Package org.biojava.nbio.alignment.io

Class StockholmFileAnnotation

  • public class StockholmFileAnnotation
extends Object
    Stores all the content parsed from the #=GF lines
    Since:
    3.0.5
    Author:
    Amr ALHOSSARY, Marko Vaz

    • Constructor Detail

      • StockholmFileAnnotation

        public StockholmFileAnnotation()

    • Method Detail

      • setDbComment

        public void setDbComment​(String dbComment)

      • addDBReference

        public void addDBReference​(String dbReferenceRepresentingString)
        Parameters:
        dbReference - the string without the initial annotation identifier ( #=GS DR )

      • getFalseDiscoveryRate

        public float getFalseDiscoveryRate()

      • setFalseDiscoveryRate

        public void setFalseDiscoveryRate​(float falseDiscoveryRate)

      • getComment

        public String getComment()

      • setNumSequences

        public void setNumSequences​(int numSequences)

      • getIdentification

        public StringBuffer getIdentification()

      • setGFIdentification

        public void setGFIdentification​(String identification)

      • setGFDefinition

        public void setGFDefinition​(String definition)

      • getAuthors

        public String[] getAuthors()

      • setGFAuthors

        public void setGFAuthors​(String authors)

      • getBuildMethod

        public String getBuildMethod()

      • addGFBuildMethod

        public void addGFBuildMethod​(String buildMethod)

      • setGFSearchMethod

        public void setGFSearchMethod​(String searchMethod)

      • setGFSourceSeed

        public void setGFSourceSeed​(String sourceSeed)

      • getSourceStructure

        public StringBuffer getSourceStructure()

      • setGFSourceStructure

        public void setGFSourceStructure​(String sourceStructure)

      • getGatheringThreshs

        public float[] getGatheringThreshs()
        Not always 2.
        It may undergo further change.
        Returns:

      • setGFGatheringThreshs

        public void setGFGatheringThreshs​(String gatheringThresh)

      • getNoiseCutoffs

        public float[] getNoiseCutoffs()
        Not always 2.
        It may undergo further change.
        Returns:

      • setGFNoiseCutoffs

        public void setGFNoiseCutoffs​(String noiseCutoff)

      • getTrustedCutoffs

        public float[] getTrustedCutoffs()
        Not always 2.
        It may undergo further change.
        Returns:

      • setGFTrustedCutoffs

        public void setGFTrustedCutoffs​(String trustedCutoff)

      • stringToFloats

        public float[] stringToFloats​(String string)

      • getTypeField

        public String getTypeField()

      • setGFTypeField

        public void setGFTypeField​(String typeField)

      • getPreviousIDs

        public String[] getPreviousIDs()

      • setGFPreviousIDs

        public void setGFPreviousIDs​(String previousIDs)

      • setFormat

        public void setFormat​(String format)

      • setVersion

        public void setVersion​(String version)

      • getAccessionNumber

        public String getAccessionNumber()

      • setGFAccessionNumber

        public void setGFAccessionNumber​(String accessionNumber)

      • isPFam

        public boolean isPFam()

      • isRFam

        public boolean isRFam()

      • getNumSequences

        public int getNumSequences()

      • setGFNumSequences

        public void setGFNumSequences​(String numSequences)

      • setGFDBComment

        public void setGFDBComment​(String dbComment)

      • setGFRefComment

        public void setGFRefComment​(String refComment)

      • setGFKeywords

        public void setGFKeywords​(String keywords)

      • addToGFComment

        public void addToGFComment​(String comment)

      • setGFPfamAccession

        public void setGFPfamAccession​(String pfamAccession)

      • setGFLocation

        public void setGFLocation​(String location)

      • setGFWikipediaLink

        public void setGFWikipediaLink​(String wikipediaLink)

      • setGFClan

        public void setGFClan​(String clan)

      • setGFMembership

        public void setGFMembership​(String membership)

      • addGFNewHampshire

        public void addGFNewHampshire​(String newHampshire)

      • addGFTreeID

        public void addGFTreeID​(String treeID)

      • addGFFalseDiscoveryRate

        public void addGFFalseDiscoveryRate​(String falseDiscoveryRate)

      • getAlignmentMethod

        public String getAlignmentMethod()

      • setAlignmentMethod

        public void setAlignmentMethod​(String alignmentMethod)