(String[])} except it weights the counts by the score of each motif.
PWM(String[]) - Constructor for class edu.dartmouth.bglab.model.PWM
Constructs a PWM from this array of strings.
PWM(String[], boolean) - Constructor for class edu.dartmouth.bglab.model.PWM
Constructs a PWM from this array of strings.
pwm - Variable in class edu.dartmouth.bglab.model.PWM
 
PWM.StringDoublePair - Class in edu.dartmouth.bglab.model
Wrapper for a string and an double; used by expand().
PWM.StringDoublePair(String, double) - Constructor for class edu.dartmouth.bglab.model.PWM.StringDoublePair
 
PWM_CRE - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
PWMEvaluator - Class in edu.dartmouth.bglab.model
Command-line program for evaluating a PWM at different stringencies.
PWMEvaluator() - Constructor for class edu.dartmouth.bglab.model.PWMEvaluator
 

Q

queue - Variable in class edu.dartmouth.bglab.util.SoftValueHashMap
Reference queue for cleared SoftReference objects.

R

R - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
radix() - Method in class edu.dartmouth.bglab.io.Scanner
Returns this scanner's default radix.
rand - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
RAND_KNOWN_RATIO - Static variable in class edu.dartmouth.bglab.beam.MLDriver
 
randomBool(double) - Static method in class edu.dartmouth.bglab.util.MoreMath
Returns a random boolean, where p is the probability that true is returned.
randomInt(int, int) - Static method in class edu.dartmouth.bglab.util.MoreMath
Returns a random integer in the range [min..max).
randomIntArray(int, int, int) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Returns an array of random ints in no particular order.
Range - Class in edu.dartmouth.bglab.util
A pair of ordered numbers.
Range(int, int) - Constructor for class edu.dartmouth.bglab.util.Range
Sets left = i and right = j.
rank - Variable in class edu.dartmouth.bglab.beam.RankedMotifPair
Intended to be the rank of the found motif, but can be any int.
RankedMotifPair - Class in edu.dartmouth.bglab.beam
A simple class used in comparing a set of identified motifs against a set of known motifs.
RankedMotifPair() - Constructor for class edu.dartmouth.bglab.beam.RankedMotifPair
This default constructor sets both motif and knownMotif to invalid motifs whose scores are -Infinity; also sets rank to -1 and found to false.
RankedMotifPair(Motif, Motif, int) - Constructor for class edu.dartmouth.bglab.beam.RankedMotifPair
Specifies the found motif, known motif, and rank of the found motif; found is set to false.
RankedMotifPair.FoundMotifComparator - Class in edu.dartmouth.bglab.beam
Compares two RankedMotifPairPair objects solely by the natural ordering of the motif instance variables.
RankedMotifPair.FoundMotifComparator() - Constructor for class edu.dartmouth.bglab.beam.RankedMotifPair.FoundMotifComparator
 
RatioScorer - Class in edu.dartmouth.bglab.score
A ratio scorer that takes two motif finders, and calculates scores as the log_2 ratio of the occurrence of a motif in the "group" motif finder over the "genomic" motif finder.
RatioScorer(MotifFinder, MotifFinder, boolean) - Constructor for class edu.dartmouth.bglab.score.RatioScorer
Sets the motif finder to be hte denominatorFinder and the group motif finder to be the numeratorFinder and tells them whether or not to discard overlaps.
rawSuffixArray - Variable in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
readGenes(String, String) - Static method in class edu.dartmouth.bglab.io.FileReaders
Intelligently reads genes from the given file; if the genes are already int, returns them as a sorted set of integers; if the genes are not int, then they're assumed to be names and are checked in the masterFile.
readGenes(String, String, String) - Static method in class edu.dartmouth.bglab.io.FileReaders
Intelligently reads genes from the given file; if the genes are already int, returns them as a sorted set of integers; if the genes are not int, then they're assumed to be names and are checked in the masterFile.
readLines(String) - Static method in class edu.dartmouth.bglab.io.FileReaders
Reads in the contents of file and returns it as a String array.
readMotif(Scanner) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
Assumes the only thing in the reader is a motif.
readMotifList(String, String, boolean, Alphabet) - Static method in class edu.dartmouth.bglab.io.FileReaders
 
readMotifList(File) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
readMotifLists(String) - Static method in class edu.dartmouth.bglab.io.FileReaders
Given a file in which each line is either empty or is a motif, constructs an array of MotifLists, where each block of motifs in the motifFile is a motif list, and blocks are seperated by empty lines; if a line has a flag, it will be read, otherwise, 'r' is assumed.
readMotifs(String, boolean, Alphabet) - Static method in class edu.dartmouth.bglab.io.FileReaders
Intelligently reads Motifs from the given file, using FileReaders.stringsToMotifs(String[], boolean, Alphabet) to convert each string into a motif.
readMotifs(String, String, boolean, Alphabet) - Static method in class edu.dartmouth.bglab.io.FileReaders
Intelligently reads Motifs from the given file, using FileReaders.stringsToMotifs(String[], boolean, Alphabet) to convert each string into a motif; if key is not null, it will only using those motifs that have the given key, as described in MoreArrays.filterByKey(String[], String).
readObject(ObjectInputStream) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
readObject(ObjectInputStream) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
Calls in.defaultReadObject() and reconstructs sa.
readObject(ObjectInputStream) - Method in class edu.dartmouth.bglab.search.MotifFinder
Calls in.defaultReadObject() and sets MotifFinder.discardOverlaps to false and MotifFinder.wildcardOptimizationCutoff to NO_WILDCARD_OPTIMIZATION.
readObject(ObjectInputStream) - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
Calls in.defaultReadObject() and reconstructs sa.
readResolve() - Method in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
readUniqMotifList(File) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
Reads motifs from the file, removes duplicates, then returns the result as a list.
reconstructFromList(Motif[], Scorer, int, int, int, int) - Static method in class edu.dartmouth.bglab.beam.Ambiguizer
Given a list of motifs, this will combine that list into an optimal ambiguous motif.
refineBipartite(Motif) - Method in class edu.dartmouth.bglab.beam.BeamDriver
Takes a (presumably) bipartite motif and runs it through the linear optimizer and the reconstructor.
regexSearchCounter - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
regexSearchCounterReportInterval - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
regexSearchThreshold - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
RelativeEntropyScorer - Class in edu.dartmouth.bglab.score
Measures the conservation of a motif m as the relative entropy of m around it's neighbors in the test motif finder versus the reference motif finder.
RelativeEntropyScorer(MotifFinder, MotifFinder, boolean, int) - Constructor for class edu.dartmouth.bglab.score.RelativeEntropyScorer
Sets the motif finder and discardOverlaps parameters of the motif finder appropriately; hammingDistance determines the space into which we will expand each motif.
relativeStart - Variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.MotifInstance
 
relativeStart - Variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.MotifInstance
 
remove() - Method in class edu.dartmouth.bglab.io.Scanner
The remove operation is not supported by this implementation of Iterator.
remove(Object) - Method in class edu.dartmouth.bglab.util.SoftValueHashMap
 
removeDuplicates() - Method in class edu.dartmouth.bglab.motif.MotifList
Removes duplicate entries, as judged by a SequenceComparator.
removeDuplicates(int[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Returns a sorted version of a without duplicates; requires the input array to be sorted.
removeDuplicates(Object[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Returns a sorted version of a with the same runtime type, with no duplicates; requires the input array to be sorted.
removeRepetitiveDegenerateMotifs(Motif[]) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Removes all repetitive degenerate sequences from this list.
removeRepetitiveDegenerateMotifs(Motif[], int) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Removes all repetitive degenerate sequences from this list.
removeRepetitiveInstantiations(Motif[]) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Returns a motif array that contains no motifs that contain repetitive instantiations.
removeRepetitiveMotifs(Motif[]) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Removes all repetitive sequences from this list.
removeRepetitiveMotifs(Motif[], int, int) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Removes all repetitive sequences from this list.
reorientedMotifSequence(Motif) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
REPORT_TOP_N - Static variable in class edu.dartmouth.bglab.beam.BackgroundDriver
 
reportStatus() - Method in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
reset() - Method in class edu.dartmouth.bglab.util.Stopwatch
Just calls start, but I like writing reset better.
resetExtraGeneSoftCache() - Static method in class edu.dartmouth.bglab.search.MotifFinder
 
