apollo.datamodel
Class FeaturePair

java.lang.Object
  apollo.datamodel.Range
      apollo.datamodel.SeqFeature
          apollo.datamodel.FeaturePair

All Implemented Interfaces:

Comparable, FeaturePairI, RangeI, SeqFeatureI, java.io.Serializable, java.lang.Cloneable

public class FeaturePair
extends SeqFeature
implements FeaturePairI

See Also:

Serialized Form

Field Summary

Fields inherited from class apollo.datamodel.SeqFeature

biotype, edit_offset_adjust, id, logger, phase, properties, ref_features, refFeature, refId, score, scores

Fields inherited from class apollo.datamodel.Range

high, low, name, refSeq, strand, type

Fields inherited from interface apollo.datamodel.RangeI

NO_NAME, NO_TYPE

Constructor Summary

FeaturePair(SeqFeatureI f1, SeqFeatureI f2)
f1 is query feature, f2 is hit feature

Method Summary

void	addProperty(java.lang.String name, java.lang.String value)
void	addScore(double score)
void	addScore(Score s)
void	addScore(java.lang.String name, double score)
void	addScore(java.lang.String name, java.lang.String score)
java.lang.String	getCigar() an explicit variable for cigar strings that are compact representations of alignments
java.lang.String	getDisplayId()
int	getEnd()
java.lang.String	getExplicitAlignment() Explicitly set alignment.
java.lang.String	getFeatureType() getType is not the "visual" type, ie the type one sees in the EvidencePanel.
int	getFrame()
int	getHend()
int	getHhigh()
int	getHigh()
SeqFeatureI	getHitFeature() shoulnt this return null? yea it should - why is it returning this??
int	getHitIndex(int genomicPosition) Gets the index into the hit strings explicitAlignment for a genomic position
int	getHitIndex(int genomicPosition, java.lang.String type)
SequenceI	getHitSequence() Returns hit.getFeatureSequence (which is start to end of hits ref seq),
int	getHlow()
java.lang.String	getHname() Set explicit hit alignment - string with gaps.
int	getHstart()
int	getHstrand()
java.lang.String	getId()
Range	getInsertionRange(int hitIndex, java.lang.String alignment)
int	getLow()
java.lang.String	getName() In the case where the range is chromosomal the name is the chromosome name
java.lang.String	getProgramName()
java.util.Hashtable	getProperties()
java.lang.String	getProperty(java.lang.String name)
SeqFeatureI	getQueryFeature()
SeqFeatureI	getRefFeature() Retrieve the parent SeqFeatureI for this SeqFeatureI, or null if it is a tree root.
java.lang.String	getRefId()
SequenceI	getRefSequence() Retrieve the SequenceI that this feature annotates.
java.lang.String	getResidues()
double	getScore()
double	getScore(java.lang.String name)
java.util.Hashtable	getScores()
int	getStart()
int	getStrand()
java.lang.String	getTopLevelType() If biotype is null, returns type
boolean	hasAlignable() Returns true if has a real alignment or if theres a "trivial" alignment from SeqFeature.getTrivialAlignable
protected boolean	hasCigar()
boolean	hasHitFeature() from SeqFeatureI
int	insertionsBefore(int hitIndex, java.lang.String alignment)
static void	main(java.lang.String[] args)
void	parseCigar() Populates getHitFeature().getAlignment() and queryAlignment using cigar string and hit and query seqs
void	removeProperty(java.lang.String key)
void	setCigar(java.lang.String cigar)
void	setEnd(int end)
void	setExplicitAlignment(java.lang.String align)
void	setFeatureType(java.lang.String type)
void	setHend(int end)
void	setHhigh(int high)
void	setHigh(int high)
void	setHitFeature(SeqFeatureI feature)
void	setHitSequence(SequenceI hit_seq)
void	setHlow(int low)
void	setHname(java.lang.String name)
void	setHstart(int start)
void	setHstrand(int strand)
void	setId(java.lang.String id)
void	setLow(int low)
void	setName(java.lang.String name)
void	setProgramName(java.lang.String name)
void	setQueryFeature(SeqFeatureI feature) Query feats hold cigars.
void	setRefFeature(SeqFeatureI feature) Set the parent SeqFeatureI.
void	setRefSequence(SequenceI seq) Set the SequenceI that this feature annotates.
void	setScore(double score)
void	setStart(int start)
void	setStrand(int strand)

