org.biojava.bio.search

Class SequenceDBSearchHit

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojava.bio.search.SequenceDBSearchHit

All Implemented Interfaces:

Annotatable, SeqSimilaritySearchHit, Changeable

Deprecated.

SimpleSeqSimilaritySearchHit has been made Annotatable and is now functionally identical.

public class SequenceDBSearchHit
extends AbstractChangeable
implements SeqSimilaritySearchHit, Annotatable

SequenceDBSearchHit objects represent a similarity search hit of a query sequence to a sequence referenced in a SequenceDB object. The core data (score, E-value, P-value) have accessors, while supplementary data are stored in the Annotation object. Supplementary data are typically the more loosely formatted details which vary from one search program to another (and between versions of those programs).

It is up to the user to define the meaning of the hit's query/subject start/end/strand with respect to its constituent sub-hits. One approach could be:

• Hit query/subject start == start of first sub-hit
• Hit query/subject end == end of last sub-hit
• Hit strand == POSITIVE if all sub-hits have strand POSITIVE
• Hit strand == NEGATIVE if all sub-hits have strand NEGATIVE
• Hit strand == UNKNOWN if sub-hits have either mixed or any UNKNOWN strands
• Hit strand == null if the concept of strandedness is inappropriate for the sequence type i.e. for protein

Since:

1.1

Author:

Keith James, Matthew Pocock

See Also:

AbstractChangeable, SeqSimilaritySearchHit, Annotatable

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.search.SeqSimilaritySearchHit

SeqSimilaritySearchHit.ByScoreComparator, SeqSimilaritySearchHit.BySubHitCountComparator

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

Fields

Modifier and Type	Field and Description
protected ChangeForwarder	annotationForwarder Deprecated.

Fields inherited from interface org.biojava.bio.search.SeqSimilaritySearchHit

byScore, bySubHitCount

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

Constructors

Constructor and Description
SequenceDBSearchHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, String subjectID, Annotation annotation, List subHits) Deprecated. Creates a new SequenceDBSearchHit object.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object other) Deprecated.
Annotation	getAnnotation() Deprecated. getAnnotation returns the Annotation associated with this hit.
protected ChangeSupport	getChangeSupport(ChangeType ct) Deprecated. Called to retrieve the ChangeSupport for this object.
double	getEValue() Deprecated. Return the overall E-value of this hit.
double	getPValue() Deprecated. Return the overall P-value of this hit.
int	getQueryEnd() Deprecated. Return the end position of the last sub-hit in the query sequence.
int	getQueryStart() Deprecated. Return the start position of the first sub-hit in the query sequence.
StrandedFeature.Strand	getQueryStrand() Deprecated. Return the strand of the hit with respect to the query sequence.
double	getScore() Deprecated. Return the overall score of this hit in the units defined by the search algorithm.
List	getSubHits() Deprecated. Return all sub-hits for this sequence similarity search hit.
int	getSubjectEnd() Deprecated. Return the end position of the last sub-hit in the subject sequence.
String	getSubjectID() Deprecated. The sequence identifier of this hit within the sequence database against which the search was performed.
int	getSubjectStart() Deprecated. Return the start position of the first sub-hit in the subject sequence.
StrandedFeature.Strand	getSubjectStrand() Deprecated. Return the strand of the sub-hit with respect to the subject sequence.
int	hashCode() Deprecated.
String	toString() Deprecated.

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

annotationForwarder

protected transient ChangeForwarder annotationForwarder

Deprecated.

Constructor Detail

SequenceDBSearchHit

public SequenceDBSearchHit(double score,
                   double eValue,
                   double pValue,
                   int queryStart,
                   int queryEnd,
                   StrandedFeature.Strand queryStrand,
                   int subjectStart,
                   int subjectEnd,
                   StrandedFeature.Strand subjectStrand,
                   String subjectID,
                   Annotation annotation,
                   List subHits)

Deprecated.

Creates a new SequenceDBSearchHit object.

Parameters:

score - a double value; the score of the hit, which may not be NaN.

eValue - a double value; the E-value of the hit, which may be NaN.

pValue - a double value; the P-value of the hit, which may be NaN.

queryStart - the start of the first sub-hit on the query sequence.

queryEnd - the end of the last sub-hit on the query sequence.

queryStrand - the strand of the sub-hits on the query sequence, which may be null for protein similarities. If they are not all positive or all negative, then this should be the unknown strand.

subjectStart - the start of the first sub-hit on the subject sequence.

subjectEnd - the end of the last sub-hit on the subject sequence.

subjectStrand - the strand of the sub-hits on the subject sequence, which may be null for protein similarities. If they are not all positive or all negative, then this should be the unknown strand.

subjectID - a String representing the ID in the SequenceDB of the sequence which was hit, which may not be null.

annotation - an Annotation object, which may not be null.

subHits - a List object containing the subhits, which may not be null. They should be sorted in the order specified by the search program.