resize(double[], int) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Returns a new array of length i containing the first i elements of a.
resize(int[], int) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Returns a new array of length i containing the first i elements of a.
resize(Object[], int) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Returns a new array of length i containing the first i elements of a and having the same runtime type.
restrictedCompare(String, int) - Method in class edu.dartmouth.bglab.util.SuffixArray
Compares the query string the suffix starting at j, but only looks at the first |query| letter of the suffix.
results - Variable in class edu.dartmouth.bglab.beam.CGIDriver
 
results - Variable in class edu.dartmouth.bglab.beam.web.WebDriver
Contains arrays of the motifs found for each stage of beam+.
ResultsEvaluator - Class in edu.dartmouth.bglab.beam
A hodgepodge of methods for evaluating results.
ResultsEvaluator() - Constructor for class edu.dartmouth.bglab.beam.ResultsEvaluator
 
retrieveFromDb - Variable in class edu.dartmouth.bglab.search.MotifFinder.GenomeSoftValueHashMap
 
retrieveMF(String) - Static method in class edu.dartmouth.bglab.search.MotifFinderFactory
Returns a motif finder that has been serialized and stored in a file called GlobalParams.objFileRoot() + mfObjFileName; returns null if retrieval is unsuccessful.
revComp - Variable in class edu.dartmouth.bglab.model.PWM
 
revComp - Variable in class edu.dartmouth.bglab.motif.Motif
 
revCompOf(String, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
 
revCompOf(String) - Method in class edu.dartmouth.bglab.motif.Motif
Returns the sequence that is the reverse compliment of the given sequence.
reverseLookup - Variable in class edu.dartmouth.bglab.util.SoftValueHashMap
 
ReverseScoreComparator - Class in edu.dartmouth.bglab.motif
A comparator for sorting motifs in ascending order of score.
ReverseScoreComparator() - Constructor for class edu.dartmouth.bglab.motif.ReverseScoreComparator
 
RIGHT - Static variable in class edu.dartmouth.bglab.motif.Motif
Defines the right (3') side of a motif.
right(int) - Method in class edu.dartmouth.bglab.util.Heap
 
right - Variable in class edu.dartmouth.bglab.util.Range
 
rnaKeyWords - Static variable in class edu.dartmouth.bglab.io.OrganismLoader
 
ROC_ROOT - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluator
 
ROOT - Static variable in class edu.dartmouth.bglab.GlobalParams
 
root() - Static method in class edu.dartmouth.bglab.GlobalParams
 
ROOT2PI - Static variable in class edu.dartmouth.bglab.util.Gaussian
 
rowIndexOf(char) - Static method in class edu.dartmouth.bglab.model.PWM
Returns the index of the row in the pwm that corresponds to b.
run() - Method in class edu.dartmouth.bglab.beam.BackgroundDriver
 
run() - Method in class edu.dartmouth.bglab.beam.BeamDriver
run() - Method in class edu.dartmouth.bglab.beam.CorruptionDriver
 
run() - Method in class edu.dartmouth.bglab.beam.FASTAdriver
Simply calls FASTAdriver.writeFASTA(GroupScorer, String) on the internal scorer, using the name of this driver and the .FASTA extension.
run() - Method in class edu.dartmouth.bglab.beam.LinearityTesterDriver
Calls scoreFile on each file in the root directory that passes PhiScoreDriver.SuffixFilter.
run() - Method in class edu.dartmouth.bglab.beam.MLDriver
 
run() - Method in class edu.dartmouth.bglab.beam.PhiScoreDriver
Calls scoreFile on each file in the root directory that passes PhiScoreDriver.SuffixFilter.
run() - Method in class edu.dartmouth.bglab.beam.ScoreDriver
 
run() - Method in class edu.dartmouth.bglab.beam.ScoreKnownsDriver
 
run() - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
run() - Method in class edu.dartmouth.bglab.beam.web.StreamPipe
 
run() - Method in class edu.dartmouth.bglab.beam.web.WebDriver
Executes BeamDriver.runBeamPlus() in a child process by using a WebDriverJr, and sends the results to the user in an email.
RUN_LISTS - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
runAmbiguizerEtc(Motif[]) - Method in class edu.dartmouth.bglab.beam.BeamDriver
Runs the ambiguizer and saves the output to *_ambiguizer.txt and *_ambiguizer.sum.
runBeam(Motif[], Scorer, Alphabet, Alphabet, UberProperties) - Static method in class edu.dartmouth.bglab.beam.Beam
Expands motifs using a beam width algorithm.
runBeam(Scorer, Alphabet, Alphabet, UberProperties) - Static method in class edu.dartmouth.bglab.beam.Beam
Generates all possible motifs of length beam.motif.length.min, then runs Beam.runBeam(Motif[], Scorer, Alphabet, Alphabet, UberProperties) on them.
runBeamEtc() - Method in class edu.dartmouth.bglab.beam.BeamDriver
Runs beam and saves the output to *_beam.txt and *_beam.sum.
runBeamPlus() - Method in class edu.dartmouth.bglab.beam.AssessmentDriver
Mirrors BeamDriver's runBeamPlus method, then reads in known motifs and evaluates how each run did.
runBeamPlus() - Method in class edu.dartmouth.bglab.beam.BeamDriver
This is the current Beam+ suite of programs.
runBeamPlus() - Method in class edu.dartmouth.bglab.beam.BiologicalBeamDriver
Mirrors BeamDriver's runBeamPlus method, then reads in known motifs and evaluates how each run did.
runBeamPlus() - Method in class edu.dartmouth.bglab.beam.CGIDriver
This is the current Beam+ suite of programs.
runBipartiteBeam(Scorer, Alphabet, Alphabet, UberProperties) - Static method in class edu.dartmouth.bglab.beam.Beam
Generates all possible motifs of length beam.motif.length.min, then runs a beam algorithm to expand them and return only the top scorers.
runBipartitesEtc() - Method in class edu.dartmouth.bglab.beam.BeamDriver
Runs bipartite beams and saves the output to *_beam.txt and *_beam.sum.
runFilterEtc(Motif[], String, double) - Method in class edu.dartmouth.bglab.beam.BeamDriver
Runs the filter specified in properties and saves the output to *_filter.txt.
runFilterEtc(Motif[], String, double) - Method in class edu.dartmouth.bglab.beam.BiologicalBeamDriver
Overrides {link #super.saveResults(Motif[], String, Stopwatch, MotifComparator)} to save the results to moduleResults for later phi scoring.
runMergeEtc(Motif[][]) - Method in class edu.dartmouth.bglab.beam.BeamDriver
Merges all the given results, and returns an array without duplicates, null values or motifs containing repetitive instantiations.
runMotifToConsensusSequenceFilter(Motif[]) - Method in class edu.dartmouth.bglab.beam.CGIDriver
This ensures that all motifs are as specific as possible.
runningProcesses - Static variable in class edu.dartmouth.bglab.beam.web.WebDriver
For storing mappings of userID's to Vectors of their running processes.
runPrism() - Method in class edu.dartmouth.bglab.beam.PRISM
 
runTestMotif() - Method in class edu.dartmouth.bglab.beam.PRISM
 
runThreads(Thread[], int) - Static method in class edu.dartmouth.bglab.util.ThreadDriver
Runs all the sourceThreads, threadCount at a time.

