object.common
Class Blast

java.lang.Object
  object.common.Blast

All Implemented Interfaces:

java.io.Serializable

public class Blast
extends java.lang.Object
implements java.io.Serializable

Description
Methodes used for executing Blast program on the server
Infos : KLB - IPMC - 08/2003

See Also:

BlastHit, Serialized Form

Field Summary

private boolean	allOk This boolean is true if the Blast program was execute well
private java.lang.String	database Database name
private java.lang.String	expectation Value of expectation value for executing Blast program
protected static java.lang.String	ext_bl2seq
protected static java.lang.String	ext_blast
protected static java.lang.String	ext_tmp
private java.lang.String	FValue Value of F value for executing Blast program
private java.util.Hashtable	hashtableBlastHit Hashtable containing the list of the BlastHit object results of the Blast
protected static java.lang.String	pathBlast
protected static java.lang.String	pathDatabase
private java.lang.String	pathFichier Path of the file where the sequence to Blast are store
protected static java.lang.String	pathFormatDB
protected static java.lang.String	pathTmp
private java.lang.String	SValue Value of S value for executing Blast program
private java.util.Vector	vectorHitOrdre Vector containing the order of the sequence in which the Blast program proceed
private java.lang.String	WValue Value of W value for executing Blast program

Constructor Summary

Blast()
Default constructor

Blast(java.lang.String database, java.lang.String expectation)
Constructs a Blast object for the Microsite web interface

Blast(java.lang.String pathFichier, java.lang.String database, java.lang.String expectation)
Constructs a Blast object

Method Summary

void	doParseBlastProgram(java.lang.String pathNameBlast) Parse the results file of the Blast program and fill the Hashtable hashtableBlastHit of this Blast object
void	doParseMegaBlastProgram(java.lang.String pathNameBlast) Parse the results file of the MegaBlast program and fill the Hashtable hashtableBlastHit of this MegaBlast object
boolean	getAllOk() This boolean is true if the Blast program was execute well
java.lang.String	getDatabase() Database name
java.lang.String	getExpectation() Value of expectation value for executing Blast program
java.lang.String	getFValue() Value of F value for executing Blast program
java.util.Hashtable	getHashtableBlastHit() Hashtable containing the list of the BlastHit object results of the Blast
java.lang.String	getPathFichier() Path of the file where the sequence to Blast are store
java.lang.String	getSValue() Value of S value for executing Blast program
java.util.Vector	getVectorHitOrdre() Vector containing the order of the sequence in which the Blast program proceed
java.lang.String	getWValue() Value of W value for executing Blast program
void	makeBlast() Lauch the process to run Blast program with all the parameters of this Blast object
void	makeFilesBlastTwoseq(org.biojava.bio.seq.Sequence sequence1, org.biojava.bio.seq.Sequence sequence2) Create both files corresponding to the two Sequence received as parameters and create a Blast database with the First one.
void	makeFileSeq(org.biojava.bio.seq.Sequence sequence) Create a file from a Sequence object received as a parameter.
void	makeFileSeq(java.util.Vector vectorSequence) Create a file from a Vector of Sequence object received as a parameter.
void	makeMegaBlast() Lauch the process to run MegaBlast program with all the parameters of this Blast object
void	setAllOk(boolean allOk)
void	setDatabase(java.lang.String database)
void	setExpectation(java.lang.String expectation)
void	setFValue(java.lang.String FValue)
void	setHashtableBlastHit(java.util.Hashtable hashtableBlastHit)
void	setPathFichier(java.lang.String pathFichier)
void	setStaticParams(java.util.Hashtable hashExtensions, java.util.Hashtable hashBlastConfiguration, java.util.Hashtable configFields) Initialize static parameters from the configuration file - ext_tmp - ext_blast - ext_bl2seq - pathBlast - pathFormatDB - pathDatabase - pathTmp
void	setSValue(java.lang.String SValue)
void	setVectorHitOrdre(java.util.Vector vectorHitOrdre)
void	setWValue(java.lang.String WValue)

Methods inherited from class java.lang.Object

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

Field Detail

database

private java.lang.String database

Database name

expectation

private java.lang.String expectation

Value of expectation value for executing Blast program

WValue

private java.lang.String WValue

Value of W value for executing Blast program

SValue

private java.lang.String SValue

Value of S value for executing Blast program

FValue

private java.lang.String FValue

Value of F value for executing Blast program

pathFichier

private java.lang.String pathFichier

Path of the file where the sequence to Blast are store

hashtableBlastHit

private java.util.Hashtable hashtableBlastHit

Hashtable containing the list of the BlastHit object results of the Blast

vectorHitOrdre

private java.util.Vector vectorHitOrdre

Vector containing the order of the sequence in which the Blast program proceed

allOk

private boolean allOk

This boolean is true if the Blast program was execute well

pathBlast

protected static java.lang.String pathBlast

pathFormatDB

protected static java.lang.String pathFormatDB

pathDatabase

protected static java.lang.String pathDatabase

pathTmp

protected static java.lang.String pathTmp

ext_blast

protected static java.lang.String ext_blast

ext_tmp

protected static java.lang.String ext_tmp

ext_bl2seq

protected static java.lang.String ext_bl2seq

Constructor Detail

Blast

public Blast()

