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java.lang.Objectorg.biojava.utils.AbstractChangeable
org.biojava.bio.search.SequenceDBSearchHit
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:
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
Deprecated. |
Fields inherited from interface org.biojava.bio.search.SeqSimilaritySearchHit |
byScore, bySubHitCount |
Fields inherited from interface org.biojava.bio.Annotatable |
ANNOTATION |
Constructor Summary | |
SequenceDBSearchHit(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)
Deprecated. Creates a new SequenceDBSearchHit object. |
Method Summary | |
boolean |
equals(java.lang.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. |
java.util.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. |
java.lang.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. |
java.lang.String |
toString()
Deprecated. |
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 |
protected transient Annotatable.AnnotationForwarder annotationForwarder
Constructor Detail |
public SequenceDBSearchHit(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)
SequenceDBSearchHit
object.
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 |
public double getScore()
SeqSimilaritySearchHit
getScore
in interface SeqSimilaritySearchHit
public double getPValue()
SeqSimilaritySearchHit
getPValue
in interface SeqSimilaritySearchHit
public double getEValue()
SeqSimilaritySearchHit
getEValue
in interface SeqSimilaritySearchHit
public int getQueryStart()
SeqSimilaritySearchHit
getQueryStart
in interface SeqSimilaritySearchHit
int
.public int getQueryEnd()
SeqSimilaritySearchHit
getQueryEnd
in interface SeqSimilaritySearchHit
int
.public StrandedFeature.Strand getQueryStrand()
SeqSimilaritySearchHit
getQueryStrand
in interface SeqSimilaritySearchHit
Strand
.public int getSubjectStart()
SeqSimilaritySearchHit
getSubjectStart
in interface SeqSimilaritySearchHit
int
.public int getSubjectEnd()
SeqSimilaritySearchHit
getSubjectEnd
in interface SeqSimilaritySearchHit
int
.public StrandedFeature.Strand getSubjectStrand()
SeqSimilaritySearchHit
getSubjectStrand
in interface SeqSimilaritySearchHit
Strand
.public java.lang.String getSubjectID()
SeqSimilaritySearchHit
getSubjectID
in interface SeqSimilaritySearchHit
public java.util.List getSubHits()
SeqSimilaritySearchHit
getSubHits
in interface SeqSimilaritySearchHit
public Annotation getAnnotation()
getAnnotation
returns the Annotation associated
with this hit.
getAnnotation
in interface Annotatable
Annotation
.public boolean equals(java.lang.Object other)
public int hashCode()
public java.lang.String toString()
protected ChangeSupport getChangeSupport(ChangeType ct)
AbstractChangeable
getChangeSupport
in class AbstractChangeable
|
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