S

s - Variable in class edu.dartmouth.bglab.model.PWM.StringDoublePair
 
S - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
sa - Variable in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
 
sameLengthHammingDistance(String, String, boolean) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
Computes the hamming distance between two strings of the same length.
sampleRandomMotifs(int, boolean, Motif, MotifFinder) - Static method in class edu.dartmouth.bglab.search.SearchUtils
Samples random Motifs from the motif finder that are the same length as m and have the same ambiguities in the same places.
sampleRandomSequence(int) - Method in class edu.dartmouth.bglab.search.MarkovModel
Samples a random sequence from the finder's sequence, ensuring that the result doesn't contain any FILLER or SPACER characters.
saveFilterResults(Motif[], String, Stopwatch) - Method in class edu.dartmouth.bglab.beam.BeamDriver
Saves the filter results to file.
saveFilterResults(Motif[], String, Stopwatch) - Method in class edu.dartmouth.bglab.beam.CGIDriver
Need to override this to do nothing so that files don't get written.
saveFilterResults(Motif[], String, Stopwatch) - Method in class edu.dartmouth.bglab.beam.web.WebDriverJr
Uses WebDriverJr.printResults(Motif[], String) to print to stdio the filtered results of only the stages that were actually run.
saveProperties() - Method in class edu.dartmouth.bglab.beam.BeamDriver
Writes the properties to fileRoot + testID + subtestID with a param extention.
saveProperties() - Method in class edu.dartmouth.bglab.beam.CGIDriver
Need to override this to do nothing so that files don't get written.
saveProperties() - Method in class edu.dartmouth.bglab.beam.web.WebDriverJr
Need to override this to do nothing so that files don't get written.
saveResults(Motif[], String, Stopwatch, MotifComparator) - Method in class edu.dartmouth.bglab.beam.BeamDriver
Saves the ambiguizer results and stats to file.
saveResults(Motif[], String, Stopwatch, MotifComparator) - Method in class edu.dartmouth.bglab.beam.CGIDriver
Need to override this to do nothing so that files don't get written.
saveResults(Motif[], String, Stopwatch, MotifComparator) - Method in class edu.dartmouth.bglab.beam.web.WebDriverJr
Uses WebDriverJr.printResults(Motif[], String) to print to stdio only the final merged results.
saveSpecialStats(Motif[], Stopwatch) - Method in class edu.dartmouth.bglab.beam.BeamDriver
Saves the special stats to file.
saveSpecialStats(Motif[], Stopwatch) - Method in class edu.dartmouth.bglab.beam.CGIDriver
Need to override this to do nothing so that files don't get written.
saveSpecialStats(Motif[], Stopwatch) - Method in class edu.dartmouth.bglab.beam.web.WebDriverJr
Need to override this to do nothing so that files don't get written.
SCALE_THICKNESS - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
SCALE_THICKNESS - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
Scanner - Class in edu.dartmouth.bglab.io
A simple text scanner which can parse primitive types and strings using regular expressions.
Scanner(File) - Constructor for class edu.dartmouth.bglab.io.Scanner
Constructs a new Scanner that produces values scanned from the specified file.
Scanner(InputStream) - Constructor for class edu.dartmouth.bglab.io.Scanner
Constructs a new Scanner that produces values scanned from the specified input stream.
Scanner(Reader) - Constructor for class edu.dartmouth.bglab.io.Scanner
Constructs a new Scanner that produces values scanned from the specified source.
Scanner(String) - Constructor for class edu.dartmouth.bglab.io.Scanner
Constructs a new Scanner that produces values scanned from the specified string.
Scope - Class in edu.dartmouth.bglab.beam
The command-line driver for BEAM, PRISM, and SPACER.
Scope() - Constructor for class edu.dartmouth.bglab.beam.Scope
 
scopeProperties - Static variable in class edu.dartmouth.bglab.beam.CGIScope
 
score - Variable in class edu.dartmouth.bglab.model.KRModel
 
score - Variable in class edu.dartmouth.bglab.model.PWM
 
score - Variable in class edu.dartmouth.bglab.motif.Motif
 
score - Variable in class edu.dartmouth.bglab.motif.Motif.ScoreData
 
score - Variable in class edu.dartmouth.bglab.motif.MotifList
 
ScoreComparator - Class in edu.dartmouth.bglab.motif
This mirrors the normal behavious of motifs for both compare() and equals(), therefore these two methods are not consistent.
ScoreComparator() - Constructor for class edu.dartmouth.bglab.motif.ScoreComparator
 
scoreData_0_0 - Static variable in class edu.dartmouth.bglab.model.ConsensusSequence
 
scoreData_1_0 - Static variable in class edu.dartmouth.bglab.model.ConsensusSequence
Returns 1.0 if generatesString(s) is true, and returns 0 otherwise.
scoreDataInfo - Static variable in class edu.dartmouth.bglab.model.KMismatchModel
Returns the number of mismatches between s and this model, normalized by the length of the model.
scoreDataInstantiationCounter - Static variable in class edu.dartmouth.bglab.motif.Motif
 
scoreDelta - Variable in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
ScoreDriver - Class in edu.dartmouth.bglab.beam
This is a simple driver that will score the known motifs of everything in the group.
ScoreDriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.ScoreDriver
Sets the file root, test ID, thread ID, properties, and scorer.
ScoreDriver(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.ScoreDriver
Sets the file root, test ID, thread ID, properties, and scorer; uses the specified group instead of pulling the group ID from the properties.
scoreFalsePositives(Motif[], Motif[], MotifComparator, int) - Static method in class edu.dartmouth.bglab.beam.ResultsEvaluator
Computes the number of false positives, as determined by the number of the first lowestRank elements in motifs tha are not in knownMotifs, as determined by comp's equality test.
scoreFile(String) - Method in class edu.dartmouth.bglab.beam.PhiScoreDriver
Calculates a phi score for the motifs in filename.
scoreInfo - Variable in class edu.dartmouth.bglab.motif.Motif
 
scoreKnownMotifs(Motif[], Motif[], MotifComparator, Scorer) - Static method in class edu.dartmouth.bglab.beam.ResultsEvaluator
Finds foundMotif - knownMotif mapping and returns the result as a RankedMotifPair[].
ScoreKnownsDriver - Class in edu.dartmouth.bglab.beam
This is a simple driver that will score the known motifs of everything in the group.
ScoreKnownsDriver(String, UberProperties) - Constructor for class edu.dartmouth.bglab.beam.ScoreKnownsDriver
Sets the file root, test ID, thread ID, properties, and scorer.
ScoreKnownsDriver(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.ScoreKnownsDriver
Sets the file root, test ID, thread ID, properties, and scorer; uses the specified group instead of pulling the group ID from the properties.
scorer - Variable in class edu.dartmouth.bglab.beam.BeamDriver
 
scorer - Variable in class edu.dartmouth.bglab.score.OccurrenceKSScorer
 
scorer - Variable in class edu.dartmouth.bglab.score.PhiComparator
 
Scorer - Class in edu.dartmouth.bglab.score
Used to calculate sig score for motifs or motif lists using a given motif finder.
Scorer(MotifFinder, boolean, int) - Constructor for class edu.dartmouth.bglab.score.Scorer
Sets the motif finder and tells it whether or not to discard overlaps and what wildcard optimization cutoff to use-- sets usePrior to true.
scorer - Variable in class edu.dartmouth.bglab.score.ZScoreScorer
 
Scorer.ScoreSoftValueHashMap - Class in edu.dartmouth.bglab.score
 
Scorer.ScoreSoftValueHashMap(Object) - Constructor for class edu.dartmouth.bglab.score.Scorer.ScoreSoftValueHashMap
 
SCORER_PACKAGE - Static variable in class edu.dartmouth.bglab.score.ScorerFactory
 
ScorerFactory - Class in edu.dartmouth.bglab.score
Contains static methods to create motif scorers.
ScorerFactory() - Constructor for class edu.dartmouth.bglab.score.ScorerFactory
 
scorerInfo - Variable in class edu.dartmouth.bglab.motif.Motif.ScoreData
 
scorerInfoMap - Static variable in class edu.dartmouth.bglab.beam.BeamDriver
 
scorers - Variable in class edu.dartmouth.bglab.score.CombinedScorer
 
scorers - Variable in class edu.dartmouth.bglab.score.MotifFilter
 
scoreString(String) - Method in class edu.dartmouth.bglab.model.ConsensusSequence
 
scoreString(String) - Method in interface edu.dartmouth.bglab.model.CREModel
Returns the score that a given model would give to a sequence.
scoreString(String) - Method in class edu.dartmouth.bglab.model.KMismatchModel
 
scoreString(String) - Method in class edu.dartmouth.bglab.model.KRModel
Returns the score of this string as Computed from the scoringTable.
scoreString(String) - Method in class edu.dartmouth.bglab.model.PWM
Returns the score of this string as computed from the scoringTable.
ScoreTester - Class in edu.dartmouth.bglab.test
For testing the .score package.
ScoreTester() - Constructor for class edu.dartmouth.bglab.test.ScoreTester
 
scoringTable - Variable in class edu.dartmouth.bglab.model.PWM
 
scrambleBases() - Method in class edu.dartmouth.bglab.motif.Motif
Returns a randomly scrambled version of this motif.
SearchTester - Class in edu.dartmouth.bglab.test
For testing the .search package.
SearchTester() - Constructor for class edu.dartmouth.bglab.test.SearchTester
 
