May 2004 Commit Log

Number of Commits:
111
Number of Active Developers:
2
westram 2004-05-27 17:29 Rev.: 2801

*** empty log message ***

15 lines of code changed in 1 file:

westram 2004-05-27 16:46 Rev.: 2800

cronjob for probe-library

0 lines of code changed in 1 file:

westram 2004-05-27 15:59 Rev.: 2799

depends updated

1 lines of code changed in 1 file:

westram 2004-05-27 15:59 Rev.: 2798

remade

1 lines of code changed in 1 file:

westram 2004-05-27 15:59 Rev.: 2797

changed extern decl for aisc_add_destroy_callback

11 lines of code changed in 1 file:

westram 2004-05-27 15:58 Rev.: 2796

make proto promotes extern "C"

1 lines of code changed in 1 file:

westram 2004-05-26 16:43 Rev.: 2795

- debugging messages
- reduced sleep values when waiting for PT- or NAME-server
- added arb_wait_for_server()
- removed unused variable servercntrl_started

44 lines of code changed in 1 file:

westram 2004-05-26 16:43 Rev.: 2794

- prototype fix
- removed servercntrl_started

1 lines of code changed in 1 file:

westram 2004-05-26 16:42 Rev.: 2793

- crashed when headline was selected in probe list (on open)
- added assert for calls to strtok
- added class ProbeMatchParser
- in the post-match-region, the SAI was displayed with the
wrong offset, if the match contained gaps in sequence (fixed).
handles special case when post-match-region is empty.
- in the pre-match-region, the SAI was displayed at the wrong
offset when that region contained less than 9 bases
- changed internal encoding of SAI color translation (now uses '0'-'9' for
configured characters and '0'-1 for all others)
- changed x/y stepping (it has used ascent instead of width).
- painting is aligned (display failed completely if probe font size was smaller
than foreground font size, now it always uses the max. size of BOTH used fonts)
- added paintProbeInfo() to paint probe string (properly aligned to x/y)
- draw vertical line showing match region
- display SAI content for all positions (not only configured ones)

276 lines of code changed in 1 file:

westram 2004-05-26 16:42 Rev.: 2792

- added sai_assert()
- store several AWARs in properties
- removed unused AWAR
- better protection for saiProbeData

43 lines of code changed in 1 file:

westram 2004-05-26 16:42 Rev.: 2791

- prototype change

1 lines of code changed in 1 file:

westram 2004-05-26 16:42 Rev.: 2790

- show 'Gene server' only if its a genome db
- fix call to arb_start_server (sleep as well)
- changed data transfer to SAI visualisation
- crashed fix (when using Auto-Match from probe design w/o opening probe match before)
- probe match event refreshes ARB_NTREE-window
- probe/SAI refreshed when matches change (changed location of callback)
- added MATCH-button to probe design result window

57 lines of code changed in 1 file:

westram 2004-05-26 16:42 Rev.: 2789

- added parameter to PT server admin

1 lines of code changed in 1 file:

westram 2004-05-26 16:42 Rev.: 2788

*** empty log message ***

11 lines of code changed in 1 file:

westram 2004-05-26 16:41 Rev.: 2787

- added match button

2 lines of code changed in 1 file:

westram 2004-05-26 13:24 Rev.: 2786

remade

38 lines of code changed in 4 files:

westram 2004-05-26 13:23 Rev.: 2785

- const fixes

3 lines of code changed in 1 file:

westram 2004-05-26 13:23 Rev.: 2784

cosmetics

1 lines of code changed in 1 file:

westram 2004-05-26 13:22 Rev.: 2783

- promotion added

4 lines of code changed in 2 files:

westram 2004-05-26 13:19 Rev.: 2782

- to update prototypes (for manual use)

28 lines of code changed in 1 file:

westram 2004-05-26 13:19 Rev.: 2781

depends

0 lines of code changed in 1 file:

westram 2004-05-26 13:19 Rev.: 2780

- optional promotion of code from .c -> .h

148 lines of code changed in 1 file:

westram 2004-05-26 13:18 Rev.: 2779

- removed (not necessary)

0 lines of code changed in 1 file:

westram 2004-05-24 17:11 Rev.: 2778

- gene-pt-server deactivated until it's fixed

6 lines of code changed in 1 file:

westram 2004-05-24 17:11 Rev.: 2777

- removed 'Sequence quality' and 'chimere' from release version
- hotkey fix

20 lines of code changed in 1 file:

westram 2004-05-24 17:10 Rev.: 2776

- hotkey fix

1 lines of code changed in 1 file:

westram 2004-05-24 17:10 Rev.: 2775

- removed warning about undefined ARB_WORKDIR etc.
- filter inserted directory links against duplicates

