charite.christo
Class BasicExecutable

java.lang.Object
  charite.christo.BasicExecutable

All Implemented Interfaces:

CanBeStopped, ChRunnable, Disposable, HasControlPanel

Direct Known Subclasses:

NativeTools, SecondaryStructure_Jnet, Toppred

public class BasicExecutable
extends java.lang.Object
implements CanBeStopped, Disposable, ChRunnable, HasControlPanel

HELP

External programs

External programs are installed in the directory ~/.StrapAlign/bin/.

Since your computer may not be prepared for installing scientific programs from WIKI:Source_code, ClustalW is also included ready to run on Windows, Macintosh and Linux. For all other external programs, WIKI:compilers and WIKI:make_(software) are required.

Compilers

Two program packages are required on your PC to install software from source code:

XXX

Testing, whether compilers are already installed

Usually, the C-compiler is started with the command "cc" and the C++ compiler with the command "c++". Fortran compilers are started with "gfortran" or "f77" or "f95". If C++ is installed then typing into the command shell "c++" produces the output

c++: no input files

But the message

c++: command not found

indicates that either C++ is not installed yet or that the PATH-variable is not set correctly. OS_DEBIAN To install the compilers on a WIKI:Debian system run the following in a terminal:

   sudo apt-get install g++ gfortran make
   

OS_SUSE To install the compilers on a WIKI:SUSE_Linux_distributions run the following in a terminal:

   sudo /sbin/yast2 --install gcc-c++ gcc-fortran make
   

OS_MAC A C++-Compiler is included in WIKI:Xcode which is found on the installation DVD of the Macintosh.

Insert Mac OS X Installation DVD. Navigate to the Optional Installs: Xcode Tools folder.

Double-click XcodeTools.mpkg. Follow the prompts, but at Installation Type, click the Customize button.

To save disk space, uncheck all the components and check only Unix Development Support.

Unfortunately, Fortran which is required for TM-align, is not included in Xcode and must be obtained from other sources. OS_WINDOWS The compilers are provided by WIKI:Cygwin. BUTTON:charite.christo.Microsoft#newCygwinButton("")! OS_OTHER To install the compilers on your system open the software manager and activate the packages

• C++-compiler
• Fortran compiler
• make

Field Summary

static java.lang.String	DEFAULT_BINARY
static java.lang.String	PFX_ADD_INCLUDE_LIMITS
static java.lang.String	PFX_DPKG
static java.lang.String	PFX_FIX_INCLUDE
static java.lang.String[][]	REPLACEME_INLCUDE_STRING
static java.lang.String	RPLC_WIN_DOT_EXE

Fields inherited from interface charite.christo.CanBeStopped

vALIGNMENTS

Fields inherited from interface charite.christo.Disposable

NONE

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

BasicExecutable()

BasicExecutable(java.lang.String n)

Method Summary

static java.lang.Class[]	checkForUpdates(java.lang.Class[] classes)
void	defineParameters(long opt, java.lang.String s)
java.io.File	dirBinaries() The directory of the installed program.
java.io.File	dirTemp() temporary directory for transient data.
void	dispose()
ChExec	exec(boolean create)
ChExec	exec(long options)
void	failedToLaunch() Show a message telling that the program could not be started
java.io.File	fileExecutable() The File of the executable.
java.io.File	fileIn() You can use this as your input file.
java.io.File	fileOut() You can use this as your output file.
javax.swing.JComponent	getControlPanel(boolean real)
java.lang.String	getName()
PrgParas	getPrgParas()
java.lang.Object	getSharedInstance()
static BasicExecutable	init(BasicExecutable e0, java.lang.String names, java.lang.String srcUrls, java.lang.String instScript)
void	initExecutable()
static void	installBioPerl() If BioPerl is not yet installed then install it or tell the user to do so.
void	installPackage()
static boolean	isBioPerlInstalled()
static boolean	isPerlInstalled()
boolean	isStopped()
static java.lang.String	msgInstallCompilers()
static java.lang.String	perlCommand()
java.lang.Object	run(java.lang.String id, java.lang.Object arg) For internal use.
void	setBinaryPackageURLs(java.lang.String... uu) Set URL of the zip-archive for the program binary.
void	setFileExecutable(java.io.File f)
BasicExecutable	setName(java.lang.String n)
void	setSharedInstance(java.lang.Object shared)
void	setSourceInstallationScript(java.lang.String shellScript)
void	setSourcePackageURLs(java.lang.String... urls) Set URL of the zip-archive for the program source.
void	stop()
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