SearchUtils - Class in edu.dartmouth.bglab.search
A general class that provides static helper methods for extracting motifs from MotifFinders; This includes methods for randomly sampling motifs from a motif finder or from a gene that is shared with a give motif, and methods for finding the instantiations of a degenerate motif that actually occur in the motif finder.
SearchUtils() - Constructor for class edu.dartmouth.bglab.search.SearchUtils
 
sendEmail(String, String, String, String) - Static method in class edu.dartmouth.bglab.beam.web.WebDriver
Sends an email to recipient using scope/email/email.sh.
separateMotifFinders - Variable in class edu.dartmouth.bglab.score.GroupScorer
 
SEPARATOR - Static variable in class edu.dartmouth.bglab.motif.Motif
The character used to separate the sequence from the flag in output and parsing.
SEQ_FILE_EXT - Static variable in class edu.dartmouth.bglab.search.MotifFinderFactory
 
seqFileRoot() - Static method in class edu.dartmouth.bglab.GlobalParams
 
seqID - Variable in class edu.dartmouth.bglab.search.MotifFinder
The ID of the biological sequence; used for determining the file name for the serialized bipartite caches.
sequence - Variable in class edu.dartmouth.bglab.io.OrganismLoader.FastaRecord
 
sequence - Variable in class edu.dartmouth.bglab.motif.Motif
 
sequence - Variable in class edu.dartmouth.bglab.motif.MotifInstance
 
sequence - Variable in class edu.dartmouth.bglab.search.MotifFinder
The biological sequence.
sequence - Variable in class edu.dartmouth.bglab.util.SuffixArray
 
SEQUENCE_BREAK - Static variable in class edu.dartmouth.bglab.motif.Alphabet
For marking breaks in biological sequences.
SequenceComparator - Class in edu.dartmouth.bglab.motif
A comparator for sorting motifs alphabetically according to their sequences.
SequenceComparator() - Constructor for class edu.dartmouth.bglab.motif.SequenceComparator
 
sequenceRegExOf(String, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
 
sequenceRegExPatternOf(String, Alphabet) - Static method in class edu.dartmouth.bglab.motif.Motif
 
sequenceSearch(Motif[], Motif) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
Returns the rank of m in arr, assuming arr is already sorted.
sequenceStartOffsets - Variable in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.beam.web.ChildProcessProblem
 
serialVersionUID - Static variable in exception edu.dartmouth.bglab.beam.web.InvalidGeneListException
 
serialVersionUID - Static variable in exception edu.dartmouth.bglab.beam.web.PrematureDeathException
 
serialVersionUID - Static variable in exception edu.dartmouth.bglab.io.IllegalFastaFileException
 
serialVersionUID - Static variable in exception edu.dartmouth.bglab.io.UnknownGeneException
 
serialVersionUID - Static variable in exception edu.dartmouth.bglab.model.ExpansionTooLargeException
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.motif.Motif
 
serialVersionUID - Static variable in exception edu.dartmouth.bglab.motif.UnknownBaseException
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.score.Scorer.ScoreSoftValueHashMap
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.AggregatedFindResults
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.CompositeMotifFinder
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.MarkovModel
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.MotifFinder.FindResultsSoftValueHashMap
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.MotifFinder.GenomeSoftValueHashMap
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.MotifFinder.UncompressedFindResults
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
serialVersionUID - Static variable in exception edu.dartmouth.bglab.search.UnsearchableMotifException
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.util.SoftValueHashMap
 
serialVersionUID - Static variable in class edu.dartmouth.bglab.util.UberProperties
 
SERVER - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
serverSocket - Variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
ServerSocketImageWriter - Class in edu.dartmouth.bglab.beam.web
 
ServerSocketImageWriter() - Constructor for class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
ServerSocketImageWriter.Gene - Class in edu.dartmouth.bglab.beam.web
 
ServerSocketImageWriter.Gene(String, int) - Constructor for class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Gene
 
ServerSocketImageWriter.Motif - Class in edu.dartmouth.bglab.beam.web
 
ServerSocketImageWriter.Motif(String, int, Color) - Constructor for class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Motif
 
ServerSocketImageWriter.MotifInstance - Class in edu.dartmouth.bglab.beam.web
 
ServerSocketImageWriter.MotifInstance(ServerSocketImageWriter.Motif, int) - Constructor for class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.MotifInstance
 
set(String, String[]) - Method in class edu.dartmouth.bglab.motif.Motif.LastExpansion
 
set(int, Motif) - Method in class edu.dartmouth.bglab.motif.MotifList
 
setAlgorithm(String) - Method in class edu.dartmouth.bglab.motif.Motif
 
setBase(char, int) - Method in class edu.dartmouth.bglab.motif.Motif
Returns a new Motif that is a clone of this motif, but it has base b in position p.
setBayesDeltaSig(double) - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
setBeta(double) - Method in class edu.dartmouth.bglab.model.KRModel
Sets the value of beta to d in the range [0..1].
setDefaults(Properties) - Method in class edu.dartmouth.bglab.util.UberProperties
Sets the default properties.
setDiscardOverlaps(boolean) - Method in class edu.dartmouth.bglab.score.GroupScorer
Sets the discard overlaps variable appropriately for the internal motif finders.
setDiscardOverlaps(boolean) - Method in class edu.dartmouth.bglab.score.Scorer
Sets the discardOverlaps value of the internal motif finders.
setDiscardOverlaps(boolean) - Method in class edu.dartmouth.bglab.search.MotifFinder
setFastaMotifFinder(MotifFinder) - Method in class edu.dartmouth.bglab.beam.BeamDriver
Makes mf the new motif finder.
setFlag(boolean) - Method in class edu.dartmouth.bglab.motif.Motif
Returns a new motif that is a clone of this motif, but with the specified flag.
setFlags(MotifList[], boolean) - Method in class edu.dartmouth.bglab.beam.PhiScoreDriver
Sets all the motif in all the motif lists of ml to flag.
setFN(int) - Method in class edu.dartmouth.bglab.util.FPFNStatBox
 
setFound(boolean) - Method in class edu.dartmouth.bglab.beam.RankedMotifPair
 
setFP(int) - Method in class edu.dartmouth.bglab.util.FPFNStatBox
 
setIoException(IOException) - Method in class edu.dartmouth.bglab.io.Scanner
 
setK(int) - Method in class edu.dartmouth.bglab.model.KMismatchModel
 
setMostParams(UberProperties) - Method in class edu.dartmouth.bglab.beam.BeamDriver
Sets all the member variables except scorer.
setMotifFinder(MotifFinder) - Method in class edu.dartmouth.bglab.score.CombinedScorer
Calls setMotifFinder on all the scorers.
setMotifFinder(MotifFinder) - Method in class edu.dartmouth.bglab.score.GroupScorer
Overrides Scorer's method to set the groupMF instead of the genomic MF.
setMotifFinder(MotifFinder) - Method in class edu.dartmouth.bglab.score.OccurrenceKSScorer
Calls setMotifFinder on all the scorers, including this one.
setMotifFinder(MotifFinder) - Method in class edu.dartmouth.bglab.score.Scorer
Sets this motif finder to the given motif finder.
setNums() - Method in class edu.dartmouth.bglab.search.MarkovModel
Sets numGenes and numBases appropriately from the finder.
setProbs(double) - Method in class edu.dartmouth.bglab.model.KRModel
Sets the probability arrays such that each probability incorporates a pseudo count.
setProgressFile(String) - Static method in class edu.dartmouth.bglab.io.FileWriters
Sets the progress file we'll use.
setRevComp(boolean) - Method in class edu.dartmouth.bglab.motif.Motif
 
setRoot(String) - Static method in class edu.dartmouth.bglab.GlobalParams
Sets the root directory (usually "SCOPE"), where the data/, src/ and tempDownloads/ are immediate sub-directories.
setScore(double) - Method in class edu.dartmouth.bglab.model.KRModel
 