40 lines of code changed in 1 file:

westram 2004-05-24 14:07 Rev.: 2774

- separated Phylogeny menu into several sub-menus
- added 'Modify branches' submenu
- order changes to "Tree" menu
- renamed some help files

35 lines of code changed in 1 file:

westram 2004-05-24 14:07 Rev.: 2773

- spelling

24 lines of code changed in 2 files:

westram 2004-05-24 14:07 Rev.: 2772

- updated

4 lines of code changed in 1 file:

westram 2004-05-24 14:07 Rev.: 2771

- added AP_tree::reset_branchlengths, bootstrap2branchlen, branchlen2bootstrap, bootstrap2branchlen

12 lines of code changed in 1 file:

westram 2004-05-24 14:06 Rev.: 2770

- added NT_reset_branchlengths + NT_move_boot_branch + NT_scale_tree

63 lines of code changed in 1 file:

westram 2004-05-24 14:06 Rev.: 2769

- added AP_tree::reset_branchlengths, scale_branchlengths, branchlen2bootstrap, bootstrap2branchlen

47 lines of code changed in 1 file:

westram 2004-05-24 14:06 Rev.: 2768

- added new parameters needed for rate variation

25 lines of code changed in 1 file:

westram 2004-05-24 14:06 Rev.: 2767

- resets branchlengths to 0.1 if values were interpreted as bootstrap values

3 lines of code changed in 1 file:

westram 2004-05-24 14:06 Rev.: 2766

- added lead tester :)

1 lines of code changed in 1 file:

westram 2004-05-24 14:01 Rev.: 2765

- help for 'Remove bootstraps'

23 lines of code changed in 1 file:

westram 2004-05-24 14:00 Rev.: 2764

- help for 'Scale branchlengths'

27 lines of code changed in 1 file:

westram 2004-05-24 14:00 Rev.: 2763

- help for 'Reset branchlengths'

23 lines of code changed in 1 file:

westram 2004-05-24 14:00 Rev.: 2762

- help for 'Justify branchlengths'

26 lines of code changed in 1 file:

westram 2004-05-24 14:00 Rev.: 2761

- help for bootstrap-branchlength-transfer

28 lines of code changed in 1 file:

meierh 2004-05-24 13:29 Rev.: 2760

genome importer "embl" imports "order"

1 lines of code changed in 1 file:

westram 2004-05-24 13:25 Rev.: 2759

- sorted phylogeny menu into several sub-menus

11 lines of code changed in 1 file:

westram 2004-05-24 13:24 Rev.: 2758

- added new parameters needed for rate variation

18 lines of code changed in 1 file:

westram 2004-05-24 13:24 Rev.: 2757

- disabled some options because they cause distance programs to crash

3 lines of code changed in 1 file:

westram 2004-05-24 13:24 Rev.: 2756

- spelling

2 lines of code changed in 1 file:

westram 2004-05-24 12:32 Rev.: 2755

- CVS version was broken (filesystem error)

48 lines of code changed in 1 file:

westram 2004-05-19 15:40 Rev.: 2754

new icons

6 lines of code changed in 2 files:

westram 2004-05-19 15:40 Rev.: 2753

*** empty log message ***

7 lines of code changed in 1 file:

westram 2004-05-19 15:40 Rev.: 2752

- layout fixed
- new button markers

31 lines of code changed in 1 file:

westram 2004-05-19 15:39 Rev.: 2751

- defined write_...- and rewrite_...-functions as macros

29 lines of code changed in 1 file:

westram 2004-05-19 15:38 Rev.: 2750

- added rewrite versions to class AW_awar (rewrite = write+touch)

8 lines of code changed in 1 file:

westram 2004-05-19 15:36 Rev.: 2749

- checks whether target is uptodate (used to avoid unnecessary linking)

82 lines of code changed in 1 file:

westram 2004-05-19 15:36 Rev.: 2748

- link applications only if necessary

28 lines of code changed in 1 file:

westram 2004-05-19 15:35 Rev.: 2747

- fixed tree admin behavior (need some further implementation)

75 lines of code changed in 1 file:

westram 2004-05-19 15:34 Rev.: 2746

- Link NTREE.a only if necessary

7 lines of code changed in 1 file:

westram 2004-05-19 15:33 Rev.: 2745

- added symbolic browser commands
- added "goto_valid_node"
- works correct when path to non-container specified
- added link to parent container
- added history
- when switching database, previously used path is restored
- added sorting

