|COGENT Version 2.4 Help|
A number of minor aspects of the behaviour of COGENT can be tailored through the application's preferences. These specify, for example, when warning and confirmation errors should be printed, or how printouts should be formatted. There are nine categories of preferences: files; help; oos; printing; archive; fonts; warnings; confirmations; and miscellaneous.
The Preference Window provides an interface to COGENT's preferences. Through this window, preferences may be inspected or changed (either temporarily or permanently). The precise layout of the Preferences Window depends on which category of preference is being displayed. In all cases, however, it consists of three regions. The top row gives the category name, with a menu button that allows other preference categories to be displayed. Beneath this is a row of four buttons which allow various operations over the particular category of preference being displayed. Beneath this, is a set of widgets which show the values of the particular preferences in the category under view and which allow those values to be altered. Any alterations take immediate effect, but such alterations will only be stored for future use if they are also saved (with the Save button). It is also possible to return to a user's default values for the current category of preferences with the Reload button. The Help button causes the appropriate version of this window to appear (a different version will appear for each category of preference), and the Done button causes the Preferences Window to close.
On UNIX and Mac systems, each user's COGENT preference values are stored in a .cogentrc file in the user's home directory. If you don't have such a file, COGENT will create one for you, using default values for all the folder paths.
On Microsoft Windows systems, each user's COGENT preference values are stored in the registry. When you first run COGENT it will prompt you for the essentials and then create the appropriate registry entries for you. These entries will be specific to individual users, and so under systems with roaming profiles, should roam with the user on different machines.
COGENT several different types of file: project/model files, print output files, import/export files, oos class files, script files, archive files, and help files. Each of these types of file may be stored in a different location. The locations are specified by two preferences specified under the File Locations section of the Preferences panel.
The project folder specifies where COGENT should look to find project files. Normally each user will keep all projects in a single folder, and this value will only need to be changed when, for example, viewing someone else's projects.
COGENT uses a scripting language to guide model execution. The scripting language is quite powerful, allowing complex experimental designs to be specified. Novice users, however, may find the scripting language an unnecessary distraction. COGENT therefore allows the user to specify a set of default scripts, contained in the script folder. When a model is created, copies of all scripts in the script folder are associated with the new model. If COGENT is correctly installed, the user should not need to change this preference, unless s/he wishes to install different default scripts.
The Help Preferences panel controls default settings for a number of preferences which govern the way the help system works.
Use online help? (default: FALSE) If this preference is set, COGENT will search for help files online, using the web address given in the "Online help URL" preference. If the preference is not set, COGENT will use local help files, using the folder given in the "Offline help folder" preference.
Online help URL (default: http://cogent.psyc.bbk.ac.uk/help/version2/)
The URL used to locate help files when "Use online help?" is set. The default value is the COGENT's home web server in the UK. Institutions could place the help files on their own server and point to that for online help.
Offline help folder (default: /usr/local/lib/cogent/help/)
This is the local folder in which help files (like this one) are stored. If use online help is not set, COGENT will search for help files in this local folder. If you are unsure of where the help files are located on your system, use online help.
Show help with index frame? (default: FALSE) Some web browsers (notably netscape) are capable of popping up help files within an index frame that provides links to all other help files. However, this behaviour is browser specific. The value of this preference specifies whether COGENT should attempt to use index frames. If in doubt, try setting the preference and popping up a help window. If you get an error from your browser, or the window doesn't appear, un-set the preference.
Help browser (default: netscape)
This preference sets the browser to use to view help files. Help files are written in HTML, so the value of this preference should be a program capable of viewing such files. This preference is not available on Windows, where the default web browser is automatically used.
Help browser accepts remote commands? (default: TRUE) Some web browsers (notable netscape, mozilla and opera) can be controlled remotely through the -remote openURL() command. If this option is set, the help browser will be opened using this option. The effect is that if a browser is already running, COGENT will open the help file in that instance of the browser, rather than opening a new browser for COGENT's help. Note that while opera supports remote control, it is not necessary: it behaves sensibly without it, and it is recommended that the option not be set if you are using opera.
The COGENT execution engine (OOS) can be configured in a variety of ways. The following preferences are relevant:
OOS executable (default: "/usr/local/bin/oos")
This string-valued preference specifies the location of the OOS executable. For the standard configuration (with the executable compiled as "oos" and located on the user's path), the default value is appropriate, but users with multiple versions of OOS available on their machines may wish to configure this preference differently.
OOS class folder (default: "/usr/local/lib/cogent/classes")
This preference specifies the location of the OOS class folder. This folder should contain the Prolog definitions of each box type, as well as declarations for operators used by OOS. If COGENT is correctly installed, the user should not need to change this preference, unless s/he wishes to install different box classes. Be warned that if this preference is incorrectly set, COGENT may produce many "syntax" errors.
OOS library folder (default: "/usr/local/lib/cogent/oos")
This preference specifies the location of optimised OOS libraries. This folder should contain the object code for each OOS library. It is only used when optimisation is on.
OOS I/O Folder (default: "~/COGENT/io")
This preference specifies the default location for output from OOS.