setScore(double) - Method in class edu.dartmouth.bglab.model.PWM
 
setScore(double, String) - Method in class edu.dartmouth.bglab.motif.Motif
 
setScore(double) - Method in class edu.dartmouth.bglab.motif.MotifList
 
setScore(Motif) - Method in class edu.dartmouth.bglab.score.Scorer
Calculates m's score and sets it.
setScore(MotifList) - Method in class edu.dartmouth.bglab.score.Scorer
Calculates m's score and sets it.
setScores(Motif[]) - Method in class edu.dartmouth.bglab.score.Scorer
Calculates and sets the scores for an array of motifs.
setScores(MotifList[]) - Method in class edu.dartmouth.bglab.score.Scorer
Calculates and sets the scores for an array of motif lists.
setScoringTable(double[]) - Method in class edu.dartmouth.bglab.model.KRModel
Sets the scoring table to be based on the specified background probabilities.
setScoringTable(double[]) - Method in interface edu.dartmouth.bglab.model.ProbCREModel
The probability that a String comes from a model or background is often computed; this allows the background to be precomputed as a scoring table based off these probs.
setScoringTable() - Method in class edu.dartmouth.bglab.model.PWM
Sets the scoring table to be the log of the probability of a given base at a given position.
setScoringTable(double[]) - Method in class edu.dartmouth.bglab.model.PWM
Sets the scoring table to be the logratio of the pwm probabilities to the probabilities derived from the given frequencies.
setSeparateMotifFinders(boolean) - Method in class edu.dartmouth.bglab.score.CombinedScorer
 
setSeparateMotifFinders(boolean) - Method in class edu.dartmouth.bglab.score.GroupScorer
If true, will cause the background probabilities to be computed from both the genomic mf and the groupMF.
setSeparateMotifFinders(boolean) - Method in class edu.dartmouth.bglab.score.OccurrenceKSScorer
 
setSequence(String) - Method in class edu.dartmouth.bglab.motif.Motif
 
setSource(String) - Method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.ROCEvalFunc
 
setStringency(double) - Method in class edu.dartmouth.bglab.model.ConsensusSequence
Does nothing.
setStringency(double) - Method in interface edu.dartmouth.bglab.model.CREModel
Sets the stringency of this model.
setStringency(double) - Method in class edu.dartmouth.bglab.model.KMismatchModel
Sets k to be s*length().
setStringency(double) - Method in class edu.dartmouth.bglab.model.KRModel
 
setStringency(double) - Method in class edu.dartmouth.bglab.model.PWM
 
setTestList(MotifList) - Method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.BackgroundEvalFunc
 
setTN(int) - Method in class edu.dartmouth.bglab.util.FPFNStatBox
 
setToMotifList(Set<Motif>) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
Returns a MotifList backed by the given set of Motifs.
setTP(int) - Method in class edu.dartmouth.bglab.util.FPFNStatBox
 
setUsePrior(boolean) - Method in class edu.dartmouth.bglab.score.CombinedScorer
 
setUsePrior(boolean) - Method in class edu.dartmouth.bglab.score.OccurrenceKSScorer
 
setUsePrior(boolean) - Method in class edu.dartmouth.bglab.score.Scorer
Sets whether or not Bayesian priors are used.
setUseVarLen(boolean) - Method in class edu.dartmouth.bglab.search.MarkovModel
 
setVerboseSave(boolean) - Method in class edu.dartmouth.bglab.beam.BeamDriver
If true, then files will be saved after every module of execution.
setWildcardOptimization(int) - Method in class edu.dartmouth.bglab.search.MotifFinder
sharedBases() - Method in class edu.dartmouth.bglab.score.MaximalMatcher
Returns the total number of shared bases between foundResult and knownResult.
shuffle(int[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Randomly rearranges the contents of an array.
shuffle(Object[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Randomly rearranges the contents of an array.
sign - Variable in class edu.dartmouth.bglab.util.Heap
 
sign(double) - Static method in class edu.dartmouth.bglab.util.MoreMath
Returns -1, 0, or 1 as d is negative, zero, or positive.
simpleFind(Motif) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns a SORTED array of the indices of where m occurs in the sequence.
simpleFindCache - Variable in class edu.dartmouth.bglab.search.MotifFinder
To speed up lookups in MotifFinder.simpleFind(Motif) when caching is turned on.
simpleScore(String) - Method in class edu.dartmouth.bglab.model.KRModel
Returns the score of this String.
SINGLETON - Static variable in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
SITE_FILE_SUFFIX - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
siteProbs - Variable in class edu.dartmouth.bglab.model.KRModel
 
sites - Variable in class edu.dartmouth.bglab.model.KRModel
 
size() - Method in class edu.dartmouth.bglab.motif.MotifList
 
size() - Method in class edu.dartmouth.bglab.search.AggregatedFindResults
 
size - Variable in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
size() - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
size() - Method in interface edu.dartmouth.bglab.search.FindResults
 
size() - Method in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
size() - Method in class edu.dartmouth.bglab.search.MotifFinder.UncompressedFindResults
 
size - Variable in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
size() - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
size() - Method in class edu.dartmouth.bglab.util.Heap
Returns the current number of objects in this heap.
size() - Method in class edu.dartmouth.bglab.util.SoftValueHashMap
 
sleep() - Static method in class edu.dartmouth.bglab.util.ThreadDriver
I know, it's silly, but it makes the code easier to read not having all those stupid try-catch blocks.
SLEEP_TIME - Static variable in class edu.dartmouth.bglab.util.ThreadDriver
Number of millis we'll sleep between various calls; this allows more processor time to be spent on the actual threads.
softCacheHits(MotifFinder, String, FindResults, boolean) - Static method in class edu.dartmouth.bglab.search.MotifFinder
 
SoftValueHashMap<K,V> - Class in edu.dartmouth.bglab.util
 
SoftValueHashMap() - Constructor for class edu.dartmouth.bglab.util.SoftValueHashMap
 
sort(char[], int[]) - Static method in class edu.dartmouth.bglab.util.SuffixArray
Copied and modified from Sun's Java source code in java.util.Arrays Sorts the specified array of ints into ascending numerical order.
sort1(char[], int[], int, int) - Static method in class edu.dartmouth.bglab.util.SuffixArray
Sorts the specified sub-array of integers into ascending order.
sortAndRemoveDuplicates(Object[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Sorts an array and removes duplicates, assuming that compareTo() is consistent with equals() for the input objects; the array returned has the same runtime type as input.
source - Variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver.ROCEvalFunc
 
SPACE - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
species - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
stackTraceElements - Variable in class edu.dartmouth.bglab.beam.web.ChildProcessProblem
 
stackTraceToString(StackTraceElement[]) - Static method in class edu.dartmouth.bglab.util.MiscUtils
 
start - Variable in class edu.dartmouth.bglab.util.Stopwatch
 
start() - Method in class edu.dartmouth.bglab.util.Stopwatch
Starts and resets the Stopwatch.
startIndex - Variable in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
startOffsets - Variable in class edu.dartmouth.bglab.search.CompositeMotifFinder
 
StatBox - Interface in edu.dartmouth.bglab.util
An empty interface that specifies that something holds statistics.
stirlingChoose(int, int) - Static method in class edu.dartmouth.bglab.util.Binomial
Returns the Choose(n,k) in log space, as computed using Stirling's approximation, where appropriate.
stirlingCumProb(int, int, double) - Static method in class edu.dartmouth.bglab.util.Binomial
Computes the cumulative probability using stirling's approximation.
stirlingProb(int, int, double) - Static method in class edu.dartmouth.bglab.util.Binomial
Computes the probability using stirling approximation, for sufficiently large N and K.
Stopwatch - Class in edu.dartmouth.bglab.util
Used for timing things, just like a real stopwatch!
Stopwatch() - Constructor for class edu.dartmouth.bglab.util.Stopwatch
Calls start.
store() - Method in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
storeIntoDb - Variable in class edu.dartmouth.bglab.search.MotifFinder.GenomeSoftValueHashMap
 
storeSpeciesAndSearchType() - Static method in class edu.dartmouth.bglab.beam.CGIScope
 
strain - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
strand - Variable in class edu.dartmouth.bglab.motif.MotifInstance
 
strandCount(Motif) - Method in class edu.dartmouth.bglab.search.MotifFinder
Counts the number of times m occurs on each strand, if and only if m.useRevComp() is true.
strandCount(MotifList) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns the sum of the strand counts of all motif in ml; no checks are made of the presence of duplicate motifs.
StreamPipe - Class in edu.dartmouth.bglab.beam.web
 
