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

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	StockholmFileAnnotation.StockholmFileAnnotationReference

Constructor Summary

Constructors

Constructor and Description
StockholmFileAnnotation()

Method Summary

Methods

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

StockholmFileAnnotation

public StockholmFileAnnotation()

Method Detail

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)