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 java.lang.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
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addDBReference(java.lang.String dbReferenceRepresentingString)
void
addGFBuildMethod(java.lang.String buildMethod)
void
addGFFalseDiscoveryRate(java.lang.String falseDiscoveryRate)
void
addGFNewHampshire(java.lang.String newHampshire)
void
addGFTreeID(java.lang.String treeID)
void
addToGFComment(java.lang.String comment)
java.lang.String
getAccessionNumber()
java.lang.String
getAlignmentMethod()
java.lang.String[]
getAuthors()
java.lang.String
getBuildMethod()
java.lang.StringBuffer
getClan()
java.lang.String
getComment()
java.lang.StringBuffer
getDbComment()
java.util.Set<StockholmStructure.DatabaseReference>
getDbReferences()
java.lang.StringBuffer
getDefinition()
java.util.Map<java.lang.String,java.util.List<java.lang.String>>
getEmbTrees()
float
getFalseDiscoveryRate()
java.lang.StringBuffer
getFormat()
float[]
getGatheringThreshs()
Not always 2.
It may undergo further change.java.lang.StringBuffer
getIdentification()
java.lang.StringBuffer
getKeywords()
java.lang.StringBuffer
getLocation()
java.lang.StringBuffer
getMembership()
float[]
getNoiseCutoffs()
Not always 2.
It may undergo further change.int
getNumSequences()
java.lang.StringBuffer
getPfamAccession()
java.lang.String[]
getPreviousIDs()
java.lang.StringBuffer
getRefComment()
java.util.Vector<StockholmFileAnnotation.StockholmFileAnnotationReference>
getReferences()
java.lang.StringBuffer
getSearchMethod()
java.lang.StringBuffer
getSourceSeed()
java.lang.StringBuffer
getSourceStructure()
float[]
getTrustedCutoffs()
Not always 2.
It may undergo further change.java.lang.String
getTypeField()
java.lang.StringBuffer
getVersion()
java.lang.StringBuffer
getWikipediaLink()
boolean
isPFam()
boolean
isRFam()
void
setAlignmentMethod(java.lang.String alignmentMethod)
void
setDbComment(java.lang.String dbComment)
void
setDbReferences(java.util.Set<StockholmStructure.DatabaseReference> dbReferences)
void
setFalseDiscoveryRate(float falseDiscoveryRate)
void
setFormat(java.lang.String format)
void
setGFAccessionNumber(java.lang.String accessionNumber)
void
setGFAuthors(java.lang.String authors)
void
setGFClan(java.lang.String clan)
void
setGFDBComment(java.lang.String dbComment)
void
setGFDefinition(java.lang.String definition)
void
setGFGatheringThreshs(java.lang.String gatheringThresh)
void
setGFIdentification(java.lang.String identification)
void
setGFKeywords(java.lang.String keywords)
void
setGFLocation(java.lang.String location)
void
setGFMembership(java.lang.String membership)
void
setGFNoiseCutoffs(java.lang.String noiseCutoff)
void
setGFNumSequences(java.lang.String numSequences)
void
setGFPfamAccession(java.lang.String pfamAccession)
void
setGFPreviousIDs(java.lang.String previousIDs)
void
setGFRefComment(java.lang.String refComment)
void
setGFSearchMethod(java.lang.String searchMethod)
void
setGFSourceSeed(java.lang.String sourceSeed)
void
setGFSourceStructure(java.lang.String sourceStructure)
void
setGFTrustedCutoffs(java.lang.String trustedCutoff)
void
setGFTypeField(java.lang.String typeField)
void
setGFWikipediaLink(java.lang.String wikipediaLink)
void
setNumSequences(int numSequences)
void
setReferences(java.util.Vector<StockholmFileAnnotation.StockholmFileAnnotationReference> references)
void
setVersion(java.lang.String version)
float[]
stringToFloats(java.lang.String string)
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Method Detail
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getDbComment
public java.lang.StringBuffer getDbComment()
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setDbComment
public void setDbComment(java.lang.String dbComment)
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getDbReferences
public java.util.Set<StockholmStructure.DatabaseReference> getDbReferences()
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setDbReferences
public void setDbReferences(java.util.Set<StockholmStructure.DatabaseReference> dbReferences)
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addDBReference
public void addDBReference(java.lang.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 java.lang.StringBuffer getRefComment()
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getKeywords
public java.lang.StringBuffer getKeywords()
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getComment
public java.lang.String getComment()
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getPfamAccession
public java.lang.StringBuffer getPfamAccession()
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getLocation
public java.lang.StringBuffer getLocation()
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getWikipediaLink
public java.lang.StringBuffer getWikipediaLink()
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getClan
public java.lang.StringBuffer getClan()
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getMembership
public java.lang.StringBuffer getMembership()
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getEmbTrees
public java.util.Map<java.lang.String,java.util.List<java.lang.String>> getEmbTrees()
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setNumSequences
public void setNumSequences(int numSequences)
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getIdentification
