June 2002 Commit Log

Number of Commits:
89
Number of Active Developers:
4
foerster 2002-06-29 23:59 Rev.: 697

(WF) bugfix PS_FileBuffer :
forgot to flush buffer in reinit() and the destructor

52 lines of code changed in 6 files:

foerster 2002-06-29 22:13 Rev.: 696

(WF) Added support for buffered IO

572 lines of code changed in 10 files:

westram 2002-06-28 14:10 Rev.: 695

new demo db containing colored species

0 lines of code changed in 1 file:

westram 2002-06-28 14:00 Rev.: 694

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102 lines of code changed in 8 files:

westram 2002-06-28 14:00 Rev.: 693

* ARB/Makefile: - removed -lAW from LIBS
- new variable GUI_LIBS (use this instead of LIBS for GUI programs)

9 lines of code changed in 1 file:

westram 2002-06-28 13:58 Rev.: 692

* AWT_dtree.cxx: - reads correct color group regardless of global flag

97 lines of code changed in 1 file:

westram 2002-06-28 13:56 Rev.: 691

* aw_color_groups.hxx: - second parameter for AW_find_color_group (to ignore global color_group usage flag)

* aw_color_groups.hxx: - added global awars for color group usage and naming of color groups

22 lines of code changed in 1 file:

westram 2002-06-28 13:56 Rev.: 690

* AW_preset.cxx: - default colors for different programs

* AW_preset.cxx: - initialization for color group awars
- window to configure color group names
- toggle for color groups usage

191 lines of code changed in 1 file:

westram 2002-06-28 13:56 Rev.: 689

* phylo.hxx: - unused define GROUPED_SUM clashing with that from awt_tree.hxx

9 lines of code changed in 1 file:

westram 2002-06-28 13:55 Rev.: 688

* PARS_main.cxx: - color collapse menu

3 lines of code changed in 1 file:

westram 2002-06-28 13:54 Rev.: 687

* NT_extern.cxx: - 'Tree/Collapse/Group all except color' submenu
- uses NT_insert_mark_submenus

27 lines of code changed in 1 file:

westram 2002-06-28 13:53 Rev.: 686

EDIT4 displays color groups

93 lines of code changed in 4 files:

westram 2002-06-28 13:51 Rev.: 685

* AWT_tree_cb.cxx: - reads correct color group regardless of global flag

231 lines of code changed in 1 file:

westram 2002-06-28 13:51 Rev.: 684

warns if title is 'Standard help file form'

10 lines of code changed in 1 file:

westram 2002-06-28 13:50 Rev.: 683

* Makefile: - skips FORM.hlp

2 lines of code changed in 1 file:

westram 2002-06-28 13:50 Rev.: 682

* oldhelp/set_meny_fields.hlp: - corrected title
* oldhelp/props_www.hlp: - updated examples
* oldhelp/join_species.hlp: - corrected title
* oldhelp/faligner.hlp: - mentioned sth about island hopper
* oldhelp/islandhopping.hlp: - basic help for island hopper

* oldhelp/markcolor.hlp: - help for marking color groups
* oldhelp/tgroupcolor.hlp: - help for group tree according to color

129 lines of code changed in 10 files:

foerster 2002-06-28 13:38 Rev.: 681

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38 lines of code changed in 3 files:

yadhu 2002-06-28 12:57 Rev.: 680

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11 lines of code changed in 1 file:

yadhu 2002-06-28 10:20 Rev.: 679

OOPS!There WAS a bug in Secondary structure editor! Danke gott! das
war fixed.

150 lines of code changed in 3 files:

richter 2002-06-27 11:25 Rev.: 678

xsub generator revitalized for building the perl interface library

13 lines of code changed in 1 file:

richter 2002-06-27 11:19 Rev.: 677

modified perl interface library files 27.06.2002

14 lines of code changed in 1 file:

westram 2002-06-26 17:35 Rev.: 676

* AWT_dtree.cxx: - list marked/all display shows color_group information
- paints "marked"-boxes in list mode as well

42 lines of code changed in 1 file:

westram 2002-06-26 17:34 Rev.: 675

* aw_commn.hxx: - AW_MAP_GC calls AW_MAP_GC_tested (tests for illegal gc number)

11 lines of code changed in 1 file:

westram 2002-06-26 17:33 Rev.: 674

* AW_preset.cxx: - AW_set_color_group always created a new ARB_color entry
(now it checks if one is present already and modifies that value)
- changed some colors for color_groups
- if gc definition string contains '--' the gc is not shown in color properties

53 lines of code changed in 1 file:

westram 2002-06-26 17:33 Rev.: 673

some assertions testing if GC is defined

4 lines of code changed in 1 file:

westram 2002-06-26 17:32 Rev.: 672

* PARS_dtree.cxx: - arb_pars uses color_groups
- inserted some dummy gcs (reserving same gc number as probes do in ARB_NTREE)

