public class CGIDriver extends BeamDriver
Modifier and Type | Class and Description |
---|---|
private class |
CGIDriver.MotifGeneListSummary |
private static class |
CGIDriver.MotifGeneSummary |
Modifier and Type | Field and Description |
---|---|
private static java.util.regex.Pattern |
aLetter |
(package private) int[] |
geneIDs |
private int |
geneLength |
private java.lang.String[] |
geneNames |
private java.util.SortedMap<java.lang.Integer,java.util.List<java.lang.String>> |
geneNumberSynonymsMap |
private static java.lang.String |
GENES_WITH_MOTIF_WHICH_DO_NOT_IMPROVE_SCORE |
private static java.lang.String |
GENES_WITH_MOTIF_WHICH_IMPROVE_SCORE |
private int[] |
groupLength |
private static java.lang.String |
INTRON_MARKER |
private boolean |
isFasta |
private java.util.SortedMap<Motif,CGIDriver.MotifGeneListSummary> |
motifGeneSummaries |
private java.util.Map<Motif,MotifInstance[]> |
motifStatsCache |
private boolean |
onlyForcedMotifs |
(package private) static java.util.regex.Pattern |
patLocation |
private java.util.Map<java.lang.String,Motif[]> |
results |
private static java.util.regex.Pattern |
synonymAndGeneNumberPattern |
AMBIGUIZER_NAME, BEAM_NAME, BIPARTITE_NAME, bpScorer, error, fileRoot, knownMotifs, MERGED_NAME, properties, scorer, scorerInfoMap, subtestID, testID, verboseSave
Constructor and Description |
---|
CGIDriver(java.lang.String threadID,
UberProperties properties) |
Modifier and Type | Method and Description |
---|---|
private static boolean |
ambiguousMatch(char a,
char b) |
private void |
createMotifListAndGeneListSummary(Motif[] mergedResult) |
protected int |
getCoverageCount(MotifInstance[] instances) |
private java.lang.String |
getGeneGroupSequenceInFastaFormat() |
private MotifInstance[] |
getMotifInstances(Motif m)
Returns an array of
MotifInstances that represent the locations in the group of the given motif. |
private java.lang.String |
getTextMotifGeneSummary(CGIDriver.MotifGeneSummary motifGeneSummary) |
private boolean |
isMotifBackwards(Motif m) |
void |
outputResultsAsText(java.io.OutputStream outputStream) |
void |
outputResultsAsXML(java.io.OutputStream outputStream) |
void |
printBestMotif(Motif m)
Need to override this to do nothing so that files don't get written.
|
private java.lang.String |
reorientedMotifSequence(Motif m) |
Motif[] |
runBeamPlus()
This is the current Beam+ suite of programs.
|
private Motif[] |
runMotifToConsensusSequenceFilter(Motif[] mergedResult)
This ensures that all motifs are as specific as possible.
|
void |
saveFilterResults(Motif[] motifs,
java.lang.String section,
Stopwatch timer)
Need to override this to do nothing so that files don't get written.
|
void |
saveProperties()
Need to override this to do nothing so that files don't get written.
|
void |
saveResults(Motif[] motifs,
java.lang.String id,
Stopwatch timer,
MotifComparator comp)
Need to override this to do nothing so that files don't get written.
|
void |
saveSpecialStats(Motif[] motifs,
Stopwatch timer)
Need to override this to do nothing so that files don't get written.
|
private void |
writeXMLGene(java.io.PrintWriter p,
java.lang.String group,
int groupLength,
int indent) |
private void |
writeXMLGenes(java.io.PrintWriter p,
java.lang.String[] groups,
int[] groupLength,
int indent) |
private void |
writeXMLHeader(java.io.PrintWriter p,
int indent) |
private void |
writeXMLIndent(java.io.PrintWriter p,
int indent) |
private void |
writeXMLMotif(java.io.PrintWriter p,
Motif m,
int indent) |
private void |
writeXMLMotifGeneListSummary(java.io.PrintWriter p,
CGIDriver.MotifGeneListSummary motifGeneListSummary,
int indent) |
private void |
writeXMLMotifGeneSummaries(java.io.PrintWriter p,
java.util.SortedSet<CGIDriver.MotifGeneSummary> geneSummariesSet,
java.lang.String listType,
int indent) |
private void |
writeXMLMotifGeneSummary(java.io.PrintWriter p,
CGIDriver.MotifGeneSummary motifGeneSummary,
int indent) |
private void |
writeXMLMotifInstance(java.io.PrintWriter p,
MotifInstance m,
int indent) |
private void |
writeXMLMotifInstances(java.io.PrintWriter p,
MotifInstance[] m,
int indent) |
private void |
writeXMLMotifPWM(java.io.PrintWriter p,
PWM pwm,
int indent) |
private void |
writeXMLMotifs(java.io.PrintWriter p,
Motif[] m,
int indent) |
private void |
writeXMLProperties(java.io.PrintWriter p,
int indent) |
private void |