StreamPipe(InputStream, OutputStream) - Constructor for class edu.dartmouth.bglab.beam.web.StreamPipe
 
STRINGENCIES - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
stringency - Variable in class edu.dartmouth.bglab.model.KRModel
 
stringency - Variable in class edu.dartmouth.bglab.model.PWM
 
stringsToIntegers(String[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Converts all the lines to Integers, ignoring non-integer lines.
stringsToMotifs(String[], boolean, Alphabet) - Static method in class edu.dartmouth.bglab.io.FileReaders
Converts an array of strings into an array of Motifs; for each string, it checks for the presence of a Motif SEPARATOR charactor; if found, it uses Motif.parseMotif(String, Alphabet) to create the motif, otherwise, it assumes the String is simply a valid sequence and creates a new motif using the defaultFlag.
stripNs() - Method in class edu.dartmouth.bglab.motif.Motif
Strips all leading and trailing N's from the sequence.
stripNsFrom(String) - Static method in class edu.dartmouth.bglab.motif.Motif
Strips all leading and trailing N's from a sequence that contains at least one non-N character.
strippedLength() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the length of the sequence not including leading and trailing N's.
stuff() - Static method in class edu.dartmouth.bglab.test.CharlieTester
 
subMotifList(MotifList, int, int) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluator
Returns a new motif list that is the given motif list in the ranges [start ..
subtestID - Variable in class edu.dartmouth.bglab.beam.BeamDriver
 
successfulGetCtr - Variable in class edu.dartmouth.bglab.score.Scorer.ScoreSoftValueHashMap
 
SuffixArray - Class in edu.dartmouth.bglab.util
A suffix array provides an efficient means of indexing all substrings of suffixArray string.
SuffixArray(String) - Constructor for class edu.dartmouth.bglab.util.SuffixArray
Builds suffixArray suffix array for the given string.
SuffixArray(String, boolean) - Constructor for class edu.dartmouth.bglab.util.SuffixArray
 
SuffixArray(String, int[]) - Constructor for class edu.dartmouth.bglab.util.SuffixArray
Builds suffixArray suffix array for the given string.
suffixArray - Variable in class edu.dartmouth.bglab.util.SuffixArray
 
SuffixArrayMotifFinder - Class in edu.dartmouth.bglab.search
Uses a SuffixArray as its internal representation of a biological sequence, allowing access to the number of occurrences of a given motif and the indices of these occurrences in the sequence.
SuffixArrayMotifFinder(String, int) - Constructor for class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
SuffixArrayMotifFinder(String, String, int) - Constructor for class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
SuffixArrayMotifFinder.SuffixArrayFindResults - Class in edu.dartmouth.bglab.search
 
SuffixArrayMotifFinder.SuffixArrayFindResults(SuffixArray, String) - Constructor for class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
SuffixArrayMotifFinder.SuffixArrayFindResults(SuffixArray, String, int, int) - Constructor for class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
sum - Variable in class edu.dartmouth.bglab.util.AveStatBox
 
summarizePhis(Object[], Object, Scorer, int, BufferedWriter, String) - Static method in class edu.dartmouth.bglab.beam.ResultsEvaluator
Given a list of motifs that is assumed to be sorted, we will calculate the phi score of each motif against the known motif, writing the first numScored to out, along with the highest scoring motif in the entire set, and returning that motif that has the highest phi score and is one of the first numScored motifs; the returned motif has its score field set to its phi score.
sumOfSqs - Variable in class edu.dartmouth.bglab.util.AveStatBox
 
supersetsOf(char) - Method in class edu.dartmouth.bglab.motif.Alphabet
Returns the set of letters that contain all of the primary bases in c.
swap(int[], int, int) - Static method in class edu.dartmouth.bglab.util.MoreArrays
 
swap(Object[], int, int) - Static method in class edu.dartmouth.bglab.util.MoreArrays
 
swap(int[], int, int) - Static method in class edu.dartmouth.bglab.util.SuffixArray
Swaps x[a] with x[b].
synonymAndGeneNumberPattern - Static variable in class edu.dartmouth.bglab.beam.CGIDriver
 
synonymAndGeneNumberPattern - Static variable in class edu.dartmouth.bglab.io.SynonymChecker
 
synonymAndGeneNumberPattern - Static variable in class edu.dartmouth.bglab.io.SynonymLoader
 
SynonymChecker - Class in edu.dartmouth.bglab.io
 
SynonymChecker() - Constructor for class edu.dartmouth.bglab.io.SynonymChecker
 
SynonymLoader - Class in edu.dartmouth.bglab.io
 
SynonymLoader() - Constructor for class edu.dartmouth.bglab.io.SynonymLoader
 

T

T - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
tempDownloadDir() - Static method in class edu.dartmouth.bglab.GlobalParams
 
TemporaryMotifFinderIdentifier - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
TEST_ON_ALL - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
testAmbiguizer(String[]) - Static method in class edu.dartmouth.bglab.test.BeamTester
 
testBiologicalDriver() - Static method in class edu.dartmouth.bglab.test.BeamTester
 
testConvertNamesToIDs() - Static method in class edu.dartmouth.bglab.test.IOTester
 
testEnt(String[]) - Static method in class edu.dartmouth.bglab.test.UtilTester
 
testFileReaders2() - Static method in class edu.dartmouth.bglab.test.IOTester
 
testGetInst(String[]) - Static method in class edu.dartmouth.bglab.test.SearchTester
 
testGetRandSequence(String[]) - Static method in class edu.dartmouth.bglab.test.BeamTester
 
testGetTop() - Static method in class edu.dartmouth.bglab.test.BeamTester
 
testID - Variable in class edu.dartmouth.bglab.beam.BeamDriver
 
testKRModel(String[]) - Static method in class edu.dartmouth.bglab.test.ModelTester
 
testModels(AffinityEvaluatorDriver.TestModel[], File[], AffinityEvaluatorDriver.EvaluatorFunction, double, boolean) - Static method in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
testMoreArrays() - Static method in class edu.dartmouth.bglab.test.UtilTester
 
testMotif - Variable in class edu.dartmouth.bglab.beam.PRISM
 
testPrior(String[]) - Static method in class edu.dartmouth.bglab.test.ScoreTester
 
testReadMotifs() - Static method in class edu.dartmouth.bglab.test.IOTester
 
testSearchUtils(String[]) - Static method in class edu.dartmouth.bglab.test.BeamTester
 
theHeap - Variable in class edu.dartmouth.bglab.util.Heap
 
ThreadDriver - Class in edu.dartmouth.bglab.util
 
ThreadDriver() - Constructor for class edu.dartmouth.bglab.util.ThreadDriver
 
TICK_HEIGHT - Static variable in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer
 
TICK_HEIGHT - Static variable in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter
 
TN - Variable in class edu.dartmouth.bglab.util.FPFNStatBox
 
toArray() - Method in class edu.dartmouth.bglab.motif.MotifList
 
toArray() - Method in class edu.dartmouth.bglab.util.Heap
Returns a shallow copy of the heap as an array.
toArray(Object[]) - Method in class edu.dartmouth.bglab.util.Heap
Like Heap.toArray(), but the runtime type of the returned array is that of the specified array.
toHashtable(String[]) - Static method in class edu.dartmouth.bglab.util.MoreArrays
Takes a string array of two fields and separates each entry into a hashtable entry, where the first field is the key and the second field is the value.
toHTMLString(String, String) - Method in class edu.dartmouth.bglab.model.PWM
Returns a HTML table representing the pwm.
toPrettyString() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the sequence with primary bases in caps and ambiguous bases as lowercase slash-separated lists of the base expansion, plus "," followed by the expansion of the reverse complement if it is used.
toSortedArray() - Method in class edu.dartmouth.bglab.util.Heap
Same as toArray, but returns it in sorted order.
toSortedArray(Object[]) - Method in class edu.dartmouth.bglab.util.Heap
Like Heap.toSortedArray(), but the runtime type of the returned array is that of the specified array.
toString() - Method in class edu.dartmouth.bglab.beam.BayesDeltaSig
 