Show debugging information (default: FALSE)
This Boolean preference determines the level of information printed in OOS's trace output window while a model is running. When the preference is set, numerous additional messages concerning the processing state of OOS are printed.
Save message logs (default: TRUE)
This Boolean preference controls whether OOS creates messages logs whilst running. Message logs consist, for each box, of all messages sent to or from that box, and can be viewed through the standard COGENT interface. The information contained in messages logs can be extremely useful for debugging purposes, but can also quickly fill most hard disks. Turn the preference off if you are happy with a model's performance and running low on disk space.
Animate box and arrow diagrams? (default: TRUE)
When this preference is TRUE and a model is run, COGENT animates box and arrow diagrams by drawing beads on arrows to show messages passing along those arrows. This slows things down a little. If the preference is FALSE, beads are not shown and COGENT runs a little faster. (This preference is only available on the registered version. In the unregistered version animation is disabled.)
Optimise (default: TRUE)
If this Boolean preference is set OOS uses a number of code optimisation. It should only affect (and improve) a model's execution speed. It is primarily for development purposes.
The Printing Preferences panel controls default settings for a number of preferences which govern the appearance and content of COGENT printouts. Note that a Print Preferences panel is also displayed when the print function is invoked. This subsidiary panel specified the preferences to be used for a particular printout, and allows default values specified in the main Printing Preferences panel to be over-ridden.
The Printing Preferences panel contains the following controls:
Print to file (default: FALSE)
This preference allows switching between sending output to a printer or saving it to a file. If the preference is TRUE, output generated by print commands is saved in a file (with filename and folder as specified by the Print file and Print folder preferences discussed below). If the preference is FALSE, output is printed using the command specified by the Print command preference.
COGENT can produce printouts of models or projects in ASCII, PostScript or HTML. The print folder specifies the default folder in which COGENT should put such print files. It's probably sensible if you intend to keep electronic copies of your printouts that you keep them all in the same place. Note that the folder in which a printout is put can also be at print time from the panel that appears when the print function is invoked.
Print file (default: cogent.ps)
This preference specifies the file in which printer output will be saved when Print to file is TRUE. The folder in which this file is placed is determined by the Print folder preference.
Printer command (default: lp -c)
The preference's value specified the print command used by COGENT to print output. When the value of Print to file is FALSE, COGENT generates a file (in the format given by Output format), prints it (via this command) and then deletes its. Likely values of this preference are lp -c (for SOLARIS and IRIX 5.X), lpr (for SUN OS 4.X), and ghostview to preview the PostScript without printing it.
Output format (default: PostScript)
This preference specifies the format in which print output is produced. Currently three formats are possible: Plain Text, PostScript, or HTML. Possible values are 0, 1 and 2 corresponding respectively to these formats.
Output page style (default: Portrait)
This preference controls the orientation and style of PostScript output. Possible values are 0, 1 and 2, corresponding to Portrait, Landscape, and Two Up, respectively. In Portrait style the long edge of the paper is vertical. In Landscape style the long edge is horizontal. Two Up page style consists of two logical pages per sheet of paper. The pages are oriented in portrait style, but reduced by a factor of 1.414 and printed side by side.
Printer font size (default: 10)
This preference controls the font size used in PostScript printouts generated by COGENT. It is ignored for other output formats.
Print new box on new page (default: FALSE)
When this preference is TRUE, COGENT will start the description of each box on a new printer page. If the preference is FALSE, then COGENT will be less wasteful and only start a new page when absolutely necessary. Note that when Output page style is set to Two Up mode two logical pages are printed on each sheet of paper, so a new page in this context means the next logical page.
Show initial contents (default: TRUE)
This preference controls whether the initial contents of boxes are included in the printout.
Show user-defined conditions (default: TRUE)
This preference specifies whether the conditions within a box should be included in full in the printout. In some views, condition definitions are peripheral "implementation details", and setting this preference to FALSE ensures that such details are excluded in the resulting printout.
Show current contents (default: TRUE)
This preference controls whether the current contents of boxes are included in the printout.
Show messages (default: TRUE)
This preference specifies whether the log of message processed by each box should be included in the printout.
Show buffer mappings (default: TRUE)
This preference specifies whether buffer mapping rules should be included in the printout.
Recurse through sub-objects (default: TRUE)
If this preference is TRUE, details of all sub-boxes of compound boxes are included in the printout.
COGENT projects that are not in progress may be "archived" in order to save space and simplify transfer of complete research programmes between machines. The archive folder specifies the folder in which COGENT stores and searches for archived projects. This folder cannot be set at the time of invoking the archive or extract functions.
Archive format: (default: CAR)
The format in which new archives will be created. See Supported Archive Formats.
Sort archives by: (default: Name)
The sorting criterion for listing archives in the archive browser. Possible values include: Name, Date, Format, Size.
Retain research programme after archiving? (default: TRUE)
If TRUE keep all files relating to the archived research programme in the research programme manager. If FALSE, delete these files when a research programme is archived.
Retain archive after extracting? (default: TRUE)
If TRUE keep the archive file after its contents have been extracted. If FALSE, delete the archive file when its contents are extracted.
