Class StockholmFileAnnotation


  • public class StockholmFileAnnotation
    extends java.lang.Object
    Stores all the content parsed from the #=GF lines
    Since:
    3.0.5
    Author:
    Amr AL-Hossary, Marko Vaz
    • Constructor Detail

      • StockholmFileAnnotation

        public StockholmFileAnnotation()
    • Method Detail

      • getDbComment

        public java.lang.StringBuffer getDbComment()
      • setDbComment

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