org.fhcrc.cpl.viewer
Class Application

java.lang.Object
  org.fhcrc.cpl.viewer.Application

All Implemented Interfaces:

ApplicationContext.ApplicationContextProvider

public class Application
extends java.lang.Object
implements ApplicationContext.ApplicationContextProvider

If the "log" arg is specified, all ApplicationContext messages and all Log4J messages will all be appended to a log file. The user can specify a file for this purpose, or one can be written in the temp dir. If this logging is on and a CommandLineModule fails execution, the full log will be appended to the failure log. If a CLM fails execution and logging is NOT on, the user is prompted to re-run the command with logging on.

Field Summary

protected boolean	_isWorkbenchInitialized
protected static boolean	enableLog
static java.lang.String	FAILURE_REPORT_ERRORMESSAGE_TEXT
static java.lang.String	FAILURE_REPORT_HEADER_TEXT
protected static java.io.File	logFile
protected static java.lang.String	LOGFILE_DUMMY_CALLER
protected static java.io.PrintWriter	logPrintWriter
protected static java.lang.String	MESSAGE_TYPE_ERROR
protected static java.lang.String	MESSAGE_TYPE_INFO

Method Summary

void	addPropertyChangeListener(java.beans.PropertyChangeListener listener)
void	addPropertyChangeListener(java.lang.String name, java.beans.PropertyChangeListener listener)
static void	closeLog()
void	errorMessage(java.lang.String message, java.lang.Throwable t)
javax.swing.JFrame	getFrame()
static Application	getInstance()
static java.io.File	getLogFile()
protected static java.io.PrintWriter	getPrintWriter(java.lang.String outFileName)
java.lang.Object	getProperty(java.lang.String name)
protected static boolean	handleHardcodedCommand(java.lang.String command, java.lang.String[] args, java.lang.String revision) Checks if the command is one of the few that we handle in a hardcoded fashion.
void	infoMessage(java.lang.String message)
static boolean	isLogEnabled()
static void	main(java.lang.String[] args) Starts the application.
static void	ms2Correct(java.lang.String[] args) TODO: we should remove this, probably
void	OpenFile(java.lang.String filename)
static boolean	processRawArguments(CommandLineModule module, java.lang.String[] args) For CommandLineModule commands, parse the argument strings, digest the relevant arguments according to the definitions provided by the module.
static void	quit()
static void	quit(int status)
static void	quit(java.lang.String err)
void	redrawWorkbench() start from scratch with a new Workbench.
protected static void	runCommand(CommandLineModule module, java.lang.String[] args) Handle arguments and run a command
static void	setMessage(java.lang.String message)
void	setProperty(java.lang.String name, java.lang.Object value)
protected static void	showHelp(CommandLineModule module) Show help for a given module
protected void	showMessage(java.lang.String text, java.lang.String messageType)
static void	showUsage() "--revision\n" + "--ms2Correct --features=ms1FeatureFile [--out=outfilename] [filterOptions] runFile" + "\n" + "--optimize [--out=outfilename] [--scanWindows=int,int,...] [--massWindows=float,float,float] [filterOptions] featureFiles..." + "\n" + "--deconvolute --quant [--out=outfilename] [--scanWindow=int] [--massWindow=float] [--lightTagWeight=float] [--heavyTagWeight=float] [--maxLabelCount=int] [--labeledResidue=char] [--intensityType={total,max,recalculated}] [--msFile=filepath] --deltaTime=[float] --deltaMass=[float][da|ppm] featureFile" + "\n" + " --deconvolute and --quant may be used together or separately\n" + "\n" + "[filterOptions] = \n" + "[--minMz=float] [--maxMz=float] [--minMass=float] [--maxMass=float]\n" + "[--minPeaks=int] [--minCharge=int] [--maxCharge=int] [--maxKL=float]\n" + "[--minIntensity=float] [--minTotalIntensity=float]\n" + "[--minTime=float] [--maxTime=float]\n" + "[--scanFirst=int] [scanLast=int] [--minScans=int]\n" + "scanFirst and scanLast filter the scan column.
void	status(java.lang.String message)

Methods inherited from class java.lang.Object

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

Field Detail

_isWorkbenchInitialized

protected boolean _isWorkbenchInitialized

enableLog

protected static boolean enableLog

logFile

protected static java.io.File logFile

logPrintWriter

protected static java.io.PrintWriter logPrintWriter

LOGFILE_DUMMY_CALLER

protected static final java.lang.String LOGFILE_DUMMY_CALLER

See Also:

Constant Field Values

MESSAGE_TYPE_INFO

protected static java.lang.String MESSAGE_TYPE_INFO

MESSAGE_TYPE_ERROR

protected static java.lang.String MESSAGE_TYPE_ERROR

FAILURE_REPORT_ERRORMESSAGE_TEXT

public static final java.lang.String FAILURE_REPORT_ERRORMESSAGE_TEXT

See Also:

