W2H: History (old 1)

• GCG version 9 is supported now (of course, together with the previous GCG versions). Not fully but reasonable fully:
  • whole new syntax of configuration files is understood
  • some new syntax is used
  • GCG html help files can be invoked directly from W2H
  However, it has also a disadvantage. A distributed tiny program seqinfo (for retrieving sequence attributes) cannot be used without having GCG source licence.
• Very nasty bug (or misunderstanding about how GCG uses shared memory) in the Intranet mode was fixed. Now there is no problem to run W2H simultaneously for many users. All of them are sharing the same memory blocks. Remember, this is only for the Intranet mode, there was no such a problem outside the Intranet mode.
• The program seqinfo is now more clever, it can better handle multiple-sequence files. With a new seqinfo only files with valid GCG file types can be added to a working list.

• Uploading of client files were improved and made stable. Also Copy and Paste feature was added there. Newly created file with uploaded data can be added automatically into your working list.
• A search set, once built, is remembered till next usage. It is a tiny change.
• Slightly changed look and feel of the Sequence selector. Buttons are now closer to the list they work with. Also better scrolling by the working list.
• We have considered once more where to take data files from when no full path is given. Hopefully, this is the last change of this behaviour (but suggestions are welcome):
  • Fetch utility takes GCG data files (so you can easily fetch files like enzyme.dat to your working directory).
  • AddSeq button prefers files from the current working directory (because mostly you want to add to working list your own files).
• The button Add specified in AddSeq window invokes pattern-matching on the specified sequence before adding to a working list. So it behaves in the similar way as the button Show matching.
• Various other bugs fixed

  * Broken pipe error message was fixed. This message appeared in the error log file of the httpd server, so not much harm, but for Netscape Enterprise server it was much more serious.

  * The killing processes from the result window was fixed. Now you can kill the time-consuming programs that were started by mistake.

  * It was necessary to stop to check if all required parameters are present because it caused troubles when the parameters were linked with dependency rules. The checking will be renewed when the dependency rules will be implemented. Sorry for that...

  * In some cases, adding a sequence to a working list forgot to put a newline character at the end of the entry. Stupid, fixed.

  * Function Upload fixed in Intranet mode.

• Changes relevant to the installation and configuration:
  • The killing processes was fixed but it brings a possible (I hope that it will not happen) portability problem. A new utility util.setpgrp was added to test it on your system.
  • W2H can run now also with the Netscape Enterprise server (let me know if not - I can check it only partly here). It required to change one configuration variable in Cfg.pl file: $SERVER_CONF was replaced with $MIMETYPES pointing directly to the mime.types file.
  • In the Intranet mode, you can enable access to the remote printers using a new variable $PRINT_ALLOWED.

• An independent program seqinfo (from Wolfgang Roemer) was added. It makes possible to add automatically or on-demand the sequence attributes (like Begin and End) from databases into your working lists.
• An incompatibility with previous versions:
  The sequence specifications typed in fetch utility and in sequence selector window which are not logical names and which have not path specified, are now searched for in the current working directory. That's slightly different from the previous versions where you had to specify ./ if you wanted to take them from your working directory.
• Various other bugs fixed

  * starting Blast was corrected, also the proper list of databases for Blast is now offered (thanks to comments from Volker Winkelmann)

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• Changes relevant to the installation and configuration:
  • Some new configuration variables were added to Cfg.pl file ($SEQINFO, $SEQINFO_AUTO, $BLAST_REMOTE, $BLAST_LOCAL, $BLAST_SITE).

• A completly new mode of usage was introduced - the Intranet mode. The mode allows to use W2H behind the company's firewall where a GCG server computer has no UNIX users accounts established. The mode can be useful also for demos during conferences or during hands-on workshops. Details are described in a separate document.
• A copy and paste mechanism was added for creating working lists.
• A logical name MyData is consulted when asking for a data file in the sequence selector or pattern chooser. Remind that you can set the logical names on-the-fly in the Setup | Session window.
• An additional validation into the Change attributes window was added (reverse and circular attributes are not modified for protein sequences).
• Finally a button Telnet was added into the Main Window. It has no special support (like automatically start of a terminal oriented GCG session), and has been added on demand to help UNIX oriented people.
• Various other bugs fixed

  * There was a nasty bug avoiding to run any program from W2H interface when the following combination happened: Apache http server and using W2H interface by the same user as the one defined in the User directive. Fortunately, fixed.