12 lines of code changed in 1 file:

westram 2002-06-26 17:32 Rev.: 671

changed menu names

7 lines of code changed in 3 files:

westram 2002-06-26 17:31 Rev.: 670

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34 lines of code changed in 2 files:

westram 2002-06-26 17:30 Rev.: 669

* AWT_tree.cxx: - tree is drawn using species color groups
- paint vertical branches in color of horizontal sub branch

81 lines of code changed in 1 file:

westram 2002-06-26 17:30 Rev.: 668

* AWT_query_and_functions.cxx: - 'Writing to a non-STRING database field may lead to conversion problems'
answer was inverted (abort->continue, continue->abort)
- 'color group 0' -> 'no color group'

26 lines of code changed in 1 file:

westram 2002-06-26 17:30 Rev.: 667

* AWT_irstree.cxx: - paint vertical branches in color of horizontal sub branch

4 lines of code changed in 1 file:

foerster 2002-06-26 16:16 Rev.: 666

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341 lines of code changed in 6 files:

foerster 2002-06-23 23:34 Rev.: 665

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283 lines of code changed in 4 files:

westram 2002-06-21 19:55 Rev.: 664

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2 lines of code changed in 1 file:

westram 2002-06-21 19:49 Rev.: 663

some bugs in call to island hopper

19 lines of code changed in 3 files:

westram 2002-06-21 18:17 Rev.: 662

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19 lines of code changed in 4 files:

westram 2002-06-21 17:48 Rev.: 661

I hopefully found the basic bug causing the last characters in XFIG to disappear.
The same bug has as well caused many general display bugs in EDIT4.

94 lines of code changed in 3 files:

westram 2002-06-21 17:45 Rev.: 660

name change

82 lines of code changed in 3 files:

westram 2002-06-21 17:44 Rev.: 659

* ED4_no_class.cxx: - corrected values calculated in ED4_calc_terminal_extentions
(only ED4_G_SEQUENCES was used for calculation, but info terminals are
drawn with ED4_G_STANDARD)

15 lines of code changed in 1 file:

westram 2002-06-21 17:44 Rev.: 658

* ED4_root.cxx: - call to ref_terminals.init uses MAXINFOWIDTH (instead of MAXCHARWIDTH; which is used for sequences)

4 lines of code changed in 1 file:

yadhu 2002-06-21 12:00 Rev.: 657

Now, expansion and contraction of helices and loops is more
INTERACTIVE.

391 lines of code changed in 6 files:

yadhu 2002-06-21 11:58 Rev.: 656

modified zoom in and zoom out mode

135 lines of code changed in 1 file:

westram 2002-06-20 15:08 Rev.: 655

Mac OSX patches from Ben Hines

2927 lines of code changed in 183 files:

westram 2002-06-20 10:59 Rev.: 654

uses GB_GROUP_NAME_MAX for groupname buffer
replaced terminal/manager name buffer size by define NAME_BUFFERSIZE

39 lines of code changed in 1 file:

westram 2002-06-20 10:59 Rev.: 653

uses GB_GROUP_NAME_MAX for groupname buffer

1 lines of code changed in 1 file:

westram 2002-06-20 10:58 Rev.: 652

uses GBT_write_group_name

3 lines of code changed in 1 file:

westram 2002-06-20 10:43 Rev.: 651

added GB_GROUP_NAME_MAX and GBT_write_group_name which automatically
shortens groupnames which are too long

27 lines of code changed in 4 files:

foerster 2002-06-19 23:40 Rev.: 650

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427 lines of code changed in 5 files:

westram 2002-06-19 16:17 Rev.: 649

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5 lines of code changed in 2 files:

westram 2002-06-19 15:44 Rev.: 648

* aw_device.hxx: - definition of AUTO_FLUSH depends on value of DEBUG_GRAPHICS

1 lines of code changed in 1 file:

westram 2002-06-19 15:44 Rev.: 647

* arb_swap_rnastr.cxx: - gets -> fgets

6 lines of code changed in 1 file:

westram 2002-06-19 15:44 Rev.: 646

* arb_primer.cxx: - gets -> fgets

12 lines of code changed in 1 file:

westram 2002-06-19 15:44 Rev.: 645

* ARB/STAT/ST_quality.cxx: - end pos in call to st_ml_add_sequence_part_to_stat was 1 behind end pos

404 lines of code changed in 2 files:

westram 2002-06-19 15:43 Rev.: 644

* ARB/config.makefile.template: - added DEBUG_GRAPHICS=0

2 lines of code changed in 1 file:

westram 2002-06-19 15:43 Rev.: 643

* ARB/Makefile: - if DEBUG_GRAPHICS=1 -> add compiler flag -DDEBUG_GRAPHICS
- fixed DEBUG (may now be 1 or 0)
- cleaned help, added rebuild

60 lines of code changed in 1 file:

westram 2002-06-14 18:46 Rev.: 642

some bugfixes for import/export

10 lines of code changed in 5 files:

westram 2002-06-14 18:44 Rev.: 641

* adlang1.c: - added pretab() to ACI
- added crop() to ACI
- added 2 aliases left() and right() to ACI

