meme
Class MemeResults

java.lang.Object
  meme.MemeResults

public class MemeResults

extends java.lang.Object

Holds the results from various parts of MemeR.

Constructor Summary

MemeResults()

Method Summary

void	appendMemeParserReport(java.lang.String data)
void	appendMemeReports(java.lang.String data)
void	appendMotifSearchResults(java.lang.String data)
void	appendSelexOligoFiles(java.lang.String data)
java.lang.String	getMemeReports()
java.lang.String	getMotifHitPlot() Rude and crude method to plot the percent hits of each motif to each file using data from motifHitSummary
java.lang.String	getMotifHitPlotText()
java.lang.String	getMotifHitsSummary() Method to return a summary of all the motif hits to each file, modify this to build an HTML table
java.lang.String	getMotifHitsSummaryText()
java.lang.String	getMotifSummary() Method to return a summary of all the motifs generated by MemeR, modify this to build an HTML table
java.lang.String	getMotifSummaryText()
java.lang.String	getResults()
void	makeFileNameHash()
void	printSave(java.lang.String newString)
void	setFileBaseName(java.lang.String data)
void	setMemeCmdLnArgs(java.lang.String data)
void	setMemeParserArrayRef(MemeParser[] data)
void	setMotifHitPlotText(java.lang.String data)
void	setMotifHitsSummaryText(java.lang.String data)
void	setMotifResults(java.util.ArrayList data)
void	setMotifSummaryText(java.lang.String data)
void	setResultsDirectory(java.lang.String data)
void	sortMotifSearchResults() method to sort the array of MotifSearchResult objects, also sets two fields based on the this.fileNameHash
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

MemeResults

public MemeResults()

Method Detail

getMotifSummary

public java.lang.String getMotifSummary()

Method to return a summary of all the motifs generated by MemeR, modify this to build an HTML table

sortMotifSearchResults

public void sortMotifSearchResults()

method to sort the array of MotifSearchResult objects, also sets two fields based on the this.fileNameHash

getMotifHitsSummary

public java.lang.String getMotifHitsSummary()

Method to return a summary of all the motif hits to each file, modify this to build an HTML table

getMotifHitPlot

public java.lang.String getMotifHitPlot()

Rude and crude method to plot the percent hits of each motif to each file using data from motifHitSummary

printSave

public void printSave(java.lang.String newString)

toString

public java.lang.String toString()

makeFileNameHash

public void makeFileNameHash()

getResults

public java.lang.String getResults()

getMemeReports

public java.lang.String getMemeReports()

getMotifSummaryText

public java.lang.String getMotifSummaryText()

getMotifHitsSummaryText

public java.lang.String getMotifHitsSummaryText()

getMotifHitPlotText

public java.lang.String getMotifHitPlotText()

setMemeParserArrayRef

public void setMemeParserArrayRef(MemeParser[] data)

setMotifHitPlotText

public void setMotifHitPlotText(java.lang.String data)

setMotifSummaryText

public void setMotifSummaryText(java.lang.String data)

setMotifHitsSummaryText

public void setMotifHitsSummaryText(java.lang.String data)

appendSelexOligoFiles

public void appendSelexOligoFiles(java.lang.String data)

setMemeCmdLnArgs

public void setMemeCmdLnArgs(java.lang.String data)

setFileBaseName

public void setFileBaseName(java.lang.String data)

setResultsDirectory

public void setResultsDirectory(java.lang.String data)

appendMemeParserReport

public void appendMemeParserReport(java.lang.String data)

appendMemeReports

public void appendMemeReports(java.lang.String data)

appendMotifSearchResults

public void appendMotifSearchResults(java.lang.String data)

setMotifResults

public void setMotifResults(java.util.ArrayList data)