public java.lang.StringBuffer getIdentification()
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setGFIdentification
public void setGFIdentification(java.lang.String identification)
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getDefinition
public java.lang.StringBuffer getDefinition()
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setGFDefinition
public void setGFDefinition(java.lang.String definition)
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getAuthors
public java.lang.String[] getAuthors()
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setGFAuthors
public void setGFAuthors(java.lang.String authors)
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getBuildMethod
public java.lang.String getBuildMethod()
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addGFBuildMethod
public void addGFBuildMethod(java.lang.String buildMethod)
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getSearchMethod
public java.lang.StringBuffer getSearchMethod()
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setGFSearchMethod
public void setGFSearchMethod(java.lang.String searchMethod)
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getSourceSeed
public java.lang.StringBuffer getSourceSeed()
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setGFSourceSeed
public void setGFSourceSeed(java.lang.String sourceSeed)
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getSourceStructure
public java.lang.StringBuffer getSourceStructure()
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setGFSourceStructure
public void setGFSourceStructure(java.lang.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(java.lang.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(java.lang.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(java.lang.String trustedCutoff)
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stringToFloats
public float[] stringToFloats(java.lang.String string)
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getTypeField
public java.lang.String getTypeField()
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setGFTypeField
public void setGFTypeField(java.lang.String typeField)
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getPreviousIDs
public java.lang.String[] getPreviousIDs()
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setGFPreviousIDs
public void setGFPreviousIDs(java.lang.String previousIDs)
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getFormat
public java.lang.StringBuffer getFormat()
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setFormat
public void setFormat(java.lang.String format)
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getVersion
public java.lang.StringBuffer getVersion()
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setVersion
public void setVersion(java.lang.String version)
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getAccessionNumber
public java.lang.String getAccessionNumber()
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setGFAccessionNumber
public void setGFAccessionNumber(java.lang.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(java.lang.String numSequences)
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setGFDBComment
public void setGFDBComment(java.lang.String dbComment)
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setGFRefComment
public void setGFRefComment(java.lang.String refComment)
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setGFKeywords
public void setGFKeywords(java.lang.String keywords)
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addToGFComment
public void addToGFComment(java.lang.String comment)
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setGFPfamAccession
public void setGFPfamAccession(java.lang.String pfamAccession)
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setGFLocation
public void setGFLocation(java.lang.String location)
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setGFWikipediaLink
public void setGFWikipediaLink(java.lang.String wikipediaLink)
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setGFClan
public void setGFClan(java.lang.String clan)
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setGFMembership
public void setGFMembership(java.lang.String membership)
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addGFNewHampshire
public void addGFNewHampshire(java.lang.String newHampshire)
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addGFTreeID
public void addGFTreeID(java.lang.String treeID)
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addGFFalseDiscoveryRate
public void addGFFalseDiscoveryRate(java.lang.String falseDiscoveryRate)
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getAlignmentMethod
public java.lang.String getAlignmentMethod()
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setAlignmentMethod
public void setAlignmentMethod(java.lang.String alignmentMethod)
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getReferences
public java.util.Vector<StockholmFileAnnotation.StockholmFileAnnotationReference> getReferences()
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setReferences
public void setReferences(java.util.Vector<StockholmFileAnnotation.StockholmFileAnnotationReference> references)
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