toString() - Method in class edu.dartmouth.bglab.beam.CGIDriver.MotifGeneSummary
 
toString() - Method in class edu.dartmouth.bglab.beam.RankedMotifPair
Prints in the following order: rank found, knownMotif.score motif.sequence knownMotif.sequence; each field is tab-delimited.
toString() - Method in class edu.dartmouth.bglab.beam.web.ChildProcessProblem
Returns the reconstructed throwable object's description.
toString() - Method in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Gene
 
toString() - Method in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.Motif
 
toString() - Method in class edu.dartmouth.bglab.beam.web.GeneMapImageDrawer.MotifInstance
 
toString() - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Gene
 
toString() - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.Motif
 
toString() - Method in class edu.dartmouth.bglab.beam.web.ServerSocketImageWriter.MotifInstance
 
toString() - Method in class edu.dartmouth.bglab.beam.web.StreamPipe
 
toString() - Method in class edu.dartmouth.bglab.io.Scanner
Returns the string representation of this Scanner.
toString() - Method in class edu.dartmouth.bglab.model.ConsensusSequence
Returns a string of the sequence and rc flag.
toString() - Method in interface edu.dartmouth.bglab.model.CREModel
Just make it pretty and informative.
toString() - Method in class edu.dartmouth.bglab.model.KMismatchModel
Returns a string of the sequence.
toString() - Method in class edu.dartmouth.bglab.model.KRModel
Returns a tab-delimited table representing the model.
toString() - Method in class edu.dartmouth.bglab.model.PWM
Returns a tab-delimited table representing the pwm.
toString() - Method in class edu.dartmouth.bglab.motif.Alphabet
 
toString() - Method in class edu.dartmouth.bglab.motif.Motif.ScoreData
 
toString() - Method in class edu.dartmouth.bglab.motif.Motif
Returns the score followed by a tab and Motif.getFlaggedSequence().
toString() - Method in class edu.dartmouth.bglab.motif.MotifInstance
 
toString() - Method in class edu.dartmouth.bglab.motif.MotifList
Returns score [tab] MotifList.getSequence().
toString() - Method in class edu.dartmouth.bglab.score.MaximalMatcher
Prints the two sets of input ranges as e1 [tab] e2 where e1 and e2 are range elements from either arr1 or arr2, which are sorted.
toString() - Method in class edu.dartmouth.bglab.search.AggregatedFindResults
 
toString() - Method in class edu.dartmouth.bglab.search.MarkovModel
Prints out a given model in order.
toString() - Method in class edu.dartmouth.bglab.search.MotifFinder.EmptyFindResults
 
toString() - Method in class edu.dartmouth.bglab.search.MotifFinder
 
toString() - Method in class edu.dartmouth.bglab.search.MotifFinder.UncompressedFindResults
 
toString() - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder.SuffixArrayFindResults
 
toString() - Method in class edu.dartmouth.bglab.util.AveStatBox
Returns mean+-stdErr.
toString() - Method in class edu.dartmouth.bglab.util.FPFNStatBox
 
toString() - Method in class edu.dartmouth.bglab.util.Histogram
 
toString() - Method in class edu.dartmouth.bglab.util.LinCorrStatBox.Point
 
toString() - Method in class edu.dartmouth.bglab.util.LinCorrStatBox
 
toString() - Method in class edu.dartmouth.bglab.util.Range
 
toString(char[], int) - Static method in class edu.dartmouth.bglab.util.SuffixArray
 
toString() - Method in class edu.dartmouth.bglab.util.UberProperties
Returns each key/value pair on its own line, in alphabetical order.
TP - Variable in class edu.dartmouth.bglab.util.FPFNStatBox
 
transform(double) - Method in class edu.dartmouth.bglab.score.LogOccurrenceScorer
 
TRUE_X_VAL - Static variable in class edu.dartmouth.bglab.model.AffinityEvaluatorDriver
 
trueMean - Variable in class edu.dartmouth.bglab.util.Histogram
 
trueSD - Variable in class edu.dartmouth.bglab.util.Histogram
 
turnOffCaching() - Method in class edu.dartmouth.bglab.search.MotifFinder
Turns off caching.
turnOnCaching() - Method in class edu.dartmouth.bglab.search.MotifFinder
Starts caching, with an estimate of the number of elements that will be cached.
turnOnCaching(int) - Method in class edu.dartmouth.bglab.search.MotifFinder
 
turnOnCaching(int, int) - Method in class edu.dartmouth.bglab.search.MotifFinder
Starts caching with an estimate of the number of elements that will be cached.

U

UberProperties - Class in edu.dartmouth.bglab.util
This class adds some helpful functionality to the Properties class, simplifying access to properties that aren't strings, improving the toString method, and supplying a default properties object.
UberProperties() - Constructor for class edu.dartmouth.bglab.util.UberProperties
Creates an empty property list with no default values.
UberProperties(Properties) - Constructor for class edu.dartmouth.bglab.util.UberProperties
Creates an empty property list with the specified defaults.
UberProperties(Properties, String) - Constructor for class edu.dartmouth.bglab.util.UberProperties
Creates a property list from the specified file, with the specified defaults.
UberProperties(String) - Constructor for class edu.dartmouth.bglab.util.UberProperties
Creates a property list from the specified file, with no default values.
undoNext() - Method in class edu.dartmouth.bglab.io.Scanner
 
UNEQUAL_GENE_LENGTHS - Static variable in class edu.dartmouth.bglab.search.MotifFinder
 
unionOf(char, char) - Method in class edu.dartmouth.bglab.motif.Alphabet
Returns the char representing the set of bases that is the union of c1 and c2.
unionOf(char[], int, char[], int, int) - Method in class edu.dartmouth.bglab.motif.Motif
Returns the char-by-char union of seq1 and seq2[seq2StartIndex] through seq2[seq2StartIndex+length], where seq1[seq1StartIndex] through seq1[seq1StartIndex+length] is matched up with seq2[seq2StartIndex] through seq2[seq2StartIndex+length], and other chars are the same as in seq1.
unionWith(Motif) - Method in class edu.dartmouth.bglab.motif.Motif
Returns the union of this motif and m; the motif returned is the length of this motiif and is the most unambiguous of all possible char-by-char unions between this and m.
unionWith(MotifList) - Method in class edu.dartmouth.bglab.motif.MotifList
Returns the union of this motif list with the given motif list; ensures that there are no duplicates, as given by the motif equals method, so long as the motifs in both this list and the given list are sorted by score.
uniteMotifs() - Method in class edu.dartmouth.bglab.motif.MotifList
Collapses this motif list into a single, ambiguous motif that represents the union of all the motifs in the list; the score of the returned motif is set to be the current score of the MotifList; strip is set to true.
uniteMotifs(boolean) - Method in class edu.dartmouth.bglab.motif.MotifList
Collapses this motif list into a single, ambiguous motif that represents the union of all the motifs in the list; the score of the returned motif is set to be the current score of the MotifList.
UnknownBaseException - Exception in edu.dartmouth.bglab.motif
A runtime exception used to notify a caller that a gene name couldn't be found.
UnknownBaseException() - Constructor for exception edu.dartmouth.bglab.motif.UnknownBaseException
 
UnknownBaseException(String) - Constructor for exception edu.dartmouth.bglab.motif.UnknownBaseException
 
UnknownBaseException(String, Throwable) - Constructor for exception edu.dartmouth.bglab.motif.UnknownBaseException
 
UnknownBaseException(Throwable) - Constructor for exception edu.dartmouth.bglab.motif.UnknownBaseException
 
UnknownGeneException - Exception in edu.dartmouth.bglab.io
An exception used to notify a caller that a gene name couldn't be found.
UnknownGeneException() - Constructor for exception edu.dartmouth.bglab.io.UnknownGeneException
 
UnknownGeneException(String) - Constructor for exception edu.dartmouth.bglab.io.UnknownGeneException
 
UnknownGeneException(String, Throwable) - Constructor for exception edu.dartmouth.bglab.io.UnknownGeneException
 
UnknownGeneException(Throwable) - Constructor for exception edu.dartmouth.bglab.io.UnknownGeneException
 
unread(int) - Method in class edu.dartmouth.bglab.io.Scanner
 
UnsearchableMotifException - Exception in edu.dartmouth.bglab.search
A runtime exception used by MotifFinder when it cannot find a motif due to the degree and distribution of ambiguity.
UnsearchableMotifException() - Constructor for exception edu.dartmouth.bglab.search.UnsearchableMotifException
 
