Constructor Detail

• StockholmFileAnnotation

  public StockholmFileAnnotation()

Method Detail

• getDbComment

  public java.lang.StringBuffer getDbComment()

• setDbComment

  public void setDbComment​(java.lang.String dbComment)

• getDbReferences

  public java.util.Set<StockholmStructure.DatabaseReference> getDbReferences()

• setDbReferences

  public void setDbReferences​(java.util.Set<StockholmStructure.DatabaseReference> dbReferences)

• addDBReference

  public void addDBReference​(java.lang.String dbReferenceRepresentingString)

  Parameters:

  dbReference - the string without the initial annotation identifier ( #=GS DR )

• getFalseDiscoveryRate

  public float getFalseDiscoveryRate()

• setFalseDiscoveryRate

  public void setFalseDiscoveryRate​(float falseDiscoveryRate)

• getRefComment

  public java.lang.StringBuffer getRefComment()

• getKeywords

  public java.lang.StringBuffer getKeywords()

• getComment

  public java.lang.String getComment()

• getPfamAccession

  public java.lang.StringBuffer getPfamAccession()

• getLocation

  public java.lang.StringBuffer getLocation()

• getWikipediaLink

  public java.lang.StringBuffer getWikipediaLink()

• getClan

  public java.lang.StringBuffer getClan()

• getMembership

  public java.lang.StringBuffer getMembership()

• getEmbTrees

  public java.util.Map<java.lang.String,​java.util.List<java.lang.String>> getEmbTrees()

• setNumSequences

  public void setNumSequences​(int numSequences)

• getIdentification

  public java.lang.StringBuffer getIdentification()

• setGFIdentification

  public void setGFIdentification​(java.lang.String identification)

• getDefinition

  public java.lang.StringBuffer getDefinition()

• setGFDefinition

  public void setGFDefinition​(java.lang.String definition)

• getAuthors

  public java.lang.String[] getAuthors()

• setGFAuthors

  public void setGFAuthors​(java.lang.String authors)

• getBuildMethod

  public java.lang.String getBuildMethod()

• addGFBuildMethod

  public void addGFBuildMethod​(java.lang.String buildMethod)

• getSearchMethod

  public java.lang.StringBuffer getSearchMethod()

• setGFSearchMethod

  public void setGFSearchMethod​(java.lang.String searchMethod)

• getSourceSeed

  public java.lang.StringBuffer getSourceSeed()

• setGFSourceSeed

  public void setGFSourceSeed​(java.lang.String sourceSeed)

• getSourceStructure

  public java.lang.StringBuffer getSourceStructure()

• setGFSourceStructure

  public void setGFSourceStructure​(java.lang.String sourceStructure)

• getGatheringThreshs

  public float[] getGatheringThreshs()

  Not always 2.
  It may undergo further change.

  Returns:

• setGFGatheringThreshs

  public void setGFGatheringThreshs​(java.lang.String gatheringThresh)

• getNoiseCutoffs

  public float[] getNoiseCutoffs()

  Not always 2.
  It may undergo further change.

  Returns:

• setGFNoiseCutoffs

  public void setGFNoiseCutoffs​(java.lang.String noiseCutoff)

• getTrustedCutoffs

  public float[] getTrustedCutoffs()

  Not always 2.
  It may undergo further change.

  Returns:

• setGFTrustedCutoffs

  public void setGFTrustedCutoffs​(java.lang.String trustedCutoff)

• stringToFloats

  public float[] stringToFloats​(java.lang.String string)

• getTypeField

  public java.lang.String getTypeField()

• setGFTypeField

  public void setGFTypeField​(java.lang.String typeField)

• getPreviousIDs

  public java.lang.String[] getPreviousIDs()

• setGFPreviousIDs

  public void setGFPreviousIDs​(java.lang.String previousIDs)

• getFormat

  public java.lang.StringBuffer getFormat()

• setFormat

  public void setFormat​(java.lang.String format)

• getVersion

  public java.lang.StringBuffer getVersion()

• setVersion

  public void setVersion​(java.lang.String version)

• getAccessionNumber

  public java.lang.String getAccessionNumber()

• setGFAccessionNumber

  public void setGFAccessionNumber​(java.lang.String accessionNumber)

• isPFam

  public boolean isPFam()

• isRFam

  public boolean isRFam()

• getNumSequences

  public int getNumSequences()

• setGFNumSequences

  public void setGFNumSequences​(java.lang.String numSequences)

• setGFDBComment

  public void setGFDBComment​(java.lang.String dbComment)

• setGFRefComment

  public void setGFRefComment​(java.lang.String refComment)

• setGFKeywords

  public void setGFKeywords​(java.lang.String keywords)

• addToGFComment

  public void addToGFComment​(java.lang.String comment)

• setGFPfamAccession

  public void setGFPfamAccession​(java.lang.String pfamAccession)

• setGFLocation

  public void setGFLocation​(java.lang.String location)

• setGFWikipediaLink

  public void setGFWikipediaLink​(java.lang.String wikipediaLink)

• setGFClan

  public void setGFClan​(java.lang.String clan)

• setGFMembership

  public void setGFMembership​(java.lang.String membership)

• addGFNewHampshire

  public void addGFNewHampshire​(java.lang.String newHampshire)

• addGFTreeID

  public void addGFTreeID​(java.lang.String treeID)

• addGFFalseDiscoveryRate

  public void addGFFalseDiscoveryRate​(java.lang.String falseDiscoveryRate)

• getAlignmentMethod

  public java.lang.String getAlignmentMethod()

• setAlignmentMethod

  public void setAlignmentMethod​(java.lang.String alignmentMethod)

• getReferences

  public java.util.Vector<StockholmFileAnnotation.StockholmFileAnnotationReference> getReferences()

• setReferences

  public void setReferences​(java.util.Vector<StockholmFileAnnotation.StockholmFileAnnotationReference> references)