charite.christo
Class Customize

java.lang.Object
  charite.christo.Customize

All Implemented Interfaces:

ChRunnable, HasModiCount, HasPanel, java.awt.event.ActionListener, java.util.EventListener

public final class Customize
extends java.lang.Object
implements java.awt.event.ActionListener, HasPanel, ChRunnable, HasModiCount

HELP The customize-dialogs are used to set program options.
Data-types:

• Single WIKI:Executable: Can be the absolute Path of an executable file such as /opt/acrobat5/acroread. Only the first line is evaluated, the other lines can be used for notes. A file-path can start with an environment variable. In Windows a shell variable can be written with a leading dollar like $ProgramFiles or with percent signs like %ProgramFiles%.
• List of shell commands: The lines contain alternative shell commands to start programs for one particular task. There are usually several programs. For example there are many different pdf-viewers around. All lines are successively executed one after the other until one line succeeds because the software designated in the line is installed on the machine. This is tested by STRAP using the WIKI:Exit_status. Note for Windows-Users: The prefix "start" which is used to start programs under Windows does not return proper exit values. As a consequence, STRAP will always assume that the respective program was successfully started.
  Comments are preceded by "#".
• Single text string
• Lists of text strings, one item per line

The settings are saved in text files in the directory ~/.StrapAlign.

Windows: The %PATH%-variable does not contain all WIKI:Executable files and therefore full file paths are often needed. Adding START at the beginning of a command line may avoid the need to enter absolute paths.


Using a new shell For using complicated shell commands with pipes, redirection, loops etc. the expression should be started with "SH " ("CYGWINSH " on Windows).

White space in file names: According to the WIKI:Url_encoding, white space in directory and file names must be encoded by "%20". Nevertheless, on standard computer systems, white space is generally avoided in file names, and this will only be the case on MS-Windows.

Setting values from file: With specific command-line options, further lines can be added. These lines are added to the default settings or if changed by the user to the text entered by the user. The command line option is formed by appending the name of the customize dialog to the prefix "customizeAdd". For example to add script lines you add the command line parameters -customizeAddScriptByRegex file. File is either a file or an URL. If the program is started from an URL, then "&customizeAddScriptByRegex=file" is added to the URL. Note that URL-encoding needs to be applied to file. JCOMPONENT:Customize#docuView()

Field Summary

static int	C_compiler
static int	CLASS_Example
static int	CLASS_ExecPath
static int	CLASS_InitCommands
static int	CLASS_LateCommands
static int	CLASSPATH
static int	CplusPlus_compiler
static int	cssAlignBrowser
static int	databases
static int	dviPsConverter
static int	dviViewer
static int	ecClassLinks
static int	error
static int	execAminoSeq
static int	execResidueSelection
static int	EXECUTABLE
static int	EXECUTABLES
static int	FILE
static int	fileBrowsers
static int	FILES
static int	FLAG_INTERN
static int	FLAG_NOTIFY_IMMEDIATELY
static int	FLAG_REPLACE
static int	FLAG_SKIP_COMMENTS
static int	fortran_compiler
static int	htmlEditors
static int	javaSourceEditor
static int	keggOrganisms
static int	laf
static int	latex
static int	LATEX
static int	latexEditors
static int	LIST
static int	LIST_OF_CLASSES
static int	LIST_OF_DIRECTORIES
static int	MAP_TO_1_FROM_N
static int	MAX_ID
static int	MAX_VARIABLE
static Customize[]	NONE
static int	openFileWith
static int	pdbLinks
static int	pdbSite
static int	pdflatex
static int	pdfViewer
static int	proteinDatabases
static int	proteinFileExtensions
static int	psPoster
static int	psViewer
static int	refuseExe
static int	scriptByRegex
static int	seqFeatureColors
static int	SHELL_SCRIPT
static int	speciesIcons
static int	testProxySelector
static int	TEXT_LINES
static int	textEditors
static int	trustExe
static int	uniprotLinks
static int	URL
static int	watchLogFile
static int	webBrowser
static int	webLinks
static int	webSearches

Fields inherited from interface charite.christo.HasPanel

NEW_PANEL, NO_NEW_PANEL

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

Customize(java.lang.String name, java.lang.String[] defaultSetting, java.lang.String help, int type)

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ev)
static void	addDialog(Customize... cc)
void	addHiddenEntries(boolean uniq, java.lang.String... ss)
void	addLine(java.lang.String s)
static void	afterDL(java.lang.String name)
static Customize[]	cc(java.lang.Object o)
static Customize	customize(int id)
static javax.swing.JComponent	docuView()
static void	downloadFiles(java.lang.String[] namesOfCustomize)
static Customize	getCustomizableForClass(java.lang.Class c, int id)
static Customize	getCustomizableForClass(java.lang.Class clazz, java.lang.String id, java.lang.String help, int type)
javax.swing.JComponent	getPanel(int options)
java.lang.String	getSetting()
java.lang.String[]	getSettings()
java.util.List<java.lang.String>	getSettingsV()
int	modificationCount()
ChButton	newButton()
static ChButton	newButton(Customize... cc)
static ChButton	newButton(int... IDs)
static ChButton	newButtonAll(java.lang.String id)
ChCombo	newComboBox()
java.lang.Object	run(java.lang.String id, java.lang.Object arg)
void	save(boolean always)
static void	setParent(ChTabPane tp, java.awt.event.ActionListener li)
static java.lang.String	toCommandLineOption(java.lang.String name)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

databases

public static final int databases

See Also:

Constant Field Values

proteinDatabases

public static final int proteinDatabases

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webLinks

public static final int webLinks

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C_compiler

public static final int C_compiler

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CplusPlus_compiler

public static final int CplusPlus_compiler

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latexEditors

public static final int latexEditors

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dviPsConverter

public static final int dviPsConverter

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dviViewer

public static final int dviViewer

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fileBrowsers

public static final int fileBrowsers

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fortran_compiler

public static final int fortran_compiler

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htmlEditors

public static final int htmlEditors

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javaSourceEditor

public static final int javaSourceEditor

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laf

public static final int laf

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pdfViewer

public static final int pdfViewer

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proteinFileExtensions

public static final int proteinFileExtensions

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psPoster

public static final int psPoster

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psViewer

public static final int psViewer

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textEditors

public static final int textEditors

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watchLogFile

public static final int watchLogFile

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webBrowser

public static final int webBrowser

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error

public static final int error

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pdbSite

public static final int pdbSite

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pdflatex

public static final int pdflatex

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latex

public static final int latex

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openFileWith

public static final int openFileWith

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scriptByRegex

public static final int scriptByRegex

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execAminoSeq

public static final int execAminoSeq

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execResidueSelection

public static final int execResidueSelection

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ecClassLinks

public static final int ecClassLinks

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webSearches

public static final int webSearches

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pdbLinks

public static final int pdbLinks

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uniprotLinks

public static final int uniprotLinks

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testProxySelector

public static final int testProxySelector

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keggOrganisms

public static final int keggOrganisms

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speciesIcons

public static final int speciesIcons

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cssAlignBrowser

public static final int cssAlignBrowser

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seqFeatureColors

public static final int seqFeatureColors

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trustExe

public static final int trustExe

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refuseExe

public static final int refuseExe

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MAX_ID

public static final int MAX_ID

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EXECUTABLE

public static final int EXECUTABLE

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EXECUTABLES

public static final int EXECUTABLES

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LATEX

public static final int LATEX

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LIST

public static final int LIST

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LIST_OF_CLASSES

public static final int LIST_OF_CLASSES

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FILE

public static final int FILE

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FILES

public static final int FILES

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TEXT_LINES

public static final int TEXT_LINES

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LIST_OF_DIRECTORIES

public static final int LIST_OF_DIRECTORIES

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SHELL_SCRIPT

public static final int SHELL_SCRIPT

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CLASSPATH

public static final int CLASSPATH

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MAP_TO_1_FROM_N

public static final int MAP_TO_1_FROM_N

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URL

public static final int URL

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MAX_VARIABLE

public static final int MAX_VARIABLE

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FLAG_SKIP_COMMENTS

public static final int FLAG_SKIP_COMMENTS

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FLAG_INTERN

public static final int FLAG_INTERN

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FLAG_REPLACE

public static final int FLAG_REPLACE

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FLAG_NOTIFY_IMMEDIATELY

public static final int FLAG_NOTIFY_IMMEDIATELY

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NONE

public static final Customize[] NONE

CLASS_Example

public static final int CLASS_Example

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CLASS_ExecPath

public static final int CLASS_ExecPath

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CLASS_InitCommands

public static final int CLASS_InitCommands

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CLASS_LateCommands

public static final int CLASS_LateCommands

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Constructor Detail

Customize

public Customize(java.lang.String name,
                 java.lang.String[] defaultSetting,
                 java.lang.String help,
                 int type)

Method Detail

docuView

public static javax.swing.JComponent docuView()

modificationCount

public int modificationCount()

Specified by:

modificationCount in interface HasModiCount

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toCommandLineOption

public static java.lang.String toCommandLineOption(java.lang.String name)

downloadFiles

public static void downloadFiles(java.lang.String[] namesOfCustomize)

afterDL

public static void afterDL(java.lang.String name)

getSettingsV

public java.util.List<java.lang.String> getSettingsV()

addHiddenEntries

public void addHiddenEntries(boolean uniq,
                             java.lang.String... ss)

getSettings

public java.lang.String[] getSettings()

getSetting

public java.lang.String getSetting()

getPanel

public javax.swing.JComponent getPanel(int options)

Specified by:

getPanel in interface HasPanel

newButtonAll

public static ChButton newButtonAll(java.lang.String id)

newButton

public static ChButton newButton(int... IDs)

newButton

public ChButton newButton()

newButton

public static ChButton newButton(Customize... cc)

newComboBox

public ChCombo newComboBox()

setParent

public static void setParent(ChTabPane tp,
                             java.awt.event.ActionListener li)

addDialog

public static void addDialog(Customize... cc)

cc

public static Customize[] cc(java.lang.Object o)

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ev)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

save

public void save(boolean always)

addLine

public void addLine(java.lang.String s)

customize

public static Customize customize(int id)

run

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

Specified by:

run in interface ChRunnable

getCustomizableForClass

public static Customize getCustomizableForClass(java.lang.Class clazz,
                                                java.lang.String id,
                                                java.lang.String help,
                                                int type)

getCustomizableForClass

public static Customize getCustomizableForClass(java.lang.Class c,
                                                int id)