76 lines of code changed in 1 file:

westram 2002-06-14 18:44 Rev.: 640

* AWTI_export.cxx: - bugfix for recursive export formats
- write new stringname to filename-input if suffix was auto-appended

28 lines of code changed in 1 file:

westram 2002-06-14 18:44 Rev.: 639

some small bug fixes and DEBUG prints (ae2.eft didn't work)

246 lines of code changed in 3 files:

westram 2002-06-14 18:43 Rev.: 638

* oldhelp/commands.hlp: - added help for pretab()
- help for left/right/crop
- added forgotten help for upper/lower/caps

11 lines of code changed in 1 file:

westram 2002-06-14 18:42 Rev.: 637

* inline.h: - header which general purpose inlines

38 lines of code changed in 1 file:

westram 2002-06-14 14:24 Rev.: 636

- added awtc_fgets (like fgets but working with MAC file format)
- changed all occurances of fgets to awtc_fgets

25 lines of code changed in 1 file:

westram 2002-06-14 12:45 Rev.: 635

fixed needed for XML tree export

39 lines of code changed in 9 files:

westram 2002-06-14 12:45 Rev.: 634

* AWT_imp_exp.cxx: - AWT_export_XML_tree/awt_export_tree_node_print_xml got option to skip folded groups

25 lines of code changed in 1 file:

westram 2002-06-14 12:44 Rev.: 633

* AWTI_import.cxx: - selection box now defaults to directory arb was called from

3 lines of code changed in 1 file:

westram 2002-06-13 20:10 Rev.: 632

button for sec.struct-usage

41 lines of code changed in 1 file:

westram 2002-06-13 20:09 Rev.: 631

- bugfixes for interpreting secondary structures

3 lines of code changed in 1 file:

westram 2002-06-13 20:08 Rev.: 630

toggle for secondary structure usage (island hopper)

8 lines of code changed in 1 file:

yadhu 2002-06-13 17:04 Rev.: 629

fixed move species bug

2 lines of code changed in 1 file:

westram 2002-06-13 13:52 Rev.: 628

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65 lines of code changed in 1 file:

westram 2002-06-13 11:53 Rev.: 627

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174 lines of code changed in 5 files:

westram 2002-06-13 11:53 Rev.: 626

added Counted<T> counter for debugging

13 lines of code changed in 1 file:

foerster 2002-06-13 09:36 Rev.: 625

new files from wolfram

593 lines of code changed in 5 files:

westram 2002-06-07 15:52 Rev.: 624

100% bootstraps only hidden at leafs

11 lines of code changed in 3 files:

westram 2002-06-07 14:28 Rev.: 623

new version from gangolf

22 lines of code changed in 5 files:

westram 2002-06-07 14:16 Rev.: 622

fixed search tool

15 lines of code changed in 1 file:

westram 2002-06-07 14:15 Rev.: 621

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39 lines of code changed in 2 files:

foerster 2002-06-04 13:49 Rev.: 620

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6 lines of code changed in 2 files:

foerster 2002-06-04 13:41 Rev.: 619

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641 lines of code changed in 4 files:

westram 2002-06-04 08:06 Rev.: 618

* arb_dnarates.c: - warnings fixed
- one internal node was not initialized
(no of internal nodes = tips*2-1-tips)
- more comprehensive error if last species in tree is unmarked
- fixed broken _CATEGORIES entry (if no categories were defined)

1019 lines of code changed in 1 file:

westram 2002-06-01 15:24 Rev.: 617

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123 lines of code changed in 4 files:

westram 2002-06-01 15:23 Rev.: 616

* SEC_main.cxx: - fixed crashes if ECOLI is missing

6 lines of code changed in 1 file:

westram 2002-06-01 13:22 Rev.: 615

new format

14 lines of code changed in 1 file:

westram 2002-06-01 13:21 Rev.: 614

* xml.hxx: - added XML_Document::add_attribute

5 lines of code changed in 1 file:

westram 2002-06-01 13:21 Rev.: 613

* ad_trees.cxx: - updates filter after opening export tree window
- filename for export tree automatically uses correct filename extension

22 lines of code changed in 1 file:

westram 2002-06-01 13:21 Rev.: 612

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40 lines of code changed in 6 files:

westram 2002-06-01 13:20 Rev.: 611

* awt_dtree.hxx: - create_group returns AW_BOOL (AW_TRUE if group was created)

1 lines of code changed in 1 file:

westram 2002-06-01 13:20 Rev.: 610

* AWT_imp_exp.cxx: - modified XML tree export according to remarks from Derek

45 lines of code changed in 1 file:

westram 2002-06-01 13:20 Rev.: 609

* AWT_dtree.cxx: - fixed bug when aborting to create a group

8 lines of code changed in 1 file:

May 2002 »

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