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jalview.annotation
Class FeatureSet  

java.lang.Object
  jalview.annotation.SeqFeature
      jalview.annotation.FeatureSet

All Implemented Interfaces:

FeatureSetI, SeqFeatureI

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public class FeatureSet

extends SeqFeature

implements FeatureSetI

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Field Summary
private  java.util.Vector	features

 

Fields inherited from class jalview.annotation.SeqFeature

end, name, primary_tag, refFeature, score, seq, source_tag, start, strand, type

 

Constructor Summary

FeatureSet()

 

Method Summary
int	_countIntrons(SeqFeatureI sf)
private  void	_setEnds()
FeatureSetI	_splitHomols(SeqFeatureI sf2)           Method to split a HOMOL feature set into pieces which are more or less contiguous (less than 10 bases between features).
void	addFeature(SeqFeatureI feature)
void	clump()
void	deleteFeature(SeqFeatureI feature)
SeqFeatureI	deleteFeatureAt(int i)
void	expand(FeatureSetI newfset)
SeqFeatureI	getFeatureAt(int i)
java.util.Vector	getFeatures()
java.util.Vector	getFeatures(long start, long end)
java.lang.String	getName()           Returns the name of the feature
int	getStrand()           Returns the strand of the feature
java.lang.String	getType()           Returns the type string of the feature.
void	group()
java.util.Hashtable	hashFeatures()
java.util.Vector	makeGeneSets(SeqFeatureI sf)
java.util.Vector	makeHomolSets(SeqFeatureI sf)
void	makeSetFeatures()
void	setFeatureAt(int i, SeqFeatureI sf)
int	size()
void	sort_by_type()

 

Methods inherited from class jalview.annotation.SeqFeature

findOverlap, getEnd, getProducedFeatures, getRefFeature, getScore, getSequenceI, getStart, overlaps, setEnd, setName, setProducedFeatures, setRefFeature, setScore, setSequenceI, setStart, setStrand, setType, toString

 

Methods inherited from class java.lang.Object

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

 

Methods inherited from interface jalview.annotation.SeqFeatureI

findOverlap, getEnd, getProducedFeatures, getRefFeature, getScore, getSequenceI, getStart, overlaps, setEnd, setName, setProducedFeatures, setRefFeature, setScore, setSequenceI, setStart, setStrand, setType

 

Field Detail

features

private java.util.Vector features

Constructor Detail

FeatureSet

public FeatureSet()

Method Detail

size

public int size()

Specified by:

size in interface FeatureSetI

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addFeature

public void addFeature(SeqFeatureI feature)

Specified by:

addFeature in interface FeatureSetI

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deleteFeature

public void deleteFeature(SeqFeatureI feature)

Specified by:

deleteFeature in interface FeatureSetI

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deleteFeatureAt

public SeqFeatureI deleteFeatureAt(int i)

Specified by:

deleteFeatureAt in interface FeatureSetI

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getFeatureAt

public SeqFeatureI getFeatureAt(int i)

Specified by:

getFeatureAt in interface FeatureSetI

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setFeatureAt

public void setFeatureAt(int i,
                         SeqFeatureI sf)

Specified by:

setFeatureAt in interface FeatureSetI

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getFeatures

public java.util.Vector getFeatures()

Specified by:

getFeatures in interface FeatureSetI

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getFeatures

public java.util.Vector getFeatures(long start,
                                    long end)

Specified by:

getFeatures in interface FeatureSetI

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hashFeatures

public java.util.Hashtable hashFeatures()

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expand

public void expand(FeatureSetI newfset)

Specified by:

expand in interface FeatureSetI

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group

public void group()

Specified by:

group in interface FeatureSetI

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clump

public void clump()

Specified by:

clump in interface FeatureSetI

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makeSetFeatures

public void makeSetFeatures()

Specified by:

makeSetFeatures in interface FeatureSetI

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sort_by_type

public void sort_by_type()

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makeHomolSets

public java.util.Vector makeHomolSets(SeqFeatureI sf)

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_splitHomols

public FeatureSetI _splitHomols(SeqFeatureI sf2)

Method to split a HOMOL feature set into pieces which are more or less contiguous (less than 10 bases between features).

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_countIntrons

public int _countIntrons(SeqFeatureI sf)

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makeGeneSets

public java.util.Vector makeGeneSets(SeqFeatureI sf)

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getStrand

public int getStrand()

Description copied from interface: SeqFeatureI

Returns the strand of the feature

Specified by:

getStrand in interface SeqFeatureI

Overrides:

getStrand in class SeqFeature

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getName

public java.lang.String getName()

Description copied from interface: SeqFeatureI

Returns the name of the feature

Specified by:

getName in interface SeqFeatureI

Overrides:

getName in class SeqFeature

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getType

public java.lang.String getType()

Description copied from interface: SeqFeatureI

Returns the type string of the feature. This is used as a more understandable replacement for the gff column source_tag

Specified by:

getType in interface SeqFeatureI

Overrides:

getType in class SeqFeature

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_setEnds

private void _setEnds()

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> jalview >> [ annotation overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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