object.common
Class BlastTwoSeq

java.lang.Object
  object.common.BlastTwoSeq

All Implemented Interfaces:

java.io.Serializable

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

Description
Object with which we can make Blast 2 sequences analysis, we can proceed to a Blast 2 sequences in several ways :
- With accession_number present in our database
- With position number on our IPMC MicroArray
- With sequence directly entered in the form
- With uploading file (not active for the moment)
Infos : KLB - IPMC - 08/2003

See Also:

Sequence, Blast, Serialized Form

Field Summary

private java.lang.String	accessionOne Accession number one
private java.lang.String	accessionTwo Accession number two
private Blast	blast Blast object in which we are going to store the Blast results
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_seq
private java.lang.String	FValue Value of F value for executing Blast program
private boolean	initialisation boolean : true if our query for align two sequence worked well
private boolean	is_accessionOne boolean : true if we want to align the first sequence from the database
private boolean	is_accessionTwo boolean : true if we want to align the second sequence from the database
private java.lang.String	message Information message
private java.lang.String	pathFichierOne Path of the file where the first sequence to Blast is store
private java.lang.String	pathFichierTwo Path of the file where the second sequence to Blast is store
protected static java.lang.String	pathTmp
private java.lang.String	seqOne The sequence entered in the first textarea of our form
private java.lang.String	seqTwo The sequence entered in the second textarea of our form
private org.biojava.bio.seq.Sequence	sequenceOne Sequence object for our first sequence to align
private org.biojava.bio.seq.Sequence	sequenceTwo Sequence object for our second sequence to align
private java.lang.String	SValue Value of S value for executing Blast program
private java.lang.String	WValue Value of W value for executing Blast program

Constructor Summary

BlastTwoSeq()
Default constructor

BlastTwoSeq(java.util.List items, int user_id)
Constructs a BlastTwoSeq object a List object and a user_id

Method Summary

boolean	formatSequence(java.lang.String fasta_seq, java.lang.String nb) Check the validity of the sequence entered by the user in the textarea or by uploading a file.
java.lang.String	getAccessionOne() Accession number one
java.lang.String	getAccessionTwo() Accession number two
Blast	getBlast() Blast object in which we are going to store the Blast results
java.lang.String	getExpectation() Value of expectation value for executing Blast program
java.lang.String	getFValue() Value of F value for executing Blast program
boolean	getInitialisation() boolean : true if our query for align two sequence worked well
boolean	getIs_accessionOne() boolean : true if we want to align the first sequence from the database
boolean	getIs_accessionTwo() boolean : true if we want to align the second sequence from the database
java.lang.String	getMessage() Information message
java.lang.String	getSeqOne() The sequence entered in the first textarea of our form
java.lang.String	getSeqTwo() The sequence entered in the second textarea of our form
org.biojava.bio.seq.Sequence	getSequenceOne() Sequence object for our first sequence to align
org.biojava.bio.seq.Sequence	getSequenceTwo() Sequence object for our second sequence to align
java.lang.String	getSValue() Value of S value for executing Blast program
java.lang.String	getWValue() Value of W value for executing Blast program
boolean	initSequenceFromFile(java.lang.String pathFic, java.lang.String nb) Initialize the sequence object of the BlastTwoSeq object if the query of the user is by uploading a file.
void	makeBlastTwoSeq() Launch Blast Two sequences for this object
void	setAccessionOne(java.lang.String accessionOne)
void	setAccessionTwo(java.lang.String accessionTwo)
void	setBlast(Blast blast)
void	setExpectation(java.lang.String expectation)
void	setFValue(java.lang.String FValue)
void	setInitialisation(boolean initialisation)
void	setIs_accessionOne(boolean is_accessionOne)
void	setIs_accessionTwo(boolean is_accessionTwo)
void	setMessage(java.lang.String message)
void	setSeqOne(java.lang.String seqOne)
void	setSeqTwo(java.lang.String seqTwo)
void	setSequenceOne(org.biojava.bio.seq.Sequence sequenceOne)
void	setSequenceTwo(org.biojava.bio.seq.Sequence sequenceTwo)
void	setStaticParams(java.util.Hashtable hashExtensions, java.util.Hashtable configFields) Initialize static parameters from the configuration file - ext_seq - ext_bl2seq - pathTmp
void	setSValue(java.lang.String SValue)
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