UnsearchableMotifException(String) - Constructor for exception edu.dartmouth.bglab.search.UnsearchableMotifException
 
UnsearchableMotifException(String, Throwable) - Constructor for exception edu.dartmouth.bglab.search.UnsearchableMotifException
 
UnsearchableMotifException(Throwable) - Constructor for exception edu.dartmouth.bglab.search.UnsearchableMotifException
 
UNSET - Static variable in class edu.dartmouth.bglab.util.LinCorrStatBox
 
unsuccessfulGetCtr - Variable in class edu.dartmouth.bglab.score.Scorer.ScoreSoftValueHashMap
 
updateLogDatabase(int, String) - Static method in class edu.dartmouth.bglab.beam.CGIScope
 
UPSTREAMLabel - Static variable in class edu.dartmouth.bglab.io.OrganismLoader
 
upstreamOffset - Variable in class edu.dartmouth.bglab.motif.MotifInstance
 
USE_REV_COMP - Static variable in class edu.dartmouth.bglab.beam.MLDriver
 
usePrior - Variable in class edu.dartmouth.bglab.score.Scorer
 
useProgressFile() - Static method in class edu.dartmouth.bglab.io.FileWriters
Returns true or false as progress file is set.
useRadix(int) - Method in class edu.dartmouth.bglab.io.Scanner
Sets this scanner's default radix to the specified radix.
useRevComp() - Method in class edu.dartmouth.bglab.model.ConsensusSequence
 
useRevComp() - Method in class edu.dartmouth.bglab.model.KRModel
Returns true if this pwm uses the reverse complement of the sequence.
useRevComp() - Method in class edu.dartmouth.bglab.model.PWM
Returns true if this pwm uses the reverse complement of the sequence.
useRevComp() - Method in class edu.dartmouth.bglab.motif.Motif
Returns true if this motif uses the reverse complement of the sequence.
userID - Variable in class edu.dartmouth.bglab.beam.web.WebDriver
 
userName - Variable in class edu.dartmouth.bglab.dataImportPreparation.GffToSql
 
useRsq - Variable in class edu.dartmouth.bglab.util.LinCorrStatBox
 
useSoftCache - Static variable in class edu.dartmouth.bglab.search.ComparatorMotifFinder
 
useVarLen - Variable in class edu.dartmouth.bglab.search.MarkovModel
 
useWholeGenome - Static variable in class edu.dartmouth.bglab.model.ModelEvaluator
 
UtilTester - Class in edu.dartmouth.bglab.test
For testing the .util package.
UtilTester() - Constructor for class edu.dartmouth.bglab.test.UtilTester
 

V

V - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
validateFasta(Scanner) - Static method in class edu.dartmouth.bglab.io.FileReaders
Validates a fasta formatted scanner and returns an array of gene names.
varLenLogProbabilityOf(String) - Method in class edu.dartmouth.bglab.search.MarkovModel
 
vecswap(int[], int, int, int) - Static method in class edu.dartmouth.bglab.util.SuffixArray
Swaps x[a ..
verboseSave - Variable in class edu.dartmouth.bglab.beam.BeamDriver
 

W

W - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
WebDriver - Class in edu.dartmouth.bglab.beam.web
A BeamDriver designed for use by a web front end.
WebDriver(String, String, UberProperties, String) - Constructor for class edu.dartmouth.bglab.beam.web.WebDriver
Calls super(String) and sets up member variables, along with making sure that there is an entry in WebDriver.runningProcesses for userID.
WebDriverJr - Class in edu.dartmouth.bglab.beam.web
A BeamDriver that has been modified so that WebDriver can run it as a child process.
WebDriverJr(String, UberProperties, int[]) - Constructor for class edu.dartmouth.bglab.beam.web.WebDriverJr
WebDriverJr(String, UberProperties, String[]) - Constructor for class edu.dartmouth.bglab.beam.web.WebDriverJr
WebScope - Class in edu.dartmouth.bglab.beam
 
WebScope() - Constructor for class edu.dartmouth.bglab.beam.WebScope
 
wildcardFind(Motif) - Method in class edu.dartmouth.bglab.search.MotifFinder
Returns a SORTED array of the indices of where m occurs in the sequence.
wildcardOptimizationCutoff - Variable in class edu.dartmouth.bglab.search.MotifFinder
The minimum amount of consecutive N's that must be in a motif to cause wildcard optimization to be used in MotifFinder.find(Motif); set to MotifFinder.NO_WILDCARD_OPTIMIZATION to turn off wildcard optimization completely.
WOC - Static variable in class edu.dartmouth.bglab.score.ConservationICScorer
The wildcard optimization cutoff used for the motif finders.
WOC - Static variable in class edu.dartmouth.bglab.score.ConservationRatioScorer
The wildcard optimization cutoff used for the motif finders.
WOC - Static variable in class edu.dartmouth.bglab.score.KSScorer
The Wilcard Optimization Cutoff; note that this is different from OccurrenceScorer because KSScorer must call find() on every search, which may change the optimization.
WOC - Static variable in class edu.dartmouth.bglab.score.LogOccurrenceScorer
The wildcard optimization cutoff used for the motif finders.
WOC - Static variable in class edu.dartmouth.bglab.score.OccurrenceScorer
The wildcard optimization cutoff used for the motif finders.
WOC - Static variable in class edu.dartmouth.bglab.score.RelativeEntropyScorer
The wildcard optimization cutoff used for the motif finders.
writeFASTA(GroupScorer, String) - Static method in class edu.dartmouth.bglab.beam.FASTAdriver
Writes the genes of the group in group scorer to the given file.
writeFile(double[], String) - Static method in class edu.dartmouth.bglab.io.FileWriters
Prints the given array in the given file, one entry per line.
writeFile(int[], String) - Static method in class edu.dartmouth.bglab.io.FileWriters
Prints the given array in the given file, one entry per line.
writeFile(Object[], String) - Static method in class edu.dartmouth.bglab.io.FileWriters
Prints the given array in the given file, one entry per line.
writeFile(Object, String) - Static method in class edu.dartmouth.bglab.io.FileWriters
Prints the toString() of the given object in the given file.
writeFile(Object[], String, String) - Static method in class edu.dartmouth.bglab.io.FileWriters
Prints the given array in the given file, one entry per line; sfx is appended at the end, with a \n between the last entry from arr and the start of sfx.
writeObject(ObjectOutputStream) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder.CompositeFindResults
 
writeObject(ObjectOutputStream) - Method in class edu.dartmouth.bglab.search.CompositeMotifFinder
Calls out.defaultWriteObject() and serializes sa.a so that sa can be restored.
writeObject(ObjectOutputStream) - Method in class edu.dartmouth.bglab.search.SuffixArrayMotifFinder
Calls out.defaultWriteObject() and serializes sa.a so that sa can be restored.
writeXMLGene(PrintWriter, String, int, int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLGenes(PrintWriter, String[], int[], int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLHeader(PrintWriter, int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLIndent(PrintWriter, int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLMotif(PrintWriter, Motif, int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLMotifGeneListSummary(PrintWriter, CGIDriver.MotifGeneListSummary, int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLMotifGeneSummaries(PrintWriter, SortedSet<CGIDriver.MotifGeneSummary>, String, int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLMotifGeneSummary(PrintWriter, CGIDriver.MotifGeneSummary, int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLMotifInstance(PrintWriter, MotifInstance, int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLMotifInstances(PrintWriter, MotifInstance[], int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLMotifPWM(PrintWriter, PWM, int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLMotifs(PrintWriter, Motif[], int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLProperties(PrintWriter, int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 
writeXMLProperty(PrintWriter, String, String, boolean, int) - Method in class edu.dartmouth.bglab.beam.CGIDriver
 

X

x - Variable in class edu.dartmouth.bglab.util.LinCorrStatBox.Point
 

Y

Y - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
y - Variable in class edu.dartmouth.bglab.util.LinCorrStatBox.Point
 

Z

ZScoreScorer - Class in edu.dartmouth.bglab.score
This is a wrapper class around Scorer that is itself a Scorer.
ZScoreScorer(Scorer, int) - Constructor for class edu.dartmouth.bglab.score.ZScoreScorer
Sets the scorer that this will use to the given scorer.

_

_N - Static variable in class edu.dartmouth.bglab.motif.Alphabet
 
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