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
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 |
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.
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