RPLC_WIN_DOT_EXE

public static final java.lang.String RPLC_WIN_DOT_EXE

See Also:

Constant Field Values

PFX_DPKG

public static final java.lang.String PFX_DPKG

See Also:

Constant Field Values

PFX_FIX_INCLUDE

public static final java.lang.String PFX_FIX_INCLUDE

See Also:

Constant Field Values

PFX_ADD_INCLUDE_LIMITS

public static final java.lang.String PFX_ADD_INCLUDE_LIMITS

See Also:

Constant Field Values

DEFAULT_BINARY

public static final java.lang.String DEFAULT_BINARY

See Also:

Constant Field Values

REPLACEME_INLCUDE_STRING

public static final java.lang.String[][] REPLACEME_INLCUDE_STRING

Constructor Detail

BasicExecutable

public BasicExecutable(java.lang.String n)

BasicExecutable

public BasicExecutable()

Method Detail

setName

public BasicExecutable setName(java.lang.String n)

getName

public final java.lang.String getName()

initExecutable

public final void initExecutable()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

dispose

public void dispose()

Specified by:

dispose in interface Disposable

dirTemp

public final java.io.File dirTemp()

temporary directory for transient data. Will be deleted after the program session.

fileIn

public final java.io.File fileIn()

You can use this as your input file.

fileOut

public final java.io.File fileOut()

You can use this as your output file.

dirBinaries

public final java.io.File dirBinaries()

The directory of the installed program.

fileExecutable

public java.io.File fileExecutable()

The File of the executable. is name() plus dot "exe"

setFileExecutable

public void setFileExecutable(java.io.File f)

setBinaryPackageURLs

public void setBinaryPackageURLs(java.lang.String... uu)

Set URL of the zip-archive for the program binary. An array of alternative URLs can be provided. Each String may contain a list of required zip files. Each URL may be followed by a file path denoting a file inside the zip archive that is the exe file.

setSourcePackageURLs

public final void setSourcePackageURLs(java.lang.String... urls)

Set URL of the zip-archive for the program source. An array of alternative URLs can be provided. Each String may contain a list of required zip files.

setSourceInstallationScript

public void setSourceInstallationScript(java.lang.String shellScript)

installPackage

public void installPackage()

failedToLaunch

public final void failedToLaunch()

Show a message telling that the program could not be started

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)

For internal use. If override please make a call super.run(...)

Specified by:

run in interface ChRunnable

perlCommand

public static java.lang.String perlCommand()

Returns:

usually "perl". If Windows and cygwin installed then returen the path to perl.exe

isPerlInstalled

public static boolean isPerlInstalled()

isBioPerlInstalled

public static boolean isBioPerlInstalled()

installBioPerl

public static void installBioPerl()

If BioPerl is not yet installed then install it or tell the user to do so.

getPrgParas

public final PrgParas getPrgParas()

setSharedInstance

public final void setSharedInstance(java.lang.Object shared)

getSharedInstance

public final java.lang.Object getSharedInstance()

defineParameters

public void defineParameters(long opt,
                             java.lang.String s)

exec

public ChExec exec(long options)

exec

public ChExec exec(boolean create)

isStopped

public boolean isStopped()

stop

public void stop()

Specified by:

stop in interface CanBeStopped

checkForUpdates

public static java.lang.Class[] checkForUpdates(java.lang.Class[] classes)

msgInstallCompilers

public static java.lang.String msgInstallCompilers()

getControlPanel

public javax.swing.JComponent getControlPanel(boolean real)

Specified by:

getControlPanel in interface HasControlPanel

init

public static BasicExecutable init(BasicExecutable e0,
                                   java.lang.String names,
                                   java.lang.String srcUrls,
                                   java.lang.String instScript)