org.biojava.bio.search
Interface SeqSimilaritySearchHit
- All Known Implementing Classes:
- SimpleSeqSimilaritySearchHit
- public interface SeqSimilaritySearchHit
- extends java.lang.Cloneable
objects of this type represent one particular hit (i.e. sequence and associated information) from a sequence
similarity search.
- Author:
- Gerald Loeffler for the
IMP
Method Summary |
java.lang.Object |
clone()
|
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 all sub-hits for this sequence similarity search hit. |
getSearchResult
public SeqSimilaritySearchResult getSearchResult()
- return the ssequence similarity search result to which this sequence similarity search hit belongs.
- Returns:
- the SeqSimilaritySearchResult object of which this object is a part. Never returns null.
getScore
public double getScore()
- return the overall score of this hit in the units defined by the search algorithm.
- Returns:
- the overall score of this hit. This is a mandatory piece of information and may hence not be NaN.
getPValue
public double getPValue()
- return the overall P-value of this hit.
- 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()
- return the overall E-value of this hit.
- 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.
getSequenceID
public java.lang.String getSequenceID()
- the sequence identifier of this hit within the sequence database against which the search was performed.
Use getSearchResult().getSequenceDB().getSequence(id) to actually retrieve the sequence with this id.
- Returns:
- the (unique) sequence identifier for this hit, valid within the sequence database against which this search
was performed. Never returns null.
getSubHits
public java.util.List getSubHits()
- return all sub-hits for this sequence similarity search hit. The sub-hits contain conrete 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.
- 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 1 entry.
clone
public java.lang.Object clone()
- Overrides:
- clone in class java.lang.Object