com.compomics.software

Class CompomicsWrapper

java.lang.Object

com.compomics.software.CompomicsWrapper

public class CompomicsWrapper
extends 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

Modifier and Type	Method and Description
static boolean	checkForNewDeployedVersion(String toolName, MavenJarFile oldMavenJarFile, URL jarRepository, String iconName, boolean deleteOldFiles, boolean startDownloadedVersion, boolean addDesktopIcon, Image normalIcon, Image waitingIcon, boolean exitJavaOnCancel) Check if a newer version of the tool is deployed in the Maven repository, and closes the tool if the user decided to update.
static void	checkForNewVersion(String currentVersion, String toolName, String googleCodeToolName) Deprecated. use the Maven repository option instead: checkForNewDeployedVersion
static void	checkForNewVersion(String currentVersion, String toolName, String googleCodeToolName, boolean closeToolWhenUpgrading, String zipFileTag, String zipFileType) Deprecated. use the Maven repository option instead: checkForNewDeployedVersion
static void	checkJavaVersion(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 boolean	downloadLatestVersion(String toolName, String groupId, String artifactId, File downloadFolder, URL jarRepository, String iconName, boolean startDownloadedVersion, boolean addDesktopIcon, Image normalIcon, Image waitingIcon, boolean exitJavaOnCancel) Check if a newer version of the tool is deployed in the Maven repository, and closes the tool if the user decided to update.
static String	getJarFilePath(String classPath, String toolName) Returns the path to the jar file.
ArrayList<String>	getJavaHomeAndOptions(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(String toolName, File jarFile, String splashName, String mainClass) Starts the launcher by calling the launch method.
void	launchTool(String toolName, File jarFile, String splashName, String mainClass, 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(String toolName,
                       File jarFile,
                       String splashName,
                       String mainClass)

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

Parameters:

toolName - the name of the tool

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(String toolName,
                       File jarFile,
                       String splashName,
                       String mainClass,
                       String[] args)

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

Parameters:

toolName - the name of the tool

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 String getJarFilePath(String classPath,
                                    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(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"

checkForNewDeployedVersion

public static boolean checkForNewDeployedVersion(String toolName,
                                                 MavenJarFile oldMavenJarFile,
                                                 URL jarRepository,
                                                 String iconName,
                                                 boolean deleteOldFiles,
                                                 boolean startDownloadedVersion,
                                                 boolean addDesktopIcon,
                                                 Image normalIcon,
                                                 Image waitingIcon,
                                                 boolean exitJavaOnCancel)

Check if a newer version of the tool is deployed in the Maven repository, and closes the tool if the user decided to update.

Parameters:

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

oldMavenJarFile - the old jar file

jarRepository - the Maven repository

iconName - the icon name

deleteOldFiles - if true, the old version of the tool is tried deleted

startDownloadedVersion - if true, the new version is started when downloaded

addDesktopIcon - if true, a desktop icon is added

normalIcon - the normal icon for the progress dialog

waitingIcon - the waiting icon for the progress dialog

exitJavaOnCancel - if true, the JVM will be shut down if the update is canceled by the user before it has started or when the update is done

Returns:

true if a new version is to be downloaded

downloadLatestVersion

public static boolean downloadLatestVersion(String toolName,
                                            String groupId,
                                            String artifactId,
                                            File downloadFolder,
                                            URL jarRepository,
                                            String iconName,
                                            boolean startDownloadedVersion,
                                            boolean addDesktopIcon,
                                            Image normalIcon,
                                            Image waitingIcon,
                                            boolean exitJavaOnCancel)

Check if a newer version of the tool is deployed in the Maven repository, and closes the tool if the user decided to update.

Parameters:

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

groupId - the group id

artifactId - the artifact id

downloadFolder - the folder to download to

jarRepository - the Maven repository

iconName - the icon name

startDownloadedVersion - if true, the new version is started when downloaded

addDesktopIcon - if true, a desktop icon is added

normalIcon - the normal icon for the progress dialog

waitingIcon - the waiting icon for the progress dialog

exitJavaOnCancel - if true, the JVM will be shut down if the update is canceled by the user before it has started or when the update is done

Returns:

true if a new version is to be downloaded

checkForNewVersion

public static void checkForNewVersion(String currentVersion,
                                      String toolName,
                                      String googleCodeToolName)

Deprecated. use the Maven repository option instead: checkForNewDeployedVersion

Check if a newer version of the tool is available on GoogleCode, and closes the tool if the user decided to update. 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(String currentVersion,
                                      String toolName,
                                      String googleCodeToolName,
                                      boolean closeToolWhenUpgrading,
                                      String zipFileTag,
                                      String zipFileType)

Deprecated. use the Maven repository option instead: checkForNewDeployedVersion

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 ArrayList<String> getJavaHomeAndOptions(String toolPath)
                                        throws FileNotFoundException,
                                               IOException,
                                               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:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

ClassNotFoundException - if a ClassNotFoundException occurs