Package eu.isas.searchgui.processbuilders

Class MakeblastdbProcessBuilder

java.lang.Object

eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

eu.isas.searchgui.processbuilders.MakeblastdbProcessBuilder

All Implemented Interfaces:

Runnable

public class MakeblastdbProcessBuilder
extends SearchGUIProcessBuilder

This class takes care of starting the Makeblastdb Process. Mandatory when using OMSSA.

Author:

Ravi Tharakan, Lennart Martens, Marc Vaudel, Harald Barsnes

Field Summary

Fields

Modifier and Type	Field	Description
static final String	EXECUTABLE_FILE_NAME	The name of the makeblastdb executable.

Fields inherited from class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

exceptionHandler, waitingHandler

Constructor Summary

Constructors

Constructor	Description
MakeblastdbProcessBuilder(String pathToJarFile, File aDatabaseFile, File makeblastdbLocation, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.exceptions.ExceptionHandler exceptionHandler)	Constructor.

Method Summary

Modifier and Type	Method	Description
void	endProcess()	Cancels the process.
String	getCurrentlyProcessedFileName()	Returns the file name of the currently processed file.
static String	getMakeblastdbFolder()	Returns the folder containing the makeblastdb script.
String	getType()	Returns the type of the process.
boolean	needsFormatting()	Checks if makeblastdb has already been run on this file.
void	startProcess()	Starts the process of a process builder, gets the input stream from the process and shows it in a JTextArea.

Methods inherited from class eu.isas.searchgui.processbuilders.SearchGUIProcessBuilder

run

Methods inherited from class java.lang.Object

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

Field Details

EXECUTABLE_FILE_NAME

public static final String EXECUTABLE_FILE_NAME

The name of the makeblastdb executable.

See Also:

• Constant Field Values

Constructor Details

MakeblastdbProcessBuilder

public MakeblastdbProcessBuilder(String pathToJarFile,
 File aDatabaseFile,
 File makeblastdbLocation,
 com.compomics.util.waiting.WaitingHandler waitingHandler,
 com.compomics.util.exceptions.ExceptionHandler exceptionHandler)

Constructor.

Parameters:

pathToJarFile - the path to the jar file

aDatabaseFile - File with the DB file to be formatted

makeblastdbLocation - the location of makeblastdb

waitingHandler - the waiting handler

exceptionHandler - the handler of exceptions

Method Details

getMakeblastdbFolder

public static String getMakeblastdbFolder()

Returns the folder containing the makeblastdb script. Depends on the operation system.

Returns:

the folder containing the makeblastdb script

needsFormatting

public boolean needsFormatting()

Checks if makeblastdb has already been run on this file.

Returns:

boolean returns true if makeblastdb has been run

startProcess

public void startProcess()
                  throws IOException

Starts the process of a process builder, gets the input stream from the process and shows it in a JTextArea. Does not close until the process is completed.

Overrides:

startProcess in class SearchGUIProcessBuilder

Throws:

IOException - Exception thrown whenever an error occurred while reading the progress stream

endProcess

public void endProcess()

Cancels the process.

Overrides:

endProcess in class SearchGUIProcessBuilder

getType

public String getType()

Description copied from class: SearchGUIProcessBuilder

Returns the type of the process.

Specified by:

getType in class SearchGUIProcessBuilder

Returns:

the type of the process

getCurrentlyProcessedFileName

public String getCurrentlyProcessedFileName()

Description copied from class: SearchGUIProcessBuilder

Returns the file name of the currently processed file.

Specified by:

getCurrentlyProcessedFileName in class SearchGUIProcessBuilder

Returns:

the file name of the currently processed file