The Font Preferences panel allows modification of some fonts used on COGENT's windows. Alternative fonts may be used to give COGENT a personalised look, or simply if something bigger or smaller is preferred. The available fonts will depend on the machine you are using, and may be accessed using the "Set" buttons on the font options panel.
History font (default: lucidasans-12)
This preference controls the font used on the Diagrammatic History window.
Diagram font (default: lucidasans-12)
This preference controls the font used for drawing project and model names on the main history diagram and model box and arrow diagrams.
Text font (default: lucidasans-12)
This preference controls the font used for text elements in graphs, weight matrices, message logs, etc.
Image font (default: lucidasans-12)
This preference controls the font used on the Current Image view of analogue buffers and the Current Display views of all buffers.
The COGENT interface is capable of generating lots of warning which require action from the user. Several categories of warning (generally less important warnings) can be suppressed by setting the appropriate control of the Warnings panel.
Reassure on success? (default: FALSE)
If TRUE, display a reassuring message whenever a file operation is successfully completed.
Warn on file access errors? (default: TRUE)
If TRUE, display a warning message whenever a file read/write fails.
Warn on syntax errors? (default: TRUE)
If TRUE, display a warning whenever a syntax error is detected in a Prolog term.
Warn on invalid model specification? (default: TRUE)
If TRUE, display a warning whenever unrecognised Prolog is found in a project or model file.
Warn on memory allocation failure? (default: TRUE)
If TRUE, display a warning whenever memory allocation fails.
Warn on miscellaneous errors? (default: TRUE)
If TRUE, display a warning on any unexpected events not covered by the above.
The COGENT interface is capable of generating lots confirmation messages which require action from the user. Many of these messages can be suppressed by setting the appropriate control of the Confirmations panel.
Confirm discard of edits? (default: FALSE)
If TRUE, seek confirmation from the user before discarding edits from any files.
Confirm project/model deletion? (default: TRUE)
If TRUE, seek confirmation from the user before deleting projects or models.
Confirm overwrite files? (default: FALSE)
If TRUE, seek confirmation from the user before over-writing all model and data files.
Confirm before printing PostScript? (default: TRUE)
If TRUE, seek confirmation from the user before printing any PostScript files. The confirmation message indicates the number of pages in the printout. This allows the user to abort printing if the file is too big.
Confirm save of model prior to running? (default: FALSE)
If TRUE, seek confirmation from the user before saving a model at execution time.
A number of further preferences control other aspects of COGENT's operation.
Double click interval (default: 400)
This preference specifies the maximum number of milliseconds that can elapse between two mouse clicks if they are to be interpreted as a double click.
Display precision (default: 2)
This value specifies the number of significant digits that COGENT stores and prints when presenting real numbers.
Show grid? (default: FALSE)
When drawing boxes on a COGENT box and arrow diagram, the boxes automatically align themselves on a grid. This value determines whether the grid is shown on the box and arrow diagram or whether it remains invisible.
Grid size (default: 5)
When drawing boxes on a COGENT box and arrow diagram, the boxes automatically align themselves on a grid. This value determines the size of that grid.
Remember window positions? (default: TRUE)
When this preference is TRUE, COGENT records the size and position of all windows associated with each model and uses this information to recreate the display state (i.e., exact window sizes and positions) of that model when it is re-opened.
Enable virtual window management? (default: FALSE)
When this preference is TRUE, COGENT allows box windows to be positioned on different virtual desktops. If the preference is FALSE, all windows are forced onto a single desktop.
Palette position: (default: Bottom of canvas)
This preference dictates the layout of the palette with respect to the main canvas on diagram, initial contents, and rules & condition definition windows. It has four values, corresponding to above, below, left and right. The default position is for the palette to be shown below the canvas.
Summarise box contents? (default: FALSE)
When this preference is TRUE, and a box of rules or data is opened, COGENT will initially show the contents in summarised form. When FALSE, the contents of such boxes are initially shown in full detail. In either case, a toggle button on appropriate canvases allows the user to switch between summarised and expanded form.
Edit on create? (default: FALSE)
If this preference is TRUE, whenever on item (either a box or a box element) is created, the appropriate editor will be automatically opened up ready to edit the new object.
Scale history? (default: TRUE)
If this preference is TRUE, the time-line display of project histories will use the creation time of models to scale the horizontal axis of the display. The horizontal distance between models on the display will then represent the difference in their creation times. If this preference is FALSE, models will be spaced equally on the history display.
Smooth scrolling of text elements? (default: TRUE)
When TRUE, COGENT performs smooth scrolling of Initial Contents windows. This looks nice, but is impracticable on slow machines. When FALSE, jump scrolling is performed.
Show scrollbars on canvases? (default: FALSE)
When this preference is TRUE, COGENT adds horizontal and vertical scrollbars to all box/arrow canvases. This is desirable when a model has lots of components, but is otherwise unnecessary.
Show toolbars on box windows? (default: TRUE)
When this preference is TRUE, COGENT adds toolbars for common commands to all box windows.
|COGENT Version 2.4 Help|