SeqFeature

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jalview.annotation
Class SeqFeature

java.lang.Object
  jalview.annotation.SeqFeature

All Implemented Interfaces:: SeqFeatureI

Direct Known Subclasses:: FeatureSet, SupportedSeqFeature

public class SeqFeature
extends java.lang.Object
implements SeqFeatureI

Field Summary

protected long end


protected java.lang.String name


protected java.lang.String primary_tag


protected SeqFeatureI refFeature


protected double score


protected SequenceI seq


protected java.lang.String source_tag


protected long start


protected int strand


protected java.lang.String type


Constructor Summary

SeqFeature()


SeqFeature(long start, long end, java.lang.String name)


Method Summary

OverlapI findOverlap(SeqFeatureI feature)
          Returns detailed information if the supplied feature overlaps with this feature.

long getEnd()
          Returns the end coordinate of the feature

java.lang.String getName()
          Returns the name of the feature

FeatureSetI getProducedFeatures()
          Returns a set of features that this feature produces from its sub features.

SeqFeatureI getRefFeature()
          Returns the parent reference feature (for nested features)

double getScore()
          Returns the score of the feature

SequenceI getSequenceI()
          Returns the underlying sequence that the feature refers to

long getStart()
          Returns the start coordinate of the feature

int getStrand()
          Returns the strand of the feature

java.lang.String getType()
          Returns the type string of the feature.

boolean overlaps(SeqFeatureI se)
          Returns whether a supplied feature overlaps with the current feature

void setEnd(long end)
          Sets the end coordinate of the feature

void setName(java.lang.String name)
          Sets the name of the feature

void setProducedFeatures(FeatureSetI producedFeatures)
          Sets the features that are produced by this feature

void setRefFeature(SeqFeatureI refFeature)
          Sets the reference parent feature

void setScore(double score)
          Sets the score of the feature.

void setSequenceI(SequenceI sequence)
          Sets the underlying sequence that the feature refers to

void setStart(long start)
          Sets the start coordinate of the feature

void setStrand(int strand)
          Sets the strand of the feature

void setType(java.lang.String type)
          Sets the type string of the feature.

java.lang.String toString()
          Convert this Object to a human-readable String.

Methods inherited from class java.lang.Object

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

Field Detail

start

protected long start

end

protected long end

name

protected java.lang.String name

source_tag

protected java.lang.String source_tag

primary_tag

protected java.lang.String primary_tag

strand

protected int strand

score

protected double score

refFeature

protected SeqFeatureI refFeature

seq

protected SequenceI seq

type

protected java.lang.String type

Constructor Detail

SeqFeature

public SeqFeature()

SeqFeature

public SeqFeature(long start,
                  long end,
                  java.lang.String name)

Method Detail