Methods inherited from class apollo.datamodel.SeqFeature

accept, addDbXref, addFeature, addFeature, addRefFeature, alignmentIsPeptide, amend_RNA, buildmRNAEditList, clearKids, clearProperties, clone, cloneFeature, compareTo, descendsFrom, flipFlop, get_cDNA, get_ORF, getAlignment, getAnalogousOppositeStrandFeature, getAnnotatedFeature, getCloneSource, getCodingDNA, getCodingProperties, getDatabase, getDbXref, getDbXrefs, getEndPhase, getFeatureAt, getFeatureContaining, getFeatureIndex, getFeaturePosition, getFeatures, getFeatureSequence, getGenomicErrors, getGenomicPosForPeptidePos, getGenomicPosition, getIdentifier, getLeafFeatsOver, getNumberOfChildren, getNumberOfDescendents, getParent, getPeptideSequence, getPhase, getPrimaryDbXref, getPropertiesMulti, getPropertyMulti, getProteinFeat, getRefFeature, getStrandedFeatSetAncestor, getSubSequence, getSyntenyLinkInfo, getTranslation, getUnpaddedAlignment, getUserObject, hasAnalogousOppositeStrandFeature, hasAnnotatedFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, hasTranslation, haveExplicitAlignment, haveRealAlignment, initWithSeqFeat, isAncestorOf, isAnnot, isAnnotTop, isClone, isCodon, isExon, isProtein, isProteinCodingGene, isSameFeat, isSequencingError, isTranscript, merge, na2aa, numberOfGenerations, replaceProperty, setAlignment, setAnalogousOppositeStrandFeature, setDatabase, setIdentifier, setPhase, setSyntenyLinkInfo, setTopLevelType, setUserObject, size, toString, translate

Methods inherited from class apollo.datamodel.Range

canHaveChildren, contains, contains, convertFromBaseOrientedToInterbase, convertFromInterbaseToBaseOriented, getEndAsString, getLeftOverlap, getRangeClone, getRightOverlap, getStartAsString, hasFeatureType, hasName, hasRefSequence, isContainedByRefSeq, isExactOverlap, isForwardStrand, isIdentical, isSequenceAvailable, length, overlaps, rangeIsUnassigned, sameRange

Methods inherited from class java.lang.Object

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

Methods inherited from interface apollo.datamodel.SeqFeatureI

accept, addDbXref, addFeature, addFeature, alignmentIsPeptide, clearKids, clearProperties, clone, cloneFeature, compareTo, descendsFrom, flipFlop, get_cDNA, getAlignment, getAnalogousOppositeStrandFeature, getAnnotatedFeature, getCloneSource, getCodingDNA, getCodingProperties, getDatabase, getDbXref, getDbXrefs, getEndPhase, getFeatureAt, getFeatureContaining, getFeatureIndex, getFeaturePosition, getFeatures, getFeatureSequence, getGenomicErrors, getGenomicPosForPeptidePos, getGenomicPosition, getLeafFeatsOver, getNumberOfChildren, getNumberOfDescendents, getParent, getPeptideSequence, getPhase, getPropertiesMulti, getPropertyMulti, getProteinFeat, getStrandedFeatSetAncestor, getSyntenyLinkInfo, getTranslation, getUnpaddedAlignment, getUserObject, hasAnalogousOppositeStrandFeature, hasAnnotatedFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, hasTranslation, haveExplicitAlignment, haveRealAlignment, isAncestorOf, isAnnot, isAnnotTop, isClone, isCodon, isExon, isProtein, isProteinCodingGene, isSameFeat, isSequencingError, isTranscript, merge, numberOfGenerations, replaceProperty, setAlignment, setAnalogousOppositeStrandFeature, setDatabase, setPhase, setSyntenyLinkInfo, setTopLevelType, setUserObject, size, translate

