'STRAP:multiple sequence alignments '

charite.christo
Class ChExec

java.lang.Object
  extended by charite.christo.ChExec
All Implemented Interfaces:
ChRunnable, HasControlPanel, java.awt.event.ActionListener, java.lang.Runnable, java.util.EventListener

public final class ChExec
extends java.lang.Object
implements java.lang.Runnable, HasControlPanel, java.awt.event.ActionListener, ChRunnable

execute external programs Several alternative command lines can be set. They are probed until one succeeds. The trying of command lines stops at an empty command line. The method error(Exception) is called when non of the alternative command lines succeeds.


Field Summary
static java.lang.String ACTION_ERROR
           
static java.lang.String ACTION_TERMINATED
           
static long CYGWIN_DLL
           
static java.lang.String CYGWINSH
           
static long DEBUG
           
static java.lang.String EXE_TM_ALIGN
           
static long IGNORE_ERROR
           
static long LOG
           
static long NOT_TO_DENY_LIST
           
static long PLEASE_INSTALL_MANUALLY
           
static long SHOW_STREAMS
           
static long STDERR
           
static long STDOUT
           
static long STDOUT_IN_TEXT_BOX
           
static boolean[] SUCCESS
           
static long WITHOUT_ASKING
           
 
Fields inherited from interface charite.christo.ChRunnable
APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, PROGRESS, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT
 
Constructor Summary
ChExec(long mode)
           
 
Method Summary
 void actionPerformed(java.awt.event.ActionEvent ev)
           
 ChExec addToEnvironement(java.lang.Object o)
           
 boolean couldNotLaunch()
           
 ChExec dir(java.io.File f)
           
 void dispose()
           
 int exitValue()
           
 boolean failedOpenDisplay()
           
 boolean finished()
           
 javax.swing.JComponent getControlPanel(boolean real)
           
 byte[] getStderr()
           
 byte[] getStdout()
           
 BA getStdoutAsBA()
           
 boolean isRunning()
           
 void kill()
           
static void log(ChExec exec, java.lang.Object o)
           
 ChExec printlnStdout(ChRunnable a)
           
 void run()
           
 java.lang.Object run(java.lang.String id, java.lang.Object arg)
           
 void setCL(java.util.List v, java.lang.Object o, boolean cygw)
          null is skipped, for List and Arrays the elements are inserted.
 ChExec setCommandLine(java.lang.Object s)
           
 ChExec setCommandLines(java.lang.String[] lines)
           
 ChExec setCommandLineV(java.lang.Object... objects)
           
 ChExec setCommandsAndArgument(java.lang.String[] commands, java.lang.Object argument0)
           
 ChExec setOptions(long m0)
           
 ChExec setStdin(java.lang.String s)
           
 ChExec showStdoutAndStderr(ChFrame f)
           
 ChExec waitFor()
           
 ChExec write(java.lang.String s)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

SUCCESS

public static final boolean[] SUCCESS

STDOUT

public static final long STDOUT
See Also:
Constant Field Values

STDERR

public static final long STDERR
See Also:
Constant Field Values

IGNORE_ERROR

public static final long IGNORE_ERROR
See Also:
Constant Field Values

CYGWIN_DLL

public static final long CYGWIN_DLL
See Also:
Constant Field Values

SHOW_STREAMS

public static final long SHOW_STREAMS
See Also:
Constant Field Values

LOG

public static final long LOG
See Also:
Constant Field Values

STDOUT_IN_TEXT_BOX

public static final long STDOUT_IN_TEXT_BOX
See Also:
Constant Field Values

PLEASE_INSTALL_MANUALLY

public static final long PLEASE_INSTALL_MANUALLY
See Also:
Constant Field Values

WITHOUT_ASKING

public static final long WITHOUT_ASKING
See Also:
Constant Field Values

NOT_TO_DENY_LIST

public static final long NOT_TO_DENY_LIST
See Also:
Constant Field Values

DEBUG

public static final long DEBUG
See Also:
Constant Field Values

ACTION_ERROR

public static final java.lang.String ACTION_ERROR
See Also:
Constant Field Values

ACTION_TERMINATED

public static final java.lang.String ACTION_TERMINATED
See Also:
Constant Field Values

CYGWINSH

public static final java.lang.String CYGWINSH
See Also:
Constant Field Values

EXE_TM_ALIGN

public static final java.lang.String EXE_TM_ALIGN
See Also:
Constant Field Values
Constructor Detail

ChExec

public ChExec(long mode)
Method Detail

setOptions

public ChExec setOptions(long m0)

finished

public boolean finished()

couldNotLaunch

public boolean couldNotLaunch()

failedOpenDisplay

public boolean failedOpenDisplay()

exitValue

public int exitValue()

kill

public void kill()

isRunning

public boolean isRunning()

dispose

public void dispose()

log

public static void log(ChExec exec,
                       java.lang.Object o)

showStdoutAndStderr

public ChExec showStdoutAndStderr(ChFrame f)

addToEnvironement

public ChExec addToEnvironement(java.lang.Object o)

setCommandLine

public ChExec setCommandLine(java.lang.Object s)

setCommandLines

public ChExec setCommandLines(java.lang.String[] lines)

setCommandsAndArgument

public ChExec setCommandsAndArgument(java.lang.String[] commands,
                                     java.lang.Object argument0)

setCL

public void setCL(java.util.List v,
                  java.lang.Object o,
                  boolean cygw)
null is skipped, for List and Arrays the elements are inserted. If arg[0] is CYGWINSH all files are written in the style /cygdrive/c/...


setCommandLineV

public ChExec setCommandLineV(java.lang.Object... objects)

printlnStdout

public ChExec printlnStdout(ChRunnable a)

setStdin

public ChExec setStdin(java.lang.String s)

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)
Specified by:
run in interface ChRunnable

write

public ChExec write(java.lang.String s)
             throws java.io.IOException
Throws:
java.io.IOException

getStderr

public byte[] getStderr()

getStdout

public byte[] getStdout()

getStdoutAsBA

public BA getStdoutAsBA()

dir

public ChExec dir(java.io.File f)

run

public void run()
Specified by:
run in interface java.lang.Runnable

waitFor

public ChExec waitFor()

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ev)
Specified by:
actionPerformed in interface java.awt.event.ActionListener

getControlPanel

public javax.swing.JComponent getControlPanel(boolean real)
Specified by:
getControlPanel in interface HasControlPanel

'STRAP:multiple sequence alignments '

'The most important classes are StrapAlign, Protein and StrapEvent.'