  * A not found help file was not redirected properly to the list of all available application help files. Fixed.

  * Fetch utility now fetches all documentation independently how many lines was defined in the Setup window (that's how a terminal oriented Fetch works).

• Changes relevant to the installation and configuration:
  • Two new checking utilities were added (util.checkcfg and w2h.checkcfg). They both help to recognize if you have badly configurated your Cfg.pl file.
  • Notes for users of Netscape Enterprise server can be found in the installation manual.
  • Slightly more talkative messages by installing help files.

• For the record: The further developement of W2H interface became a collaborative project between DKFZ (German Cancer Research Center, Heidelberg, Germany) and EMBL-EBI (European Bioinformatics Institute, Hinxton, UK). The main contact person remains the same (Martin Senger) but now with a new e-mail address senger@EBI.ac.uk.
• The graphical viewer uses now automatically a default set of colors.
• Running an application (and saving parameters as well) is now better indicated by a small message window which gives also a direct button to the result window.
• An application window is now by default automatically closed after the application was started. This can be changed in Setup|Globals window.
• Some explanatory texts added into various windows (e.g. loading an application, or changing attributes of a working list).
• It is now possible to use ftp to upload the client files directly from W2H interface (buttons Upload | Ftp).
• The uploading client sequences can be automatically converted into GCG format.
• A list of available databases was added to Search Set buttons in Application Windows. It is helpful in (often) cases when a user wishes to specify a whole database as the command line parameter.
• There was a very unpleasant bug in specifying a search set. The W2H was very keen to add always a @ character to a search set on the command line. It was fixed and in the same time the function of the button Add Specified (in the Search Set Builder window) was changed (now it only copies what specified without trying to be too smart).
• Removing a working list: When you remove all items from a working list then the working list itself is removed as well.
• A new working list was always really a new one. It was a bug because the New button in the main window should make access also to the existing working lists (in the not-current directories). Fixed.
• The limits of some range parameters are dependent on values of other parameters. Unfortunately, W2H interface cannot (yet) change the limits dynamically according to the actual values of the others. It was not fixed but now W2H recognizes that the limits are dependent and ignore them. It was a serious bug, because you could not even enter some values.
• Various other bugs fixed

  * Application window: Better formatting of the application explanatory text.

  * Setup graphical devices: Even the last user defined device is possible to remove now.

  * Validation of entered numbers is probably better now.

  * Default values which are dependent on the sequence ranges are now evaluated properly (e.g. an expression like eval (MIN (6, (SQ1.End-SQ1.Begin+1)/2)) should work now).

  * A sporadic error "Word too long" should not occur anymore.

• Changes relevant to the installation and configuration:
  • The $APPMENU variable was changed to be able to merge two or more application menu files together (GCG and EGCG for example).
  • A new $DISABLED_APPS variable was introduced to be able to avoid to start the applications whose config files are not correctly parsed.
  • More configuration files can be parsed now without the syntax errors (but program lookup is still not parsable).
  • Better configuration for generating help files (see variable $START_DOC).
  • The variable $SERVER_ROOT was renamed to $SERVER_CONF because it better expresses its contents.

See also changes mentioned in Version 1.08beta below because the last "official" version put on ftp was 1.07beta and the main changes (for ecample the GIF output) happened from 1.07b to 1.08b.

• Only useful graphical devices are offered in the Setup Window (the terminal oriented devices are ignored).
• Logical names are partially supported (not in file browsers - where is easy to implement it but I am not sure if it is reasonable enough because logical naming requires to re-start current GCG session - let us wait for users reactions).
• Various bugs fixed

  Wrong command-line menu-arguments were generated if they have value zero (e.g. by Blimps).

  The help system for the applications was completely re-written to work with standard GCG distribution (surprisingly it was not true before).

