uk.ac.ebi.intact.application.intSeq.business
Class CallingSrs

java.lang.Object
  |
  +--uk.ac.ebi.intact.application.intSeq.business.CallingSrs

All Implemented Interfaces:

CallingSrsIF

public class CallingSrs

extends java.lang.Object

implements CallingSrsIF

This class allows to retrieve AC and Description fields from the SRS engine, with the SPTr database. So, it executes first the Wgetz command to call SRS, with the user request. Results are record in a file. The first request returns a list of AC and Description. Afterwards, the second request returns one sequence which corresponds to an AC.

Version:

: $Id: CallingSrs.java,v 1.4 2003/11/14 15:06:43 skerrien Exp $

Author:

shuet (shuet@ebi.ac.uk)

Field Summary

protected boolean	matchWithIntactId
protected java.lang.String	proteinTopic protein feature which has been captured by the user
protected ManagerFilesSrs	resultWgetzQuery
protected java.lang.String	srsCommand
protected boolean	srsError the first idea is that there will be none error during the SRS running
protected IntactUserI	theUser

Constructor Summary

CallingSrs()
constructor by default

CallingSrs(java.lang.String id)
constructor which allows to check if the protein topic exists in IntAct.

CallingSrs(java.lang.String proteintopic, java.lang.String command)
constructor which allows to call the SRS engine in case of lack of the request in IntAct

Method Summary

protected void	ExecFinalCommand(boolean acOrSeqRequest) This method decides which command will be executed (Wgetz or Getz) and put the file in the provided directory: to organize the numerous generated files into two separate directories.
boolean	GetBooleanIntactId() later, a method will allow to look for an IntAct entry from a protein topic (no SRS process in this case)
static long	getId() Returns the unique id based on the current time; the ids are unique for a session.
java.lang.String	GetSequenceFasta() Wgetz execution + parsing of the WGETZ output file get the sequence one by one in a fasta format string because the SequenceSimilarityAction requires a protein sequence in a String format (don't forget that the Fasta Format is required)
java.util.ArrayList	RetrieveAccDes() Wgetz execution + parsing of the WGETZ output file
protected void	WebSrs(java.lang.String path) This method manages the execution of the Wgetz URL.

Methods inherited from class java.lang.Object

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

Field Detail

theUser

protected IntactUserI theUser

proteinTopic

protected java.lang.String proteinTopic

protein feature which has been captured by the user

srsCommand

protected java.lang.String srsCommand

srsError

protected boolean srsError

the first idea is that there will be none error during the SRS running

resultWgetzQuery

protected ManagerFilesSrs resultWgetzQuery

matchWithIntactId

protected boolean matchWithIntactId

Constructor Detail

CallingSrs

public CallingSrs()

constructor by default

CallingSrs

public CallingSrs(java.lang.String id)

constructor which allows to check if the protein topic exists in IntAct. (later)

Parameters:

id - String which represents a protein feature (protein reference or simply a word)

CallingSrs

public CallingSrs(java.lang.String proteintopic,
                  java.lang.String command)

constructor which allows to call the SRS engine in case of lack of the request in IntAct

Parameters:

proteintopic - String which represents a protein feature (protein reference or simply a word)

command - String the Wgetz command to make a request on SRS

Method Detail

getId

public static long getId()

Returns the unique id based on the current time; the ids are unique for a session.

GetBooleanIntactId

public boolean GetBooleanIntactId()

later, a method will allow to look for an IntAct entry from a protein topic (no SRS process in this case)

Specified by:

GetBooleanIntactId in interface CallingSrsIF

Returns:

the boolean answer.

RetrieveAccDes

public java.util.ArrayList RetrieveAccDes()
                                   throws IntactException

Wgetz execution + parsing of the WGETZ output file

Specified by:

RetrieveAccDes in interface CallingSrsIF

Returns:

a list of Accession Number and Description got from the SRS request

IntactException

GetSequenceFasta

public java.lang.String GetSequenceFasta()
                                  throws IntactException

Wgetz execution + parsing of the WGETZ output file get the sequence one by one in a fasta format string because the SequenceSimilarityAction requires a protein sequence in a String format (don't forget that the Fasta Format is required)

Specified by:

GetSequenceFasta in interface CallingSrsIF

Returns:

a list of Accession Number and Description got from the SRS request

IntactException

ExecFinalCommand

protected void ExecFinalCommand(boolean acOrSeqRequest)
                         throws IntactException

This method decides which command will be executed (Wgetz or Getz) and put the file in the provided directory: to organize the numerous generated files into two separate directories.

Parameters:

acOrSeqRequest - the boolean which will put the generated file in the good directory. true means that it is the AC-Description result file

IntactException

WebSrs

protected void WebSrs(java.lang.String path)
               throws IntactException

This method manages the execution of the Wgetz URL.

Parameters:

path - the string which will add the good extension for the temporary file of which name is rendered randomly.

IntactException