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java.lang.Objectprocope.methods.interologs.blast.BlastHit
public class BlastHit
A single BLAST hit.
Constructor Summary | |
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BlastHit(int queryID,
int hitID,
float identity,
int alignlen,
int mismatches,
int gapopenings,
int querystart,
int queryend,
int hitstart,
int hitend,
double evalue,
float bitscore)
Creates an new BLAST hit object. |
Method Summary | |
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int |
compareTo(BlastHit o)
Orders the hits by their hit ID. |
int |
getAlignmentLength()
Returns the length of the alignment |
float |
getBitScore()
Returns the bit score of the hit |
double |
getEvalue()
Returns the e-value of the hit |
int |
getGapOpenings()
Returns the gap openings in the alignment |
int |
getHitEnd()
Returns the hit end coordinate of the hit |
int |
getHitID()
Returns the internal ID of the hit protein |
int |
getHitStart()
Returns the hit start coordinate of the hit |
float |
getIdentity()
Returns the identity of the alignment |
int |
getMismatches()
Returns the number of mismatches in the alignment |
int |
getQueryEnd()
Returns the query end coordinate of the hit |
int |
getQueryID()
Returns the internal ID of the query protein |
int |
getQueryStart()
Returns the query start coordinate of the hit |
String |
toString()
Returns a simple string representation of the hit. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public BlastHit(int queryID, int hitID, float identity, int alignlen, int mismatches, int gapopenings, int querystart, int queryend, int hitstart, int hitend, double evalue, float bitscore)
queryID
- internal ID of the query proteinhitID
- internal ID of the hit protein (database protein)identity
- identity of the alignmentalignlen
- length of the alignmentmismatches
- number of mismatches in the alignmentgapopenings
- gap openings in the alignmentquerystart
- start coordinate in the query sequencequeryend
- end coordinate in the query sequencehitstart
- start coordinate in the hit sequencehitend
- end coordinate in the hit sequenceevalue
- e-value of the hitbitscore
- bitscore of the hitProteinManager
Method Detail |
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public int getHitID()
public int getQueryID()
public float getIdentity()
public int getAlignmentLength()
public int getMismatches()
public int getGapOpenings()
public int getQueryStart()
public int getQueryEnd()
public int getHitStart()
public int getHitEnd()
public double getEvalue()
public float getBitScore()
public String toString()
toString
in class Object
public int compareTo(BlastHit o)
compareTo
in interface Comparable<BlastHit>
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