Methods inherited from interface apollo.datamodel.RangeI

canHaveChildren, contains, contains, convertFromBaseOrientedToInterbase, convertFromInterbaseToBaseOriented, getLeftOverlap, getRangeClone, getRightOverlap, hasFeatureType, hasName, hasRefSequence, isContainedByRefSeq, isExactOverlap, isForwardStrand, isIdentical, isSequenceAvailable, length, overlaps, rangeIsUnassigned, sameRange

Constructor Detail

FeaturePair

public FeaturePair(SeqFeatureI f1,
                   SeqFeatureI f2)

f1 is query feature, f2 is hit feature

Method Detail

setQueryFeature

public void setQueryFeature(SeqFeatureI feature)

Description copied from class: SeqFeature

Query feats hold cigars. This gives hit feats access to query feat & its cigar

Specified by:

setQueryFeature in interface FeaturePairI

Specified by:

setQueryFeature in interface SeqFeatureI

Overrides:

setQueryFeature in class SeqFeature

getQueryFeature

public SeqFeatureI getQueryFeature()

Specified by:

getQueryFeature in interface FeaturePairI

setHitFeature

public void setHitFeature(SeqFeatureI feature)

Specified by:

setHitFeature in interface FeaturePairI

getHitFeature

public SeqFeatureI getHitFeature()

Description copied from class: SeqFeature

shoulnt this return null? yea it should - why is it returning this??

Specified by:

getHitFeature in interface SeqFeatureI

Overrides:

getHitFeature in class SeqFeature

hasHitFeature

public boolean hasHitFeature()

from SeqFeatureI

Specified by:

hasHitFeature in interface SeqFeatureI

Overrides:

hasHitFeature in class SeqFeature

setLow

public void setLow(int low)

Specified by:

setLow in interface RangeI

Overrides:

setLow in class Range

getLow

public int getLow()

Specified by:

getLow in interface RangeI

Overrides:

getLow in class Range

setHigh

public void setHigh(int high)

Specified by:

setHigh in interface RangeI

Overrides:

setHigh in class Range

getHigh

public int getHigh()

Specified by:

getHigh in interface RangeI

Overrides:

getHigh in class Range

setStart

public void setStart(int start)

Specified by:

setStart in interface RangeI

Overrides:

setStart in class Range

getStart

public int getStart()

Specified by:

getStart in interface RangeI

Overrides:

getStart in class Range

setEnd

public void setEnd(int end)

Specified by:

setEnd in interface RangeI

Overrides:

setEnd in class Range

getEnd

public int getEnd()

Specified by:

getEnd in interface RangeI

Overrides:

getEnd in class Range

setStrand

public void setStrand(int strand)

Specified by:

setStrand in interface RangeI

Overrides:

setStrand in class Range

getStrand

public int getStrand()

Specified by:

getStrand in interface RangeI

Overrides:

getStrand in class Range

Returns:

1 for forward strand, -1 for reverse strand, 0 for strandless

setName

public void setName(java.lang.String name)

Specified by:

setName in interface RangeI

Overrides:

setName in class Range

getName

public java.lang.String getName()

Description copied from interface: RangeI

In the case where the range is chromosomal the name is the chromosome name

Specified by:

getName in interface RangeI

Overrides:

getName in class Range

setId

public void setId(java.lang.String id)

Specified by:

setId in interface SeqFeatureI

Overrides:

setId in class SeqFeature

getId

public java.lang.String getId()

Specified by:

getId in interface SeqFeatureI

Overrides:

getId in class SeqFeature

getScore

public double getScore()

Specified by:

getScore in interface SeqFeatureI

Overrides:

getScore in class SeqFeature

getScore

public double getScore(java.lang.String name)

Specified by:

getScore in interface SeqFeatureI

Overrides:

getScore in class SeqFeature

getScores

public java.util.Hashtable getScores()

Specified by:

getScores in interface SeqFeatureI

Overrides:

getScores in class SeqFeature

setScore

public void setScore(double score)

Specified by:

setScore in interface SeqFeatureI

Overrides:

setScore in class SeqFeature

addScore

public void addScore(Score s)

Specified by:

addScore in interface SeqFeatureI

Overrides:

addScore in class SeqFeature

addScore

public void addScore(double score)

