Package org.biojava.nbio.alignment.io
Class StockholmFileAnnotation
- java.lang.Object
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- org.biojava.nbio.alignment.io.StockholmFileAnnotation
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public class StockholmFileAnnotation extends Object
Stores all the content parsed from the #=GF lines- Since:
- 3.0.5
- Author:
- Amr AL-Hossary, Marko Vaz
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
StockholmFileAnnotation.StockholmFileAnnotationReference
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Constructor Summary
Constructors Constructor Description StockholmFileAnnotation()
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Method Summary
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Constructor Detail
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StockholmFileAnnotation
public StockholmFileAnnotation()
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Method Detail
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getDbComment
public StringBuffer getDbComment()
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setDbComment
public void setDbComment(String dbComment)
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getDbReferences
public Set<StockholmStructure.DatabaseReference> getDbReferences()
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setDbReferences
public void setDbReferences(Set<StockholmStructure.DatabaseReference> dbReferences)
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addDBReference
public void addDBReference(String dbReferenceRepresentingString)
- Parameters:
dbReference
- the string without the initial annotation identifier ( #=GS DR )
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getFalseDiscoveryRate
public float getFalseDiscoveryRate()
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setFalseDiscoveryRate
public void setFalseDiscoveryRate(float falseDiscoveryRate)
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getRefComment
public StringBuffer getRefComment()
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getKeywords
public StringBuffer getKeywords()
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getComment
public String getComment()
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getPfamAccession
public StringBuffer getPfamAccession()
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getLocation
public StringBuffer getLocation()
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getWikipediaLink
public StringBuffer getWikipediaLink()
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getClan
public StringBuffer getClan()
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getMembership
public StringBuffer getMembership()
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getEmbTrees
public Map<String,List<String>> getEmbTrees()
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setNumSequences
public void setNumSequences(int numSequences)
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getIdentification
public StringBuffer getIdentification()
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setGFIdentification
public void setGFIdentification(String identification)
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getDefinition
public StringBuffer getDefinition()
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setGFDefinition
public void setGFDefinition(String definition)
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getAuthors
public String[] getAuthors()
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setGFAuthors
public void setGFAuthors(String authors)
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getBuildMethod
public String getBuildMethod()
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addGFBuildMethod
public void addGFBuildMethod(String buildMethod)
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getSearchMethod
public StringBuffer getSearchMethod()
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setGFSearchMethod
public void setGFSearchMethod(String searchMethod)
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getSourceSeed
public StringBuffer getSourceSeed()
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setGFSourceSeed
public void setGFSourceSeed(String sourceSeed)
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getSourceStructure
public StringBuffer getSourceStructure()
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setGFSourceStructure
public void setGFSourceStructure(String sourceStructure)
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getGatheringThreshs
public float[] getGatheringThreshs()
Not always 2.
It may undergo further change.- Returns:
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setGFGatheringThreshs
public void setGFGatheringThreshs(String gatheringThresh)
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getNoiseCutoffs
public float[] getNoiseCutoffs()
Not always 2.
It may undergo further change.- Returns:
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setGFNoiseCutoffs
public void setGFNoiseCutoffs(String noiseCutoff)
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getTrustedCutoffs
public float[] getTrustedCutoffs()
Not always 2.
It may undergo further change.- Returns:
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setGFTrustedCutoffs
public void setGFTrustedCutoffs(String trustedCutoff)
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stringToFloats
public float[] stringToFloats(String string)
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getTypeField
public String getTypeField()
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setGFTypeField
public void setGFTypeField(String typeField)
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getPreviousIDs
public String[] getPreviousIDs()
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setGFPreviousIDs
public void setGFPreviousIDs(String previousIDs)
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getFormat
public StringBuffer getFormat()
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getVersion
public StringBuffer getVersion()
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setVersion
public void setVersion(String version)
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getAccessionNumber
public String getAccessionNumber()
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setGFAccessionNumber
public void setGFAccessionNumber(String accessionNumber)
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isPFam
public boolean isPFam()
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isRFam
public boolean isRFam()
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getNumSequences
public int getNumSequences()
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setGFNumSequences
public void setGFNumSequences(String numSequences)
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setGFDBComment
public void setGFDBComment(String dbComment)
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setGFRefComment
public void setGFRefComment(String refComment)
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setGFKeywords
public void setGFKeywords(String keywords)
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addToGFComment
public void addToGFComment(String comment)
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setGFPfamAccession
public void setGFPfamAccession(String pfamAccession)
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setGFLocation
public void setGFLocation(String location)
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setGFWikipediaLink
public void setGFWikipediaLink(String wikipediaLink)
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setGFMembership
public void setGFMembership(String membership)
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addGFNewHampshire
public void addGFNewHampshire(String newHampshire)
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addGFTreeID
public void addGFTreeID(String treeID)
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addGFFalseDiscoveryRate
public void addGFFalseDiscoveryRate(String falseDiscoveryRate)
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getAlignmentMethod
public String getAlignmentMethod()
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setAlignmentMethod
public void setAlignmentMethod(String alignmentMethod)
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getReferences
public Vector<StockholmFileAnnotation.StockholmFileAnnotationReference> getReferences()
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setReferences
public void setReferences(Vector<StockholmFileAnnotation.StockholmFileAnnotationReference> references)
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