org.biojava.bio.search
Interface SeqSimilaritySearchSubHit

All Known Implementing Classes:
SimpleSeqSimilaritySearchSubHit

public interface SeqSimilaritySearchSubHit
extends java.lang.Cloneable

objects of this type represent one particular sub-hit (i.e. one concrete sequence stretch within a sequence and associated information) from a sequence similarity search hit.

Author:
Gerald Loeffler for the IMP

Field Summary
static java.lang.String QUERY_LABEL
          this object is used as the label for the query sequence in the alignment of the query sequence with this sub-hit sequence
 
Method Summary
 java.lang.Object clone()
           
 Alignment getAlignment()
          return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence.
 double getEValue()
          return the E-value of this sub-hit.
 SeqSimilaritySearchHit getHit()
          return the ssequence similarity search hit to which this sequence similarity search sub-hit belongs.
 double getPValue()
          return the P-value of this sub-hit.
 double getScore()
          return the score of this sub-hit in the units defined by the search algorithm.
 

Field Detail

QUERY_LABEL

public static final java.lang.String QUERY_LABEL
this object is used as the label for the query sequence in the alignment of the query sequence with this sub-hit sequence
Method Detail

getHit

public SeqSimilaritySearchHit getHit()
return the ssequence similarity search hit to which this sequence similarity search sub-hit belongs.
Returns:
the SeqSimilaritySearchHit object of which this object is a part. Never returns null.

getScore

public double getScore()
return the score of this sub-hit in the units defined by the search algorithm.
Returns:
the score of this sub-hit. This is a mandatory piece of information and may hence not be NaN.

getPValue

public double getPValue()
return the P-value of this sub-hit.
Returns:
the P-value of this sub-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 E-value of this sub-hit.
Returns:
the E-value of this sub-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.

getAlignment

public Alignment getAlignment()
return an alignment of (possibly part of) the query sequence against (possibly part of) this hit sequence. In this alignment, the query is identified by the label given by the static field QUERY_LABEL.
Returns:
the alignment of the query sequence against this hit sequence. May return null.

clone

public java.lang.Object clone()
Overrides:
clone in class java.lang.Object