Specified by:

addScore in interface SeqFeatureI

Overrides:

addScore in class SeqFeature

addScore

public void addScore(java.lang.String name,
                     double score)

Specified by:

addScore in interface SeqFeatureI

Overrides:

addScore in class SeqFeature

addScore

public void addScore(java.lang.String name,
                     java.lang.String score)

Specified by:

addScore in interface SeqFeatureI

Overrides:

addScore in class SeqFeature

addProperty

public void addProperty(java.lang.String name,
                        java.lang.String value)

Specified by:

addProperty in interface SeqFeatureI

Overrides:

addProperty in class SeqFeature

removeProperty

public void removeProperty(java.lang.String key)

Specified by:

removeProperty in interface SeqFeatureI

Overrides:

removeProperty in class SeqFeature

getProperty

public java.lang.String getProperty(java.lang.String name)

Specified by:

getProperty in interface SeqFeatureI

Overrides:

getProperty in class SeqFeature

getProperties

public java.util.Hashtable getProperties()

Specified by:

getProperties in interface SeqFeatureI

Overrides:

getProperties in class SeqFeature

setFeatureType

public void setFeatureType(java.lang.String type)

Specified by:

setFeatureType in interface RangeI

Overrides:

setFeatureType in class Range

getTopLevelType

public java.lang.String getTopLevelType()

Description copied from class: SeqFeature

If biotype is null, returns type

Specified by:

getTopLevelType in interface SeqFeatureI

Overrides:

getTopLevelType in class SeqFeature

getFeatureType

public java.lang.String getFeatureType()

Description copied from class: Range

getType is not the "visual" type, ie the type one sees in the EvidencePanel. getType returns the "logical" type(the type from the data). These are the types in the squiggly brackets in the tiers file that map to the visual type listed before the squigglies. gui.scheme.FeatureProperty maps logical types to visual types (convenience function in DetailInfo.getPropertyType)

Specified by:

getFeatureType in interface RangeI

Overrides:

getFeatureType in class Range

setProgramName

public void setProgramName(java.lang.String name)

Specified by:

setProgramName in interface SeqFeatureI

Overrides:

setProgramName in class SeqFeature

getProgramName

public java.lang.String getProgramName()

Specified by:

getProgramName in interface SeqFeatureI

Overrides:

getProgramName in class SeqFeature

getResidues

public java.lang.String getResidues()

Specified by:

getResidues in interface RangeI

Overrides:

getResidues in class Range

setRefSequence

public void setRefSequence(SequenceI seq)

Description copied from interface: RangeI

Set the SequenceI that this feature annotates.

Specified by:

setRefSequence in interface RangeI

Overrides:

setRefSequence in class Range

Parameters:

seq - the new parent SequenceI

getRefSequence

public SequenceI getRefSequence()

Description copied from interface: RangeI

Retrieve the SequenceI that this feature annotates.

Specified by:

getRefSequence in interface RangeI

Overrides:

getRefSequence in class Range

Returns:

the current parent SequenceI

getRefId

public java.lang.String getRefId()

Specified by:

getRefId in interface SeqFeatureI

Overrides:

getRefId in class SeqFeature

getRefFeature

public SeqFeatureI getRefFeature()

Description copied from interface: SeqFeatureI

Retrieve the parent SeqFeatureI for this SeqFeatureI, or null if it is a tree root.

Specified by:

getRefFeature in interface SeqFeatureI

Overrides:

getRefFeature in class SeqFeature

Returns:

the parent SeqFeatureI Couldnt this return a FeatureSetI, doesnt a ref feature have to be a FeatureSetI?

setRefFeature

public void setRefFeature(SeqFeatureI feature)

Description copied from interface: SeqFeatureI

Set the parent SeqFeatureI.

When building a part-whole hieracy of features, you must both add a feature to its parent, and then call child.setRefFeature(parent). It is possible for a feature to be added to multiple feature sets, but there is only one legitimate parent.

