charite.christo.blast
Class BlastResult

java.lang.Object
  charite.christo.blast.BlastResult

public final class BlastResult
extends java.lang.Object

This class provids an object oriented structure of BLAST results. It can be initialized with an XML BLAST output. A human readable text can be created with the method toText(). There is a significant difference between the numbering in BLAST output files and this API: In contrast to the output written by the BLAST program counting in this model starts at zero and not at one. For example queryStart 1 queryEnd 100 in the BLAST output would means 100 residues with indices 0 to index 99 here in this class. There is a difference between the XML format at NCBI and at ebi.ac.uk. This parser can cope with both formats.

Field Summary

static long

WRITE_MARK_NOVEL

Constructor Summary

BlastResult(BA xml)

Method Summary

void	addDatabase(BlastDatabase database)
void	addHit(BlastHit bh)
void	dispose()
BlastDatabase[]	getDatabases()
BlastHit[]	getHits()
boolean[]	getMatchingAminoacids(byte[] sequence)
java.lang.String	getProgramName()
java.lang.String	getProgramVersion()
java.lang.String	getQuerySeq(java.lang.String s)
static BlastResult	newInstance(SequenceBlaster blaster, java.lang.String label, java.lang.String icon)
void	setMatrix(java.lang.String s)
void	setProgramName(java.lang.String s)
void	setProgramVersion(java.lang.String s)
void	setQuerySeq(java.lang.String s)
void	writeFile(java.io.File f, int outputWidth)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

WRITE_MARK_NOVEL

public static final long WRITE_MARK_NOVEL

See Also:

Constant Field Values

Constructor Detail

BlastResult

public BlastResult(BA xml)

Method Detail

dispose

public void dispose()

getHits

public BlastHit[] getHits()

addDatabase

public void addDatabase(BlastDatabase database)

getDatabases

public BlastDatabase[] getDatabases()

setQuerySeq

public void setQuerySeq(java.lang.String s)

getQuerySeq

public java.lang.String getQuerySeq(java.lang.String s)

addHit

public void addHit(BlastHit bh)

setProgramName

public void setProgramName(java.lang.String s)

getProgramName

public java.lang.String getProgramName()

setProgramVersion

public void setProgramVersion(java.lang.String s)

getProgramVersion

public java.lang.String getProgramVersion()

setMatrix

public void setMatrix(java.lang.String s)

writeFile

public void writeFile(java.io.File f,
                      int outputWidth)
               throws java.io.IOException

Throws:

java.io.IOException

getMatchingAminoacids

public boolean[] getMatchingAminoacids(byte[] sequence)

newInstance

public static BlastResult newInstance(SequenceBlaster blaster,
                                      java.lang.String label,
                                      java.lang.String icon)