SeqFeatureI

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jalview.annotation
Interface SeqFeatureI

All Known Subinterfaces:: FeaturePairI, FeatureSetI, SupportedSeqFeatureI

All Known Implementing Classes:: FeatureSet, SeqFeature, SupportedSeqFeature

public interface SeqFeatureI

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 feature)
          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.

Method Detail

getName

public java.lang.String getName()

Returns the name of the feature

setName

public void setName(java.lang.String name)

Sets the name of the feature

getStart

public long getStart()

Returns the start coordinate of the feature

setStart

public void setStart(long start)

Sets the start coordinate of the feature

getEnd

public long getEnd()

Returns the end coordinate of the feature

setEnd

public void setEnd(long end)

Sets the end coordinate of the feature

getSequenceI

public SequenceI getSequenceI()

Returns the underlying sequence that the feature refers to

setSequenceI

public void setSequenceI(SequenceI sequence)

Sets the underlying sequence that the feature refers to

getRefFeature

public SeqFeatureI getRefFeature()

Returns the parent reference feature (for nested features)

setRefFeature

public void setRefFeature(SeqFeatureI refFeature)

Sets the reference parent feature

getProducedFeatures

public FeatureSetI getProducedFeatures()

Returns a set of features that this feature produces from its sub features. For instances this could be a set of coding exons from an mRNA

setProducedFeatures

public void setProducedFeatures(FeatureSetI producedFeatures)

Sets the features that are produced by this feature

getStrand

public int getStrand()

Returns the strand of the feature

setStrand

public void setStrand(int strand)

Sets the strand of the feature

getType

public java.lang.String getType()

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

setType

public void setType(java.lang.String type)

Sets the type string of the feature. This is where the gff source_tag value should go.

getScore

public double getScore()

Returns the score of the feature

setScore

public void setScore(double score)

Sets the score of the feature.

overlaps

public boolean overlaps(SeqFeatureI feature)

Returns whether a supplied feature overlaps with the current feature

findOverlap

public OverlapI findOverlap(SeqFeatureI feature)

Returns detailed information if the supplied feature overlaps with this feature.