442 lines of code changed in 1 file:

westram 2004-05-19 15:31 Rev.: 2744

- avoid linking of applications if not necessary

102 lines of code changed in 1 file:

westram 2004-05-13 13:10 Rev.: 2743

dependencies updated

9 lines of code changed in 5 files:

westram 2004-05-13 13:07 Rev.: 2742

- simply ignores all arguments

4 lines of code changed in 1 file:

westram 2004-05-13 13:06 Rev.: 2741

- call GB_install_error_handler
- made many functions static
- removed debug printout

49 lines of code changed in 1 file:

westram 2004-05-13 13:06 Rev.: 2740

- renamed some GB_getenv...() functions
- show system call

3 lines of code changed in 1 file:

westram 2004-05-13 13:05 Rev.: 2739

- spelling

2 lines of code changed in 2 files:

westram 2004-05-13 13:05 Rev.: 2738

- automatically announce property database to browser
- spelling

4 lines of code changed in 1 file:

westram 2004-05-13 13:04 Rev.: 2737

- removed create_help_entry + macro_message_cb

2 lines of code changed in 1 file:

westram 2004-05-13 13:03 Rev.: 2736

- menu item for db browser
- awars for db browser
- cleaned up save windows

14 lines of code changed in 1 file:

westram 2004-05-13 13:02 Rev.: 2735

- cleanup

0 lines of code changed in 1 file:

westram 2004-05-13 13:02 Rev.: 2734

- fixed writing order of AWAR_DB_PATH and AWAR_DB"directory"
- announce main DB to browser

23 lines of code changed in 1 file:

westram 2004-05-13 12:59 Rev.: 2733

redesigned

32 lines of code changed in 1 file:

westram 2004-05-13 12:59 Rev.: 2732

window for db browser

27 lines of code changed in 1 file:

westram 2004-05-13 12:58 Rev.: 2731

- changed user name detection

25 lines of code changed in 8 files:

westram 2004-05-13 12:55 Rev.: 2730

- added REARRANGE parameter to comment

1 lines of code changed in 1 file:

westram 2004-05-13 12:55 Rev.: 2729

- warning fix

9 lines of code changed in 1 file:

westram 2004-05-13 12:54 Rev.: 2728

- renamed some GB_getenv...() functions
- show system call

2 lines of code changed in 1 file:

westram 2004-05-13 12:54 Rev.: 2727

- renamed some GB_getenv...() functions

6 lines of code changed in 1 file:

westram 2004-05-13 12:54 Rev.: 2726

- added database browser interface
- added AWT_is_link()

7 lines of code changed in 1 file:

westram 2004-05-13 12:53 Rev.: 2725

- added AWT_db_browser.o

9 lines of code changed in 1 file:

westram 2004-05-13 12:53 Rev.: 2724

cleanup

0 lines of code changed in 1 file:

westram 2004-05-13 12:52 Rev.: 2723

- replaced stat by lstat (stat cannot detect symbolic links)
- added special file browser entries: 'hide-subdirs' and 'sort'
- fixed several bugs in file browser (had problems with links)

134 lines of code changed in 1 file:

westram 2004-05-13 12:51 Rev.: 2722

- database browser

502 lines of code changed in 1 file:

westram 2004-05-13 12:50 Rev.: 2721

*** empty log message ***

7 lines of code changed in 2 files:

westram 2004-05-13 12:49 Rev.: 2720

- rewrote GB_internal_error (uses gb_error_handler)

31 lines of code changed in 1 file:

westram 2004-05-13 12:49 Rev.: 2719

- renamed some GB_getenv...() functions
- added GB_is_executablefile()
- added GB_find_executable()
- do some checks in GB_getenv..() functions (check whether is executable or is directory)
- print info at system()-call with GB_information()
- treats empty environment variables as "not defined"

206 lines of code changed in 1 file:

westram 2004-05-07 15:51 Rev.: 2718

- updated

14 lines of code changed in 1 file:

westram 2004-05-06 16:54 Rev.: 2717

- note

1 lines of code changed in 1 file:

westram 2004-05-06 16:54 Rev.: 2716

- uses AWAR_ERROR_MESSAGES
- increased scrollback size in message window from 50 to 500
- splitted aw_insert_message_in_tmp_message into 2 functions
- skip refresh of list while receiving new messages
- prints clock instead of counter in front of messages
- several functions made static
- cleanups
- removed write_with_success_or_exit

