apollo.gui.detailviewers.sequencealigner
Interface TierI

All Superinterfaces:

AnnotationChangeListener, java.util.EventListener, org.bdgp.util.Range

All Known Implementing Classes:

Tier

public interface TierI
extends org.bdgp.util.Range, AnnotationChangeListener

A Tier is a container class that holds a set of non overlapping SeqFeatureI's. When referencing a position the 0th position corresponds to the first base in the reference sequence. The level of a tier is related to the different perspectives at which you can look at a tier. The LEVEL_TOP is a view of the tier at a transcript level while the LEVEL_BOTTOM corresponds to the exon level view. At each level a position is associated with a range, if that range corresponds to a feature then a position is also associated to that feature. The strand of a tier identifies how to translate from a tier position to a chromosome relative position. When adding features to a strand they should all be of the same strand type, and phase. Additionally all added features should be within the bounds of the reference sequence. Are type and phase needed?

Nested Class Summary

static class

TierI.Level

Method Summary

boolean	addFeature(SeqFeatureI feature)
java.util.Collection<SeqFeatureI>	addFeatures(java.util.Collection<SeqFeatureI> features)
char	charAt(int pos)
void	clear()
SeqFeatureI	featureAt(int position, TierI.Level level)
boolean	featureExsitsAt(int position, TierI.Level level)
SeqFeatureI	featureIn(org.bdgp.util.Range range, boolean exact, TierI.Level level)
java.util.Collection<SeqFeatureI>	featuresIn(org.bdgp.util.Range range, TierI.Level level)
int	getBasePair(int position)
int	getBoundaryType(int position, TierI.Level level)
java.util.Collection<SeqFeatureI>	getFeatures(TierI.Level level)
SeqFeatureI	getNextFeature(int position, TierI.Level level)
int	getPosition(int basePair)
SeqFeatureI	getPrevFeature(int position, TierI.Level level)
ReadingFrame	getReadingFrame()
SequenceI	getReference()
Strand	getStrand()
SequenceType	getType()
int	numFeatures(TierI.Level level)
org.bdgp.util.Range	rangeAt(int position, TierI.Level level)
void	removeFeature(SeqFeatureI feature)
void	setReadingFrame(ReadingFrame rf)
void	setReference(SequenceI s)
void	setStrand(Strand s)
boolean	willOverlap(SeqFeatureI feature)

Methods inherited from interface org.bdgp.util.Range

getHigh, getLow

Methods inherited from interface apollo.editor.AnnotationChangeListener

handleAnnotationChangeEvent

Method Detail

getReference

SequenceI getReference()

setReference

void setReference(SequenceI s)

charAt

char charAt(int pos)

rangeAt

org.bdgp.util.Range rangeAt(int position,
                            TierI.Level level)

addFeature

boolean addFeature(SeqFeatureI feature)

addFeatures

java.util.Collection<SeqFeatureI> addFeatures(java.util.Collection<SeqFeatureI> features)

removeFeature

void removeFeature(SeqFeatureI feature)

numFeatures

int numFeatures(TierI.Level level)

featureExsitsAt

boolean featureExsitsAt(int position,
                        TierI.Level level)

featureAt

SeqFeatureI featureAt(int position,
                      TierI.Level level)

featureIn

SeqFeatureI featureIn(org.bdgp.util.Range range,
                      boolean exact,
                      TierI.Level level)

featuresIn

java.util.Collection<SeqFeatureI> featuresIn(org.bdgp.util.Range range,
                                             TierI.Level level)

getBasePair

int getBasePair(int position)

getPosition

int getPosition(int basePair)

getStrand

Strand getStrand()

setStrand

void setStrand(Strand s)

getReadingFrame

ReadingFrame getReadingFrame()

setReadingFrame

void setReadingFrame(ReadingFrame rf)

clear

void clear()

getFeatures

java.util.Collection<SeqFeatureI> getFeatures(TierI.Level level)

willOverlap

boolean willOverlap(SeqFeatureI feature)

getBoundaryType

int getBoundaryType(int position,
                    TierI.Level level)

getNextFeature

SeqFeatureI getNextFeature(int position,
                           TierI.Level level)

getPrevFeature

SeqFeatureI getPrevFeature(int position,
                           TierI.Level level)

getType

SequenceType getType()