com.compomics.software

Class CompomicsWrapper

java.lang.Object

com.compomics.software.CompomicsWrapper

public class CompomicsWrapper
extends java.lang.Object

A general wrapper for compomics tools. All tools shall contain a resources/conf folder. In it a JavaOptions.txt and splash screen. Eventually JavaHome.txt and proxy/uniprotjapi.properties.

Author:

Harald Barsnes, Marc Vaudel, Davy Maddelein

Constructor Summary

Constructors

Constructor and Description
CompomicsWrapper() Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
static void	checkForNewVersion(java.lang.String currentVersion, java.lang.String toolName, java.lang.String googleCodeToolName) Check if a newer version of the tool is available on GoogleCode, and closes the tool if the user decided to upgrade.
static void	checkForNewVersion(java.lang.String currentVersion, java.lang.String toolName, java.lang.String googleCodeToolName, boolean closeToolWhenUpgrading, java.lang.String zipFileTag, java.lang.String zipFileType) Check if a newer version of the tool is available on GoogleCode.
static void	checkJavaVersion(java.lang.String toolName) Checks if the user is running Java 64 bit and shows a warning if not, and shows a dialog with a warning and a link to the JavaTroubleShooting page if not.
static java.lang.String	getJarFilePath(java.lang.String classPath, java.lang.String toolName) Returns the path to the jar file.
java.util.ArrayList<java.lang.String>	getJavaHomeAndOptions(java.lang.String toolPath) Returns an array list containing the Java home plus any parameters to the JVM.
static boolean	is64BitJava() Returns if the Java version used is 64 bit.
void	launchTool(java.lang.String toolName, java.io.File jarFile, java.lang.String splashName, java.lang.String mainClass) Starts the launcher by calling the launch method.
void	launchTool(java.lang.String toolName, java.io.File jarFile, java.lang.String splashName, java.lang.String mainClass, java.lang.String[] args) Starts the launcher by calling the launch method.

Methods inherited from class java.lang.Object

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

Constructor Detail

CompomicsWrapper

public CompomicsWrapper()

Constructor.

Method Detail

launchTool

public void launchTool(java.lang.String toolName,
              java.io.File jarFile,
              java.lang.String splashName,
              java.lang.String mainClass)

Starts the launcher by calling the launch method. Use this as the main class in the jar file.

Parameters:

toolName -

jarFile - the jar file to execute

splashName - the splash name, for example peptide-shaker-splash.png

mainClass - the main class to execute, for example eu.isas.peptideshaker.gui.PeptideShakerGUI

launchTool

public void launchTool(java.lang.String toolName,
              java.io.File jarFile,
              java.lang.String splashName,
              java.lang.String mainClass,
              java.lang.String[] args)

Starts the launcher by calling the launch method. Use this as the main class in the jar file.

Parameters:

toolName -

jarFile - the jar file to execute

splashName - the splash name, for example peptide-shaker-splash.png, can be null

mainClass - the main class to execute, for example eu.isas.peptideshaker.gui.PeptideShakerGUI

args - the arguments to pass to the tool (ignored if null)

getJarFilePath

public static java.lang.String getJarFilePath(java.lang.String classPath,
                              java.lang.String toolName)

Returns the path to the jar file. Verifies that the path exists and tries to decode from Unicode if not.

Parameters:

classPath - the class path to extract the jar file path from

toolName - the name of the tool, e.g., "PeptideShaker" or "SearchGUI".

Returns:

the path to the jar file

is64BitJava

public static boolean is64BitJava()

Returns if the Java version used is 64 bit.

Returns:

true if the Java version is 64 bit

checkJavaVersion

public static void checkJavaVersion(java.lang.String toolName)

Checks if the user is running Java 64 bit and shows a warning if not, and shows a dialog with a warning and a link to the JavaTroubleShooting page if not.

Parameters:

toolName - the name of the tool, e.g., "PeptideShaker"

checkForNewVersion

public static void checkForNewVersion(java.lang.String currentVersion,
                      java.lang.String toolName,
                      java.lang.String googleCodeToolName)

Check if a newer version of the tool is available on GoogleCode, and closes the tool if the user decided to upgrade. No zip file tag used (see the other checkForNewVersion method).

Parameters:

currentVersion - the version number of the tool currently running

toolName - the name of the tool, e.g., "PeptideShaker"

googleCodeToolName - the GoogleCode name of the tool, e.g., "peptide-shaker"

checkForNewVersion

public static void checkForNewVersion(java.lang.String currentVersion,
                      java.lang.String toolName,
                      java.lang.String googleCodeToolName,
                      boolean closeToolWhenUpgrading,
                      java.lang.String zipFileTag,
                      java.lang.String zipFileType)

Check if a newer version of the tool is available on GoogleCode.

Parameters:

currentVersion - the version number of the tool currently running

toolName - the name of the tool, e.g., "PeptideShaker"

googleCodeToolName - the GoogleCode name of the tool, e.g., "peptide-shaker"

closeToolWhenUpgrading - if true, the tool will close when the download page is opened, false only opens the download page

zipFileTag - the zip file tag, e.g., SearchGUI-1.10.4_windows.zip has the tag "_windows"

zipFileType - the zip file type, e.g., ".zip" or ".tar.gz"

getJavaHomeAndOptions

public java.util.ArrayList<java.lang.String> getJavaHomeAndOptions(java.lang.String toolPath)
                                                            throws java.io.FileNotFoundException,
                                                                   java.io.IOException,
                                                                   java.lang.ClassNotFoundException

Returns an array list containing the Java home plus any parameters to the JVM. The fist index in the list will always contain the Java home. Note that this method assumes that the tool has folder called resources/conf in the same folder as the jar file.

Parameters:

toolPath - the path to the jar file of the tool

Returns:

an array list containing the Java home plus any parameters to the JVM

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.ClassNotFoundException