Method Detail

getScore

public double getScore()

Deprecated.

Description copied from interface: SeqSimilaritySearchHit

Return the overall score of this hit in the units defined by the search algorithm.

Specified by:

getScore in interface SeqSimilaritySearchHit

Returns:

the overall score of this hit. This is a mandatory piece of information and hence may not be NaN.

getPValue

public double getPValue()

Deprecated.

Description copied from interface: SeqSimilaritySearchHit

Return the overall P-value of this hit.

Specified by:

getPValue in interface SeqSimilaritySearchHit

Returns:

the overall P-value of this hit. This is an optional (but desired) piece of information and implementations of this interface may return NaN if a P-value is not available for this hit.

getEValue

public double getEValue()

Deprecated.

Description copied from interface: SeqSimilaritySearchHit

Return the overall E-value of this hit.

Specified by:

getEValue in interface SeqSimilaritySearchHit

Returns:

the overall E-value of this hit. This is an optional (but desired) piece of information and implementations of this interface may return NaN if an E-value is not available for this hit.

getQueryStart

public int getQueryStart()

Deprecated.

Description copied from interface: SeqSimilaritySearchHit

Return the start position of the first sub-hit in the query sequence.

Specified by:

getQueryStart in interface SeqSimilaritySearchHit

Returns:

an int.

getQueryEnd

public int getQueryEnd()

Deprecated.

Description copied from interface: SeqSimilaritySearchHit

Return the end position of the last sub-hit in the query sequence.

Specified by:

getQueryEnd in interface SeqSimilaritySearchHit

Returns:

an int.

getQueryStrand

public StrandedFeature.Strand getQueryStrand()

Deprecated.

Description copied from interface: SeqSimilaritySearchHit

Return the strand of the hit with respect to the query sequence. If the sub-hits are not all on the same strand this should return the unknown strand. This may be null for protein sequences.

Specified by:

getQueryStrand in interface SeqSimilaritySearchHit

Returns:

a Strand.

getSubjectStart

public int getSubjectStart()

Deprecated.

Description copied from interface: SeqSimilaritySearchHit

Return the start position of the first sub-hit in the subject sequence.

Specified by:

getSubjectStart in interface SeqSimilaritySearchHit

Returns:

an int.

getSubjectEnd

public int getSubjectEnd()

Deprecated.

Description copied from interface: SeqSimilaritySearchHit

Return the end position of the last sub-hit in the subject sequence.

Specified by:

getSubjectEnd in interface SeqSimilaritySearchHit

Returns:

an int.

getSubjectStrand

public StrandedFeature.Strand getSubjectStrand()

Deprecated.

Description copied from interface: SeqSimilaritySearchHit

Return the strand of the sub-hit with respect to the subject sequence. If the sub-hits are not all on the same strand this should return the unknown strand. This may be null for protein sequences.

Specified by:

getSubjectStrand in interface SeqSimilaritySearchHit

Returns:

a Strand.

getSubjectID

public String getSubjectID()

Deprecated.

Description copied from interface: SeqSimilaritySearchHit

The sequence identifier of this hit within the sequence database against which the search was performed.

Specified by:

getSubjectID in interface SeqSimilaritySearchHit

Returns:

the (unique) sequence identifier for this hit, valid within the sequence database against which this search was performed. Never returns null.

getSubHits

public List getSubHits()

Deprecated.

Description copied from interface: SeqSimilaritySearchHit

Return all sub-hits for this sequence similarity search hit. The sub-hits contain concrete alignments (and scores) for sequence stretches from the sequence of this hit. The sub-hits in the list returned by this method are sorted from best to worst.

Specified by:

getSubHits in interface SeqSimilaritySearchHit

Returns:

a List of SeqSimilaritySearchSubHit objects containing all sub-hits for this hit. Never returns null and the List is guaranteed to contain at least one entry.

getAnnotation

public Annotation getAnnotation()

Deprecated.

getAnnotation returns the Annotation associated with this hit.

Specified by:

getAnnotation in interface Annotatable

Returns:

an Annotation.

equals

public boolean equals(Object other)

Deprecated.

Overrides:

equals in class Object

hashCode

public int hashCode()

Deprecated.

Overrides:

hashCode in class Object

toString

public String toString()

Deprecated.

Overrides:

toString in class Object

getChangeSupport

protected ChangeSupport getChangeSupport(ChangeType ct)

Deprecated.

Description copied from class: AbstractChangeable

Called to retrieve the ChangeSupport for this object.

Your implementation of this method should have the following structure:

 ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
 

It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.

Overrides:

getChangeSupport in class AbstractChangeable