StockholmFileAnnotation (biojava 5.3.0 API)

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

Nested Classes
Modifier and Type	Class and Description
`static class`	`StockholmFileAnnotation.StockholmFileAnnotationReference`

Constructor Summary

Constructors
Constructor and Description

StockholmFileAnnotation()

Constructors
Constructor and Description
`StockholmFileAnnotation()`

Method Summary

All Methods Instance Methods Concrete 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.
`StringBuffer`	`getIdentification()`
`StringBuffer`	`getKeywords()`
`StringBuffer`	`getLocation()`
`StringBuffer`	`getMembership()`
`float[]`	`getNoiseCutoffs()` Not always 2.
`int`	`getNumSequences()`
`StringBuffer`	`getPfamAccession()`
`String[]`	`getPreviousIDs()`
`StringBuffer`	`getRefComment()`
`Vector<StockholmFileAnnotation.StockholmFileAnnotationReference>`	`getReferences()`
`StringBuffer`	`getSearchMethod()`
`StringBuffer`	`getSourceSeed()`
`StringBuffer`	`getSourceStructure()`
`float[]`	`getTrustedCutoffs()` Not always 2.
`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)

Class StockholmFileAnnotation

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

StockholmFileAnnotation

Method Detail

getDbComment

setDbComment

getDbReferences

setDbReferences

addDBReference

getFalseDiscoveryRate

setFalseDiscoveryRate

getRefComment

getKeywords

getComment

getPfamAccession

getLocation

getWikipediaLink

getClan

getMembership

getEmbTrees

setNumSequences

getIdentification

setGFIdentification

getDefinition

setGFDefinition

getAuthors

setGFAuthors

getBuildMethod

addGFBuildMethod

getSearchMethod

setGFSearchMethod

getSourceSeed

setGFSourceSeed

getSourceStructure

setGFSourceStructure

getGatheringThreshs

setGFGatheringThreshs

getNoiseCutoffs

setGFNoiseCutoffs

getTrustedCutoffs

setGFTrustedCutoffs

stringToFloats

getTypeField

setGFTypeField

getPreviousIDs

setGFPreviousIDs

getFormat

setFormat

getVersion

setVersion

getAccessionNumber

setGFAccessionNumber

isPFam

isRFam

getNumSequences

setGFNumSequences

setGFDBComment

setGFRefComment

setGFKeywords

addToGFComment

setGFPfamAccession

setGFLocation

setGFWikipediaLink

setGFClan

setGFMembership

addGFNewHampshire

addGFTreeID

addGFFalseDiscoveryRate

getAlignmentMethod

setAlignmentMethod

getReferences

setReferences