org.biojava.bio.search
Class SimpleSeqSimilaritySearchSubHit

java.lang.Object
  |
  +--org.biojava.bio.search.SimpleSeqSimilaritySearchSubHit

public class SimpleSeqSimilaritySearchSubHit
extends java.lang.Object
implements SeqSimilaritySearchSubHit, java.lang.Cloneable

a simple implementation of interface SeqSimilaritySearchSubHit that takes care of all the house-keeping. Objects of this class are immutable.

Author:
Gerald Loeffler for the IMP

Fields inherited from interface org.biojava.bio.search.SeqSimilaritySearchSubHit
QUERY_LABEL
 
Constructor Summary
SimpleSeqSimilaritySearchSubHit(SeqSimilaritySearchHit hit, double score, double pValue, double eValue, Alignment alignment)
          construct an immutable object of this class by providing all properties.
 
Method Summary
 java.lang.Object clone()
           
 boolean equals(java.lang.Object o)
           
 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.
 int hashCode()
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
 

Constructor Detail

SimpleSeqSimilaritySearchSubHit

public SimpleSeqSimilaritySearchSubHit(SeqSimilaritySearchHit hit,
                                       double score,
                                       double pValue,
                                       double eValue,
                                       Alignment alignment)
construct an immutable object of this class by providing all properties.
Parameters:
hit - the SeqSimilaritySearchHit object of which this object is a part. Not null.
score - the score of this hit. This is a mandatory piece of information and may hence not be NaN.
pValue - the P-value of this hit. May be NaN.
eValue - the E-value of this hit. May be NaN.
alignment - the alignment of the query sequence against this hit sequence. May be null.
Method Detail

getHit

public SeqSimilaritySearchHit getHit()
Description copied from interface: SeqSimilaritySearchSubHit
return the ssequence similarity search hit to which this sequence similarity search sub-hit belongs.
Specified by:
getHit in interface SeqSimilaritySearchSubHit
Tags copied from interface: SeqSimilaritySearchSubHit
Returns:
the SeqSimilaritySearchHit object of which this object is a part. Never returns null.

getScore

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

getPValue

public double getPValue()
Description copied from interface: SeqSimilaritySearchSubHit
return the P-value of this sub-hit.
Specified by:
getPValue in interface SeqSimilaritySearchSubHit
Tags copied from interface: SeqSimilaritySearchSubHit
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()
Description copied from interface: SeqSimilaritySearchSubHit
return the E-value of this sub-hit.
Specified by:
getEValue in interface SeqSimilaritySearchSubHit
Tags copied from interface: SeqSimilaritySearchSubHit
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()
Description copied from interface: SeqSimilaritySearchSubHit
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.
Specified by:
getAlignment in interface SeqSimilaritySearchSubHit
Tags copied from interface: SeqSimilaritySearchSubHit
Returns:
the alignment of the query sequence against this hit sequence. May return null.

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

equals

public boolean equals(java.lang.Object o)
Overrides:
equals in class java.lang.Object

hashCode

public int hashCode()
Overrides:
hashCode in class java.lang.Object

clone

public java.lang.Object clone()
Specified by:
clone in interface SeqSimilaritySearchSubHit
Overrides:
clone in class java.lang.Object