Centre for Molecular and Biomolecular Informatics
Radboud University Nijmegen
To exit the file manager/xmenu program.
The view menu allows you to control how and in which order files (and directories) are displayed in the file selection box.
Three Sort types are supported:
Two Display types are supported:
Finally, the toggle option Dot Files controls whether the "dot" or "." files (files having a name starting with a period) are included in the listing or not. On a Unix system dot files are widely used by applications as configuration files, and it may be convenient to exclude them from view.
The tools currently available in the Cheminformatics menu are:
The general (i.e., not Cheminformatics) commands available from the file manager appear under four headings:
The file manager allows you to define:
These commands can be added, edited, and deleted. All three type of commands use the same syntax. Any changes to the definition of these commands, can be made permanent by clicking the Save Configuration menu item. The configuration is kept in the file .filemanrc in the user's home directory.
|Command syntax for configuring xmenu|
The user can either start external applications or use Tcl syntax. The latter has to be declared by using the macro INTERNAL (Use only CAPITALS for macros). The INTERNAL syntax is used by some of the predefined commands, but will not be of much use for the general user. With one exception, you can use the internal browser to browse the output of external (NON-interactive) commands or to display the contents of a file.
Example: INTERNAL BrowseCmd "zcat OLDFILE"
OLDFILE is an other macro. A macro is one of the below reserved keywords, with usually triggers some action to be performed before the actual execution of the command:
|OLDFILE||OLDFILE is substituted by the selected filename(s)|
|OLDFILECHECK||OLDFILE is substituted by the selected filename(s), after user confirmation|
|NEWFILE||NEWFILE is substituted by the user supplied filename|
|NEWDIR||NEWDIR is substituted by the user supplied directory name|
|ADDARGS||ADDARGS is substituted by the user supplied argument|
|UPDATELIST||UPDATELIST triggers the display of the file selection box to be refreshed after the execution of a command|
Use the & (ampersand) symbol at the end of the command definition to force execution in the background. In this way the file manager does not have to wait for the external application to finish before continuing.
In the last example the environment variable TA_ROOT is used.
|The internal file browser|
The file manager has in internal browser which can be used for browsing through the contents of a text file or the output of a command. If the output contains special character attributes (such as bold or underlining) the characters will be displayed in different colors. Colors and fonts can be configured.
Close will close the browser. Search will search for the string typed in the box to the right. Regular expressions are supported.
|Help on xmenu|
Clicking on this button causes a web browser to be invoked with help on the file manager.
|Change the size of the xmenu window|
Clicking the Small button will cause the file manager window to shrink. Only the menubar will be visible. You can click on the Big button (note the name change!) to display the full file manager again.
|Filter the files listed|
In this text field you can supply a file name filter.
For instance, "*.ps" will only list the
files with filenames ending in ".ps" (these will be
PostScript files), and "abc*"
will list all files having names starting with "abc".
An * (asterisk) means all files.
Hit the Enter key to activate (alternatively, you can click on refresh). Clicking with the third mouse button in this field will bring up a popup window which lists the currently defined file extensions. (See the Configure section on how to add new file extensions.)
|The display field for selected files|
Here the currently selected file(s) is/are displayed. See the file selection box section on how select files.
|The display field for the current directory|
There are three ways of changing the current directory:
|The file selection box|
Directories are listed first in the list and are denoted with a "/" (slash). The first entry is always "../" denoting the directory just above the current one. You can go to a directory by Double Clicking its entry in the list, and you can select a file by Clicking its entry in the list. You can select a range of files by pressing the first mouse button on the first entry, dragging down the pointer to the last entry and finally releasing the mouse button (you can also use the shift key for the same effect). The selected file(s) will show up in the Filename: field. Double clicking an ordinary file will trigger the action associated with its file extension. Example: Double clicking a file with the file extension .pdf might bring up Acrobat Reader (a PDF viewer). (See the Configure section on how to add new file extensions and how to define the action associated with it.)
|The button box|
The button box shows the predefined buttons of the file manager. (See the Configure section on how to add your own buttons.)
|Create a new file|
You will be prompted for the name of the file to be newly created, and then an xterm session with the standard Unix file editor vi will be started (with an empty file).
|Edit the selected file|
Starts an xterm session with the standard Unix text file editor vi on the selected file.
|Type (show the contents of) the selected file|
Displays the selected file in the internal browser and allows you to browse its contents.
|Copy the selected file to a new one|
Copies the selected file(s). You can copy one file to a new one, or one or more files to an existing directory. You will be prompted for the destination and for confirmation. If you supply (for the destination) an existing directory the file(s) will be copied to that directory.
|Rename the selected file to a new one|
Renames (moves) the selected file(s). You can rename one file to a new one, or one or more files to an existing directory. You will be prompted for the destination and for confirmation. If you supply (for the destination) an existing directory the file(s) will be moved to that directory.
|Delete the selected file|
Deletes (removes) the selected file(s). You will be prompted for confirmation. For directories, use Delete Dir.
|Execute the selected file|
Executes the selected file. Note that the file must be executable (i.e., it must be a valid script or binary program and the execute permission must have been set). See the file permissions section.
|Change the permissions of the selected file|
Change the file permissions of the selected file(s). On Unix systems a file has an owner and belongs to a group. File permissions are defined for three different sort of users, the owner (User), the users who belong to the files group (Group) and all other users (Other). If just one file is selected, its existing file permissions are shown in the file permissions window. When multiple files are selected the new permissions will overwrite all existing ones.
Note: You can only change file permissions of files which you own.
|Create a new directory|
You will be prompted for the name of a newly to be created directory.
|Delete the selected directory|
Prompts for confirmation and tries to delete the selected directory Note that the directory should already be empty for the removal to succeed.
|Select all files|
Selects all files and directories in the file selection box, both visible and unvisible.
|Refresh the file listing|
The file manager refreshes the file selection box whenever one of its predefined actions (such as Delete) is likely to alter the contents of the current directory. But external processes, other applications, and terminal sessions may also alter the contents of a directory. Clicking on Refresh will force the display of the file selection box to be refreshed.
|List the home directory|
Puts the file manager in the user's home directory.
|Go up one directory level|
Double clicking the .. in the file selection box will put the file manager in the directory just above the current directory. However, the .. may not always be visible in the file selection box. Clicking Up will have the same effect.