procope.methods.interologs.blast
Class BlastHit

java.lang.Object
  extended by procope.methods.interologs.blast.BlastHit
All Implemented Interfaces:
Comparable<BlastHit>

public class BlastHit
extends Object
implements Comparable<BlastHit>

A single BLAST hit.

Author:
Jan Krumsiek

Constructor Summary
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
 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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

BlastHit

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)
Creates an new BLAST hit object.

Parameters:
queryID - internal ID of the query protein
hitID - internal ID of the hit protein (database protein)
identity - identity of the alignment
alignlen - length of the alignment
mismatches - number of mismatches in the alignment
gapopenings - gap openings in the alignment
querystart - start coordinate in the query sequence
queryend - end coordinate in the query sequence
hitstart - start coordinate in the hit sequence
hitend - end coordinate in the hit sequence
evalue - e-value of the hit
bitscore - bitscore of the hit
See Also:
ProteinManager
Method Detail

getHitID

public int getHitID()
Returns the internal ID of the hit protein

Returns:
internal ID of the hit protein

getQueryID

public int getQueryID()
Returns the internal ID of the query protein

Returns:
internal ID of the query protein

getIdentity

public float getIdentity()
Returns the identity of the alignment

Returns:
identity of the alignment

getAlignmentLength

public int getAlignmentLength()
Returns the length of the alignment

Returns:
length of the alignment

getMismatches

public int getMismatches()
Returns the number of mismatches in the alignment

Returns:
number of mismatches in the alignment

getGapOpenings

public int getGapOpenings()
Returns the gap openings in the alignment

Returns:
gap openings in the alignment

getQueryStart

public int getQueryStart()
Returns the query start coordinate of the hit

Returns:
query start coordinate of the hit

getQueryEnd

public int getQueryEnd()
Returns the query end coordinate of the hit

Returns:
query end coordinate of the hit

getHitStart

public int getHitStart()
Returns the hit start coordinate of the hit

Returns:
hit start coordinate of the hit

getHitEnd

public int getHitEnd()
Returns the hit end coordinate of the hit

Returns:
hit end coordinate of the hit

getEvalue

public double getEvalue()
Returns the e-value of the hit

Returns:
e-value of the hit

getBitScore

public float getBitScore()
Returns the bit score of the hit

Returns:
bit score of the hit

toString

public String toString()
Returns a simple string representation of the hit. This contains the query and hit protein as well as the e-value.

Overrides:
toString in class Object

compareTo

public int compareTo(BlastHit o)
Orders the hits by their hit ID. Used for internal purposes.

Specified by:
compareTo in interface Comparable<BlastHit>