writeXMLProperty(java.io.PrintWriter p,
java.lang.String name,
java.lang.String value,
boolean dft,
int indent) |
getScorer, refineBipartite, run, runAmbiguizerEtc, runBeamEtc, runBipartitesEtc, runFilterEtc, runMergeEtc, setFastaMotifFinder, setMostParams, setVerboseSave
activeCount, checkAccess, clone, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield
private static final java.lang.String GENES_WITH_MOTIF_WHICH_IMPROVE_SCORE
private static final java.lang.String GENES_WITH_MOTIF_WHICH_DO_NOT_IMPROVE_SCORE
private static final java.lang.String INTRON_MARKER
private static final java.util.regex.Pattern aLetter
static final java.util.regex.Pattern patLocation
private static final java.util.regex.Pattern synonymAndGeneNumberPattern
int[] geneIDs
private int geneLength
private java.lang.String[] geneNames
private final int[] groupLength
private boolean isFasta
private java.util.SortedMap<Motif,CGIDriver.MotifGeneListSummary> motifGeneSummaries
private final java.util.Map<Motif,MotifInstance[]> motifStatsCache
private boolean onlyForcedMotifs
private java.util.Map<java.lang.String,Motif[]> results
private final java.util.SortedMap<java.lang.Integer,java.util.List<java.lang.String>> geneNumberSynonymsMap
public CGIDriver(java.lang.String threadID, UberProperties properties) throws UnknownGeneException, java.io.IOException
UnknownGeneException
java.io.IOException
private static boolean ambiguousMatch(char a, char b)
private void createMotifListAndGeneListSummary(Motif[] mergedResult)
protected int getCoverageCount(MotifInstance[] instances)
private java.lang.String getGeneGroupSequenceInFastaFormat()
private MotifInstance[] getMotifInstances(Motif m)
MotifInstances
that represent the locations in the group of the given motif. Uses a cache to
speed up multiple lookups of the same motif by a user.private java.lang.String getTextMotifGeneSummary(CGIDriver.MotifGeneSummary motifGeneSummary)
private boolean isMotifBackwards(Motif m)
public void outputResultsAsText(java.io.OutputStream outputStream) throws java.io.IOException
java.io.IOException
public void outputResultsAsXML(java.io.OutputStream outputStream)
public void printBestMotif(Motif m)
printBestMotif
in class BeamDriver
private java.lang.String reorientedMotifSequence(Motif m)
public Motif[] runBeamPlus() throws java.io.IOException
runBeamPlus
in class BeamDriver
java.io.IOException
private Motif[] runMotifToConsensusSequenceFilter(Motif[] mergedResult)
mergedResult
- public void saveFilterResults(Motif[] motifs, java.lang.String section, Stopwatch timer) throws java.io.IOException
saveFilterResults
in class BeamDriver
java.io.IOException
public void saveProperties() throws java.io.IOException
saveProperties
in class BeamDriver
java.io.IOException
public void saveResults(Motif[] motifs, java.lang.String id, Stopwatch timer, MotifComparator comp) throws java.io.IOException
saveResults
in class BeamDriver
java.io.IOException
public void saveSpecialStats(Motif[] motifs, Stopwatch timer)
saveSpecialStats
in class BeamDriver
private void writeXMLGene(java.io.PrintWriter p, java.lang.String group, int groupLength, int indent)
private void writeXMLGenes(java.io.PrintWriter p, java.lang.String[] groups, int[] groupLength, int indent)
private void writeXMLHeader(java.io.PrintWriter p, int indent)
private void writeXMLIndent(java.io.PrintWriter p, int indent)
private void writeXMLMotif(java.io.PrintWriter p, Motif m, int indent)
private void writeXMLMotifGeneListSummary(java.io.PrintWriter p, CGIDriver.MotifGeneListSummary motifGeneListSummary, int indent)
private void writeXMLMotifGeneSummaries(java.io.PrintWriter p, java.util.SortedSet<CGIDriver.MotifGeneSummary> geneSummariesSet, java.lang.String listType, int indent)
private void writeXMLMotifGeneSummary(java.io.PrintWriter p, CGIDriver.MotifGeneSummary motifGeneSummary, int indent)
private void writeXMLMotifInstance(java.io.PrintWriter p, MotifInstance m, int indent)
private void writeXMLMotifInstances(java.io.PrintWriter p, MotifInstance[] m, int indent)
private void writeXMLMotifPWM(java.io.PrintWriter p, PWM pwm, int indent)
private void writeXMLMotifs(java.io.PrintWriter p, Motif[] m, int indent)
private void writeXMLProperties(java.io.PrintWriter p, int indent)
private void writeXMLProperty(java.io.PrintWriter p, java.lang.String name, java.lang.String value, boolean dft, int indent)