- 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
-
- 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
-
- 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 - 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
-
- 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 - 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- enumerateMotifs(int, boolean, int, int) - Static method in class edu.dartmouth.bglab.motif.MotifUtils
-
- 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
-
- 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
-
- 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 - 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- getComparator() - Method in class edu.dartmouth.bglab.model.KRModel
-
- getComparator() - Method in class edu.dartmouth.bglab.model.PWM
-
- 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
-
- 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
-
- 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
-
- getHits(String) - Method in class edu.dartmouth.bglab.model.PWM
-
- 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
-
- 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 - 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
-
- hashCode() - Method in class edu.dartmouth.bglab.motif.MotifList
-
- 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
-
- 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
-
- 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
-
- 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
-
- MaximalMatcher(Motif, MotifList, MotifFinder) - Constructor for class edu.dartmouth.bglab.score.MaximalMatcher
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- 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
-
- readMotifs(String, String, boolean, Alphabet) - Static method in class edu.dartmouth.bglab.io.FileReaders
-
- 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
-
- 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
-
- 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
-
- run() - Method in class edu.dartmouth.bglab.beam.LinearityTesterDriver
-
- run() - Method in class edu.dartmouth.bglab.beam.MLDriver
-
- run() - Method in class edu.dartmouth.bglab.beam.PhiScoreDriver
-
- 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
-
- 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
-
- 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 - 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
-
- 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
-
- 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
-
- 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
-
- 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
-