• The conversion of graphical outputs into the GIF format was added. It is done by converting an HP-GL printer language. The result is a graphical viewer displaying directly in the Navigator and allowing zooming, rotating, changing colors and line thicknesses interactively.
• A directory browser (file chooser) was added. That also means that the pages using the directory browser were slightly changed.
• A special parameter -wwwid was added to the command line of each application. This can be used for accounting purposes.
• The button New in the main window creates a new list file even if it is empty. Previously a new file was created only after being populated by a description or by some sequences. It seemed to be confusing.
• Also, the sequence selector is automatically invoked when a New working list is wanted. It seems to be a good default action.
• The Help button was added to some pages (e.g. to Sequence Selector).
• A default masking for directory listings is (nearly) the same as in the UNIX ls command. That means that files starting with a dot are not shown. Use a file mask '.*' to see all files.
• A View button was added to the main window to have quicker access to the file/directoy viewer. Functionality is the same as a corresponding button in the Results window.
• Various bugs fixed

  Directory listing: files with null length are displayed with a zero in the size column

  Directory listing: file names containing "<" or ">" characters are displayed properly now

  When no working list is specified (neither from the previous session, nor from WPI history file), then a default list is offered with a name username_default.list

  Sequence selector: button List File works properly even when using after button Show matching. Previously, it always displayed the last used specification from the left frame.

• The uploading client files added.
• The enzyme/pattern chooser added.
• Search set button for blast added.
• The Fetch utility was added making possible viewing and storing the selected sequences.
• Changing attributes of items in the working list is possible now.
• The scrollbars were changed where two of them interacted badly together. It was in the case where a long list was in a frame. There were scrollbars by the frame AND by the list. Now it is hopefully more user friendly.
• More information displayed in the Status frame (under Setup button).
• Various bugs fixed

  Some help pages could not be closed properly.

  In some cases a new working list was created without 'two-dots' header. It does not mind because W2H does not insist on this separator but it should be there for re-usability also in WPI. Fixed.

  Viewing of list files wrongly marked the 2-dots separator as a reference to the parent directory. Fixed.

  The name of a search set, when goes into the command line, gets '@' at the beginning. I hope that it is correct behaviour, but...

  Results window: Using 'Refresh' button after using 'View file' button, you got often a strange JavaScript error message. Fixed.

• Viewing files was completely rewritten resulting with quicker access. But more important: now a user can view her/his files even if her/his home directory is readable only for her/him. Also the authentication dialog appears only once.
• The functions for maintaining the working lists were implemented. Now it is possible to add/remove sequences, or save only selected subset into a new working list. The sequence selection is supported by a list of available databases.
• A new global option was added allowing to define the file-name masks for working lists. Default is still *.list as before but now you can set to get automatically more types of files into your list of working lists (e.g. *.list *.fil *.seq).
• The working lists do not need more to have a header separator (two dots). If there is no such a separator, the whole file is considered as a sequence list.
• The help about an application is now accessible by a special link named Help on... in the application window.
• The help references (links to the other applications) in the application helps pages are now created only in some sections (Description, Related programs).
• The terminal oriented application are still not yet supported but are properly recognized and a simple telnet access is offered directly from the WWW page.
• Program documentation for developers was writen and make available.
• Various bugs fixed

  The error LOGNAME/USER - undefined variable does not occur more

  The history file is properly updated by exit (that means that the next session knows about setting from the previous one).

  Some Close buttons produced a JavaScript syntax error with a new version of Netscape (Atlas). Fixed.

  Hitting Enter after specifying a display variable (in graphical devices) produced an error message. Fixed.

  Some simple working lists did not work (because of lacking a space after a sequence name). Fixed.

  A direct typed sequence in the main window is now correctly propagated into an application window.

• The original GCG programs are marked with the GCG logo, the EGCG programs with the EGCG logo
• More configuration files distributed for a easier configuration
• Various bugs fixed

  Optional parameters are restored properly

  Graphical output works also for programs without -PLOT option

  Some bugs for MS Windows platform disappeared

Multi-lines prompts (e.g. Print or SaveAs) displayed only partly

Buttons have no colors, are not proportional