message

private java.lang.String message

Information message

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

pathFichierOne

private java.lang.String pathFichierOne

Path of the file where the first sequence to Blast is store

pathFichierTwo

private java.lang.String pathFichierTwo

Path of the file where the second sequence to Blast is store

accessionOne

private java.lang.String accessionOne

Accession number one

accessionTwo

private java.lang.String accessionTwo

Accession number two

is_accessionOne

private boolean is_accessionOne

boolean : true if we want to align the first sequence from the database

is_accessionTwo

private boolean is_accessionTwo

boolean : true if we want to align the second sequence from the database

seqOne

private java.lang.String seqOne

The sequence entered in the first textarea of our form

seqTwo

private java.lang.String seqTwo

The sequence entered in the second textarea of our form

sequenceOne

private org.biojava.bio.seq.Sequence sequenceOne

Sequence object for our first sequence to align

sequenceTwo

private org.biojava.bio.seq.Sequence sequenceTwo

Sequence object for our second sequence to align

blast

private Blast blast

Blast object in which we are going to store the Blast results

initialisation

private boolean initialisation

boolean : true if our query for align two sequence worked well

pathTmp

protected static java.lang.String pathTmp

ext_seq

protected static java.lang.String ext_seq

ext_bl2seq

protected static java.lang.String ext_bl2seq

Constructor Detail

BlastTwoSeq

public BlastTwoSeq()

Default constructor

BlastTwoSeq

public BlastTwoSeq(java.util.List items,
                   int user_id)

Constructs a BlastTwoSeq object a List object and a user_id

Parameters:

items - List object containing the datas of the query

user_id - ID of the user who want to proceed to a Blast two sequences

See Also:

Common, Common.getSEQForGID(int), Common.getGIDForAN(String), formatSequence(String,String), initSequenceFromFile(String,String)

Method Detail

setStaticParams

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

Initialize static parameters from the configuration file
- ext_seq
- ext_bl2seq
- pathTmp

getMessage

public java.lang.String getMessage()

Information message

setMessage

public void setMessage(java.lang.String message)

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)

getAccessionOne

public java.lang.String getAccessionOne()

Accession number one

setAccessionOne

public void setAccessionOne(java.lang.String accessionOne)

getAccessionTwo

public java.lang.String getAccessionTwo()

Accession number two

setAccessionTwo

public void setAccessionTwo(java.lang.String accessionTwo)

getIs_accessionOne

public boolean getIs_accessionOne()

boolean : true if we want to align the first sequence from the database

setIs_accessionOne

public void setIs_accessionOne(boolean is_accessionOne)

getIs_accessionTwo

public boolean getIs_accessionTwo()

boolean : true if we want to align the second sequence from the database

setIs_accessionTwo

public void setIs_accessionTwo(boolean is_accessionTwo)

getSeqOne

public java.lang.String getSeqOne()

The sequence entered in the first textarea of our form

setSeqOne

public void setSeqOne(java.lang.String seqOne)

getSeqTwo

public java.lang.String getSeqTwo()

The sequence entered in the second textarea of our form

setSeqTwo

public void setSeqTwo(java.lang.String seqTwo)

getSequenceOne

public org.biojava.bio.seq.Sequence getSequenceOne()

Sequence object for our first sequence to align

setSequenceOne

public void setSequenceOne(org.biojava.bio.seq.Sequence sequenceOne)

getSequenceTwo

public org.biojava.bio.seq.Sequence getSequenceTwo()

Sequence object for our second sequence to align

setSequenceTwo

public void setSequenceTwo(org.biojava.bio.seq.Sequence sequenceTwo)

getInitialisation

public boolean getInitialisation()

boolean : true if our query for align two sequence worked well

setInitialisation

public void setInitialisation(boolean initialisation)

getBlast

public Blast getBlast()

Blast object in which we are going to store the Blast results

setBlast

public void setBlast(Blast blast)

formatSequence

public boolean formatSequence(java.lang.String fasta_seq,
                              java.lang.String nb)

Check the validity of the sequence entered by the user in the textarea or by uploading a file.
This validity is based on a regxep which is : "^[atgcATGCnNkKyYrRsSdDwWmM]+$"

Parameters:

fasta_seq - String sequence supposed in the FASTA format

nb - String could be 1 or 2 corresponding to the sequence number

initSequenceFromFile

public boolean initSequenceFromFile(java.lang.String pathFic,
                                    java.lang.String nb)

Initialize the sequence object of the BlastTwoSeq object if the query of the user is by uploading a file.

Parameters:

pathFic - Path of the file in which is stored the sequence

nb - String could be 1 or 2 corresponding to the sequence number

See Also:

formatSequence(String,String)

makeBlastTwoSeq

public void makeBlastTwoSeq()

Launch Blast Two sequences for this object

See Also:

Blast, Blast.makeFilesBlastTwoseq(Sequence,Sequence), Blast.makeBlast()