Package org.biojava.nbio.alignment.io

Class StockholmFileAnnotation

java.lang.Object
org.biojava.nbio.alignment.io.StockholmFileAnnotation
public class StockholmFileAnnotation extends Object
Stores all the content parsed from the #=GF lines
Since:
3.0.5
Author:
Amr AL-Hossary, Marko Vaz

  • Constructor Details

    • StockholmFileAnnotation

      public StockholmFileAnnotation()

  • Method Details

    • getDbComment

      public StringBuffer getDbComment()

    • setDbComment

      public void setDbComment(String dbComment)

    • getDbReferences

      public Set<StockholmStructure.DatabaseReference> getDbReferences()

    • setDbReferences

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

    • 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)

    • getRefComment

      public StringBuffer getRefComment()

    • getKeywords

      public StringBuffer getKeywords()

    • getComment

      public String getComment()

    • getPfamAccession

      public StringBuffer getPfamAccession()

    • getLocation

      public StringBuffer getLocation()

    • getWikipediaLink

      public StringBuffer getWikipediaLink()

    • getClan

      public StringBuffer getClan()

    • getMembership

      public StringBuffer getMembership()

    • getEmbTrees

      public Map<String,List<String>> getEmbTrees()

    • setNumSequences

      public void setNumSequences(int numSequences)

    • getIdentification

      public StringBuffer getIdentification()

    • setGFIdentification

      public void setGFIdentification(String identification)

    • getDefinition

      public StringBuffer getDefinition()

    • 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)

    • getSearchMethod

      public StringBuffer getSearchMethod()

    • setGFSearchMethod

      public void setGFSearchMethod(String searchMethod)

    • getSourceSeed

      public StringBuffer getSourceSeed()

    • 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)

    • getFormat

      public StringBuffer getFormat()

    • setFormat

      public void setFormat(String format)

    • getVersion

      public StringBuffer getVersion()

    • 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)

    • getReferences

      public Vector<StockholmFileAnnotation.StockholmFileAnnotationReference> getReferences()

    • setReferences

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