SimpleSeqSimilaritySearchHit (biojava 1.30 API)

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org.biojava.bio.search
Class SimpleSeqSimilaritySearchHit

java.lang.Object
  |
  +--org.biojava.utils.AbstractChangeable
        |
        +--org.biojava.bio.search.SimpleSeqSimilaritySearchHit

All Implemented Interfaces:: Annotatable, Changeable, SeqSimilaritySearchHit

public class SimpleSeqSimilaritySearchHit
extends AbstractChangeable
implements SeqSimilaritySearchHit

SimpleSeqSimilaritySearchHit 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, Gerald Loeffler
See Also:: AbstractChangeable, SeqSimilaritySearchHit, Annotatable

Nested Class Summary

Nested classes inherited from class org.biojava.bio.search.SeqSimilaritySearchHit

SeqSimilaritySearchHit.ByScoreComparator, SeqSimilaritySearchHit.BySubHitCountComparator

Nested classes inherited from class org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Field Summary

protected Annotatable.AnnotationForwarder annotationForwarder


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

byScore, bySubHitCount

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

SimpleSeqSimilaritySearchHit(double score, double eValue, double pValue, int queryStart, int queryEnd, StrandedFeature.Strand queryStrand, int subjectStart, int subjectEnd, StrandedFeature.Strand subjectStrand, java.lang.String subjectID, Annotation annotation, java.util.List subHits)
          Creates a new SimpleSeqSimilaritySearchHit object.

Method Summary

boolean equals(java.lang.Object other)


Annotation getAnnotation()
          getAnnotation returns the Annotation associated with this hit.

protected ChangeSupport getChangeSupport(ChangeType ct)
          Called to retrieve the ChangeSupport for this object

double getEValue()
          Return the overall E-value of this hit.

double getPValue()
          Return the overall P-value of this hit.

int getQueryEnd()
          Return the end position of the last sub-hit in the query sequence.

int getQueryStart()
          Return the start position of the first sub-hit in the query sequence.

StrandedFeature.Strand getQueryStrand()
          Return the strand of the hit with respect to the query sequence.

double getScore()
          Return the overall score of this hit in the units defined by the search algorithm.

java.util.List getSubHits()
          Return all sub-hits for this sequence similarity search hit.

int getSubjectEnd()
          Return the end position of the last sub-hit in the subject sequence.

java.lang.String getSubjectID()
          The sequence identifier of this hit within the sequence database against which the search was performed.

int getSubjectStart()
          Return the start position of the first sub-hit in the subject sequence.

StrandedFeature.Strand getSubjectStrand()
          Return the strand of the sub-hit with respect to the subject sequence.

int hashCode()


java.lang.String toString()


Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, 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 Annotatable.AnnotationForwarder annotationForwarder

Constructor Detail

SimpleSeqSimilaritySearchHit

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

Creates a new SimpleSeqSimilaritySearchHit 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.; 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