Default constructor

Blast

public Blast(java.lang.String pathFichier,
             java.lang.String database,
             java.lang.String expectation)

Constructs a Blast object

Parameters:

pathFichier - Path of the file to Blast

database - The name of the database against which the file must be Blast

expectation - Expectation value for executing Blast program

Blast

public Blast(java.lang.String database,
             java.lang.String expectation)

Constructs a Blast object for the Microsite web interface

Parameters:

database - The name of the database against which the file must be Blast

expectation - Expectation value for executing Blast program

Method Detail

setStaticParams

public void setStaticParams(java.util.Hashtable hashExtensions,
                            java.util.Hashtable hashBlastConfiguration,
                            java.util.Hashtable configFields)

Initialize static parameters from the configuration file
- ext_tmp
- ext_blast
- ext_bl2seq
- pathBlast
- pathFormatDB
- pathDatabase
- pathTmp

getDatabase

public java.lang.String getDatabase()

Database name

setDatabase

public void setDatabase(java.lang.String database)

getExpectation

public java.lang.String getExpectation()

Value of expectation value for executing Blast program

setExpectation

public void setExpectation(java.lang.String expectation)

getWValue

public java.lang.String getWValue()

Value of W value for executing Blast program

setWValue

public void setWValue(java.lang.String WValue)

getSValue

public java.lang.String getSValue()

Value of S value for executing Blast program

setSValue

public void setSValue(java.lang.String SValue)

getFValue

public java.lang.String getFValue()

Value of F value for executing Blast program

setFValue

public void setFValue(java.lang.String FValue)

getPathFichier

public java.lang.String getPathFichier()

Path of the file where the sequence to Blast are store

setPathFichier

public void setPathFichier(java.lang.String pathFichier)

getAllOk

public boolean getAllOk()

This boolean is true if the Blast program was execute well

setAllOk

public void setAllOk(boolean allOk)

getHashtableBlastHit

public java.util.Hashtable getHashtableBlastHit()

Hashtable containing the list of the BlastHit object results of the Blast

setHashtableBlastHit

public void setHashtableBlastHit(java.util.Hashtable hashtableBlastHit)

getVectorHitOrdre

public java.util.Vector getVectorHitOrdre()

Vector containing the order of the sequence in which the Blast program proceed

setVectorHitOrdre

public void setVectorHitOrdre(java.util.Vector vectorHitOrdre)

makeBlast

public void makeBlast()

Lauch the process to run Blast program with all the parameters of this Blast object

See Also:

Process, Runtime, doParseBlastProgram(String)

makeMegaBlast

public void makeMegaBlast()

Lauch the process to run MegaBlast program with all the parameters of this Blast object

See Also:

Process, Runtime, doParseBlastProgram(String)

doParseBlastProgram

public void doParseBlastProgram(java.lang.String pathNameBlast)

Parse the results file of the Blast program and fill the Hashtable hashtableBlastHit of this Blast object

Parameters:

pathNameBlast - Path of the file to parse

See Also:

BlastHit

doParseMegaBlastProgram

public void doParseMegaBlastProgram(java.lang.String pathNameBlast)

Parse the results file of the MegaBlast program and fill the Hashtable hashtableBlastHit of this MegaBlast object

Parameters:

pathNameBlast - Path of the file to parse

See Also:

BlastHit

makeFilesBlastTwoseq

public void makeFilesBlastTwoseq(org.biojava.bio.seq.Sequence sequence1,
                                 org.biojava.bio.seq.Sequence sequence2)

Create both files corresponding to the two Sequence received as parameters and create a Blast database with the First one.

Parameters:

sequence1 - Sequence corresponding to the Blast database for the Blast two sequences

sequence2 - Sequence query for the Blast two sequences

See Also:

Process, Runtime

makeFileSeq

public void makeFileSeq(org.biojava.bio.seq.Sequence sequence)

Create a file from a Sequence object received as a parameter.

makeFileSeq

public void makeFileSeq(java.util.Vector vectorSequence)

Create a file from a Vector of Sequence object received as a parameter.

Parameters:

vectorSequence - Vector of Sequence object