public class StockholmFileAnnotation
extends java.lang.Object
Modifier and Type | Class and Description |
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static class |
StockholmFileAnnotation.StockholmFileAnnotationReference |
Constructor and Description |
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StockholmFileAnnotation() |
Modifier and Type | Method and Description |
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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) |
public java.lang.StringBuffer getDbComment()
public void setDbComment(java.lang.String dbComment)
public java.util.Set<StockholmStructure.DatabaseReference> getDbReferences()
public void setDbReferences(java.util.Set<StockholmStructure.DatabaseReference> dbReferences)
public void addDBReference(java.lang.String dbReferenceRepresentingString)
dbReference
- the string without the initial annotation identifier ( #=GS DR )public float getFalseDiscoveryRate()
public void setFalseDiscoveryRate(float falseDiscoveryRate)
public java.lang.StringBuffer getRefComment()
public java.lang.StringBuffer getKeywords()
public java.lang.String getComment()
public java.lang.StringBuffer getPfamAccession()
public java.lang.StringBuffer getLocation()
public java.lang.StringBuffer getWikipediaLink()
public java.lang.StringBuffer getClan()
public java.lang.StringBuffer getMembership()
public java.util.Map<java.lang.String,java.util.List<java.lang.String>> getEmbTrees()
public void setNumSequences(int numSequences)
public java.lang.StringBuffer getIdentification()
public void setGFIdentification(java.lang.String identification)
public java.lang.StringBuffer getDefinition()
public void setGFDefinition(java.lang.String definition)
public java.lang.String[] getAuthors()
public void setGFAuthors(java.lang.String authors)
public java.lang.String getBuildMethod()
public void addGFBuildMethod(java.lang.String buildMethod)
public java.lang.StringBuffer getSearchMethod()
public void setGFSearchMethod(java.lang.String searchMethod)
public java.lang.StringBuffer getSourceSeed()
public void setGFSourceSeed(java.lang.String sourceSeed)
public java.lang.StringBuffer getSourceStructure()
public void setGFSourceStructure(java.lang.String sourceStructure)
public float[] getGatheringThreshs()
public void setGFGatheringThreshs(java.lang.String gatheringThresh)
public float[] getNoiseCutoffs()
public void setGFNoiseCutoffs(java.lang.String noiseCutoff)
public float[] getTrustedCutoffs()
public void setGFTrustedCutoffs(java.lang.String trustedCutoff)
public float[] stringToFloats(java.lang.String string)
public java.lang.String getTypeField()
public void setGFTypeField(java.lang.String typeField)
public java.lang.String[] getPreviousIDs()
public void setGFPreviousIDs(java.lang.String previousIDs)
public java.lang.StringBuffer getFormat()
public void setFormat(java.lang.String format)
public java.lang.StringBuffer getVersion()
public void setVersion(java.lang.String version)
public java.lang.String getAccessionNumber()
public void setGFAccessionNumber(java.lang.String accessionNumber)
public boolean isPFam()
public boolean isRFam()
public int getNumSequences()
public void setGFNumSequences(java.lang.String numSequences)
public void setGFDBComment(java.lang.String dbComment)
public void setGFRefComment(java.lang.String refComment)
public void setGFKeywords(java.lang.String keywords)
public void addToGFComment(java.lang.String comment)
public void setGFPfamAccession(java.lang.String pfamAccession)
public void setGFLocation(java.lang.String location)
public void setGFWikipediaLink(java.lang.String wikipediaLink)
public void setGFClan(java.lang.String clan)
public void setGFMembership(java.lang.String membership)
public void addGFNewHampshire(java.lang.String newHampshire)
public void addGFTreeID(java.lang.String treeID)
public void addGFFalseDiscoveryRate(java.lang.String falseDiscoveryRate)
public java.lang.String getAlignmentMethod()
public void setAlignmentMethod(java.lang.String alignmentMethod)
public java.util.Vector<StockholmFileAnnotation.StockholmFileAnnotationReference> getReferences()
public void setReferences(java.util.Vector<StockholmFileAnnotation.StockholmFileAnnotationReference> references)