Constant Field Values

FAILURE_REPORT_HEADER_TEXT

public static final java.lang.String FAILURE_REPORT_HEADER_TEXT

See Also:

Constant Field Values

Method Detail

getInstance

public static Application getInstance()

setMessage

public static void setMessage(java.lang.String message)

redrawWorkbench

public void redrawWorkbench()

start from scratch with a new Workbench. For language changing

status

public void status(java.lang.String message)

Specified by:

status in interface ApplicationContext.ApplicationContextProvider

errorMessage

public void errorMessage(java.lang.String message,
                         java.lang.Throwable t)

Specified by:

errorMessage in interface ApplicationContext.ApplicationContextProvider

infoMessage

public void infoMessage(java.lang.String message)

Specified by:

infoMessage in interface ApplicationContext.ApplicationContextProvider

showMessage

protected void showMessage(java.lang.String text,
                           java.lang.String messageType)

getFrame

public javax.swing.JFrame getFrame()

Specified by:

getFrame in interface ApplicationContext.ApplicationContextProvider

setProperty

public void setProperty(java.lang.String name,
                        java.lang.Object value)

Specified by:

setProperty in interface ApplicationContext.ApplicationContextProvider

getProperty

public java.lang.Object getProperty(java.lang.String name)

Specified by:

getProperty in interface ApplicationContext.ApplicationContextProvider

addPropertyChangeListener

public void addPropertyChangeListener(java.beans.PropertyChangeListener listener)

Specified by:

addPropertyChangeListener in interface ApplicationContext.ApplicationContextProvider

addPropertyChangeListener

public void addPropertyChangeListener(java.lang.String name,
                                      java.beans.PropertyChangeListener listener)

Specified by:

addPropertyChangeListener in interface ApplicationContext.ApplicationContextProvider

OpenFile

public void OpenFile(java.lang.String filename)

runCommand

protected static void runCommand(CommandLineModule module,
                                 java.lang.String[] args)

Handle arguments and run a command

Parameters:

module -

args -

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Starts the application. Application can be started in either interactive mode or specifically to find peptides in a file. Interactive Mode: Application [mzxmlfile] Find Peptides: Application --findPeptides [--out=outfile] mzxmlfile If outfile is not specified, outfile is mzxmlfile.peptides.tsv

Parameters:

args -

Throws:

java.lang.Exception

handleHardcodedCommand

protected static boolean handleHardcodedCommand(java.lang.String command,
                                                java.lang.String[] args,
                                                java.lang.String revision)

Checks if the command is one of the few that we handle in a hardcoded fashion. if so, do something about it and return true (or throw an exception, shut down, whatever). If not, return false;

Parameters:

command -

args -

revision -

Returns:

true iff the command entered is one we handle hardcoded

showHelp

protected static void showHelp(CommandLineModule module)

Show help for a given module

Parameters:

module -

processRawArguments

public static boolean processRawArguments(CommandLineModule module,
                                          java.lang.String[] args)

For CommandLineModule commands, parse the argument strings, digest the relevant arguments according to the definitions provided by the module. If any undefined arguments are specified, die

Parameters:

args -

Returns:

closeLog

public static void closeLog()

quit

public static void quit()

quit

public static void quit(java.lang.String err)

quit

public static void quit(int status)

showUsage

public static void showUsage()

"--revision\n" + "--ms2Correct --features=ms1FeatureFile [--out=outfilename] [filterOptions] runFile" + "\n" + "--optimize [--out=outfilename] [--scanWindows=int,int,...] [--massWindows=float,float,float] [filterOptions] featureFiles..." + "\n" + "--deconvolute --quant [--out=outfilename] [--scanWindow=int] [--massWindow=float] [--lightTagWeight=float] [--heavyTagWeight=float] [--maxLabelCount=int] [--labeledResidue=char] [--intensityType={total,max,recalculated}] [--msFile=filepath] --deltaTime=[float] --deltaMass=[float][da|ppm] featureFile" + "\n" + " --deconvolute and --quant may be used together or separately\n" + "\n" + "[filterOptions] = \n" + "[--minMz=float] [--maxMz=float] [--minMass=float] [--maxMass=float]\n" + "[--minPeaks=int] [--minCharge=int] [--maxCharge=int] [--maxKL=float]\n" + "[--minIntensity=float] [--minTotalIntensity=float]\n" + "[--minTime=float] [--maxTime=float]\n" + "[--scanFirst=int] [scanLast=int] [--minScans=int]\n" + "scanFirst and scanLast filter the scan column. minScans filters the scanCount column. Other filter parameters filter the column matching their name.";

getPrintWriter

protected static java.io.PrintWriter getPrintWriter(java.lang.String outFileName)
                                             throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

ms2Correct

public static void ms2Correct(java.lang.String[] args)
                       throws java.lang.Exception

TODO: we should remove this, probably

Parameters:

args -

Throws:

java.lang.Exception

isLogEnabled

public static boolean isLogEnabled()

getLogFile

public static java.io.File getLogFile()