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java.lang.Object | +--org.biojava.bio.search.SimpleSeqSimilaritySearchHit
a simple implementation of interface SeqSimilaritySearchHit that takes care of all the housekeeping. Objects of this class are immutable.
Constructor Summary | |
SimpleSeqSimilaritySearchHit(SeqSimilaritySearchResult searchResult,
double score,
double pValue,
double eValue,
java.lang.String sequenceID,
java.util.List subHits)
construct an immutable object from the values of all properties. |
Method Summary | |
java.lang.Object |
clone()
|
boolean |
equals(java.lang.Object o)
|
double |
getEValue()
return the overall E-value of this hit. |
double |
getPValue()
return the overall P-value of this hit. |
double |
getScore()
return the overall score of this hit in the units defined by the search algorithm. |
SeqSimilaritySearchResult |
getSearchResult()
return the ssequence similarity search result to which this sequence similarity search hit belongs. |
java.lang.String |
getSequenceID()
the sequence identifier of this hit within the sequence database against which the search was performed. |
java.util.List |
getSubHits()
return an unmodifiable view of the sub-hits list. |
int |
hashCode()
|
java.lang.String |
toString()
|
Methods inherited from class java.lang.Object |
finalize,
getClass,
notify,
notifyAll,
wait,
wait,
wait |
Constructor Detail |
public SimpleSeqSimilaritySearchHit(SeqSimilaritySearchResult searchResult, double score, double pValue, double eValue, java.lang.String sequenceID, java.util.List subHits)
searchResult
- the search result of which this search hit is a part. Not null.score
- the overall score of this hit. This is a mandatory piece of information and may hence not be NaN.pValue
- the overall P-value of this hit. May be NaN.eValue
- the overall E-value of this hit. May be NaN.sequenceID
- the (unique) sequence identifier for this hit, valid within the sequence database against which
this search was performed. Not null.subHits
- a List of SeqSimilaritySearchSubHit objects containing all sub-hits for this hit. Not null.Method Detail |
public SeqSimilaritySearchResult getSearchResult()
public double getScore()
public double getPValue()
public double getEValue()
public java.lang.String getSequenceID()
public java.util.List getSubHits()
public java.lang.String toString()
public boolean equals(java.lang.Object o)
public int hashCode()
public java.lang.Object clone()
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