Specified by:

setRefFeature in interface SeqFeatureI

Overrides:

setRefFeature in class SeqFeature

Parameters:

feature - the new parent SeqFeatureI

getFrame

public int getFrame()

Specified by:

getFrame in interface SeqFeatureI

Overrides:

getFrame in class SeqFeature

Returns:

1,2,3 for frame, or -1 if no frame

getHname

public java.lang.String getHname()

Description copied from class: SeqFeature

Set explicit hit alignment - string with gaps. The compact alternative to this is cigars(which should be migrated to this interface from FeaturePairI). For an alignment to work you must set both setHitAlignmnet and setRefAlignment. Previously this was set with hit.setProperty("alignment")

Specified by:

getHname in interface SeqFeatureI

Overrides:

getHname in class SeqFeature

setHname

public void setHname(java.lang.String name)

getHstart

public int getHstart()

Specified by:

getHstart in interface SeqFeatureI

Overrides:

getHstart in class SeqFeature

setHstart

public void setHstart(int start)

Specified by:

setHstart in interface FeaturePairI

getHend

public int getHend()

Specified by:

getHend in interface SeqFeatureI

Overrides:

getHend in class SeqFeature

setHend

public void setHend(int end)

Specified by:

setHend in interface FeaturePairI

setHlow

public void setHlow(int low)

Specified by:

setHlow in interface FeaturePairI

getHlow

public int getHlow()

Specified by:

getHlow in interface SeqFeatureI

Overrides:

getHlow in class SeqFeature

setHhigh

public void setHhigh(int high)

Specified by:

setHhigh in interface FeaturePairI

getHhigh

public int getHhigh()

Specified by:

getHhigh in interface SeqFeatureI

Overrides:

getHhigh in class SeqFeature

setHstrand

public void setHstrand(int strand)

Specified by:

setHstrand in interface FeaturePairI

getHstrand

public int getHstrand()

Specified by:

getHstrand in interface SeqFeatureI

Overrides:

getHstrand in class SeqFeature

getHitIndex

public int getHitIndex(int genomicPosition)

Gets the index into the hit strings explicitAlignment for a genomic position

getHitIndex

public int getHitIndex(int genomicPosition,
                       java.lang.String type)

insertionsBefore

public int insertionsBefore(int hitIndex,
                            java.lang.String alignment)

getInsertionRange

public Range getInsertionRange(int hitIndex,
                               java.lang.String alignment)

getHitSequence

public SequenceI getHitSequence()

Returns hit.getFeatureSequence (which is start to end of hits ref seq),

Specified by:

getHitSequence in interface FeaturePairI

Specified by:

getHitSequence in interface SeqFeatureI

Overrides:

getHitSequence in class SeqFeature

setHitSequence

public void setHitSequence(SequenceI hit_seq)

Specified by:

setHitSequence in interface FeaturePairI

main

public static void main(java.lang.String[] args)

getDisplayId

public java.lang.String getDisplayId()

setCigar

public void setCigar(java.lang.String cigar)

Specified by:

setCigar in interface SeqFeatureI

Overrides:

setCigar in class SeqFeature

getCigar

public java.lang.String getCigar()

Description copied from class: SeqFeature

an explicit variable for cigar strings that are compact representations of alignments

Specified by:

getCigar in interface SeqFeatureI

Overrides:

getCigar in class SeqFeature

hasCigar

protected boolean hasCigar()

Overrides:

hasCigar in class SeqFeature

getExplicitAlignment

public java.lang.String getExplicitAlignment()

Explicitly set alignment. no padding

Specified by:

getExplicitAlignment in interface SeqFeatureI

Overrides:

getExplicitAlignment in class SeqFeature

setExplicitAlignment

public void setExplicitAlignment(java.lang.String align)

Specified by:

setExplicitAlignment in interface SeqFeatureI

Overrides:

setExplicitAlignment in class SeqFeature

parseCigar

public void parseCigar()

Populates getHitFeature().getAlignment() and queryAlignment using cigar string and hit and query seqs

Specified by:

parseCigar in interface SeqFeatureI

Overrides:

parseCigar in class SeqFeature

hasAlignable

public boolean hasAlignable()

Returns true if has a real alignment or if theres a "trivial" alignment from SeqFeature.getTrivialAlignable

Specified by:

hasAlignable in interface SeqFeatureI

Overrides:

hasAlignable in class SeqFeature