103 lines of code changed in 1 file:

westram 2004-05-06 16:38 Rev.: 2715

- prints error message if wrong argument etc. to aw_message
- changed position where several messages are sent

11 lines of code changed in 1 file:

westram 2004-05-06 16:36 Rev.: 2714

- if \n is used in shell script it is unencoded
now arb_message scans and replaces these \n's

16 lines of code changed in 1 file:

westram 2004-05-06 16:35 Rev.: 2713

- added info message about fixed protml crash

3 lines of code changed in 1 file:

westram 2004-05-06 16:34 Rev.: 2712

- redefined ARBMACROHOME to ~/.arb_prop/arb_macros
- added ARBMACRO (defaults to $ARBHOME/lib/macros)
- always shows used $ARBHOME

22 lines of code changed in 1 file:

westram 2004-05-06 16:31 Rev.: 2711

- DOCU change
- commented sections
- formatted interface
- commented-out functions: MATCHLIST/INFO_HEADER und MATCHLIST/INFO

181 lines of code changed in 1 file:

westram 2004-05-06 16:31 Rev.: 2710

updated

0 lines of code changed in 1 file:

westram 2004-05-06 16:30 Rev.: 2709

- GBS_strclose changed
- cleanup

8 lines of code changed in 1 file:

westram 2004-05-06 16:30 Rev.: 2708

- cosmetics

1 lines of code changed in 1 file:

westram 2004-05-06 16:30 Rev.: 2707

- replaced get_match_info and get_match_hinfo by formatting versions
- detect_format_props() scans column widths for output
- added cat_...() for easy formatting
- GBS_strclose changed

182 lines of code changed in 1 file:

westram 2004-05-06 16:25 Rev.: 2706

- hotkey fix
- uses AWAR_ERROR_MESSAGES
- fixed message handling in NT_show_message

20 lines of code changed in 1 file:

westram 2004-05-06 16:06 Rev.: 2705

- fixed PRG=name in tree comment (contained 'xterm -e')

4 lines of code changed in 1 file:

westram 2004-05-06 16:05 Rev.: 2704

- fixed a typo causing failure when using amino acids

1 lines of code changed in 1 file:

westram 2004-05-06 16:05 Rev.: 2703

- call $DISPLAY_FUNC only if treefile exists

1 lines of code changed in 1 file:

westram 2004-05-06 16:04 Rev.: 2702

- if 'star decomposition' and 'rearrangement' were used together
protml crashed, because of undefined vectors and matrixes

12 lines of code changed in 1 file:

westram 2004-05-06 16:03 Rev.: 2701

- assertion macro

24 lines of code changed in 1 file:

westram 2004-05-06 16:03 Rev.: 2700

- added assertions (avoiding to create empty ?vector, ?matrix and ?cube)

46 lines of code changed in 1 file:

westram 2004-05-06 16:02 Rev.: 2699

- beautified
- added 'pwdx' to adawcbstruct

74 lines of code changed in 1 file:

westram 2004-05-06 16:01 Rev.: 2698

- use additional default directory (ARBMACRO) in macro selection box

1 lines of code changed in 1 file:

westram 2004-05-06 16:01 Rev.: 2697

- awt_create_selection_box_cb: tweaked soft links
- added PT_SERVER_HOME to awt_get_base_directory
- awt_create_selection_box allows multiple directories in parameter pwd

75 lines of code changed in 1 file:

westram 2004-05-06 15:57 Rev.: 2696

GBS_strclose changed

51 lines of code changed in 33 files:

westram 2004-05-06 15:50 Rev.: 2695

- GBT_message() never appends to AWAR "tmp/message", always overwrites.
Needed because messages were duplicated.
- uses AWAR_ERROR_MESSAGES
- GBT_message checks for NULL msg
- GBS_strclose changed

18 lines of code changed in 1 file:

westram 2004-05-06 15:49 Rev.: 2694

- removed (ignored) parameter 'optimize' from GBS_strclose
- GBS_fread_string changed

12 lines of code changed in 1 file:

westram 2004-05-06 15:49 Rev.: 2693

- added support for 'ARBMACRO'
- GBS_strclose changed

14 lines of code changed in 1 file:

westram 2004-05-06 15:49 Rev.: 2692

updated

2 lines of code changed in 1 file:

westram 2004-05-06 15:48 Rev.: 2691

- GBS_strclose changed

11 lines of code changed in 4 files:

April 2004 »

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