February 2008 Commit Log

Number of Commits:
113
Number of Active Developers:
4
westram 2008-02-29 19:41 Rev.: 5156

- indented

5653 lines of code changed in 17 files:

westram 2008-02-29 19:18 Rev.: 5155

- removed register keywords

936 lines of code changed in 65 files:

westram 2008-02-29 17:36 Rev.: 5154

- updated

1 lines of code changed in 1 file:

westram 2008-02-29 17:36 Rev.: 5153

- fake define -DARB_OPENGL for make depends.
Otherwise dependencies change depending on current build.
Bad, cause dependencies are stored in CVS.

1 lines of code changed in 1 file:

westram 2008-02-29 17:26 Rev.: 5152

- gb_main -> GLOBAL_gb_main

18 lines of code changed in 1 file:

westram 2008-02-29 17:26 Rev.: 5151

- added GB_SETSMDMALLOC_UNINITIALIZED to allocate w/o initializing.
used to get rid of some warnings in ARBDB

39 lines of code changed in 1 file:

westram 2008-02-29 17:26 Rev.: 5150

- use GB_SETSMDMALLOC_UNINITIALIZED
- removed register-modifiers (gcc knows better)

37 lines of code changed in 1 file:

westram 2008-02-29 17:26 Rev.: 5149

- removed marker line from 'clean'

0 lines of code changed in 1 file:

westram 2008-02-29 16:56 Rev.: 5148

- replaced global gb_main by GLOBAL_gb_main

1228 lines of code changed in 79 files:

westram 2008-02-29 16:53 Rev.: 5147

- remove parameter names and AWUSE()

4 lines of code changed in 1 file:

westram 2008-02-29 16:52 Rev.: 5146

- reverted to revision 1.26 (reverts part of [5141])

1 lines of code changed in 1 file:

westram 2008-02-29 16:52 Rev.: 5145

- reverted to revision 1.10 (reverts part of [5141])

2 lines of code changed in 1 file:

westram 2008-02-29 16:51 Rev.: 5144

- again changed variables names (renamed to ugly tmp_... by joerg)

134 lines of code changed in 16 files:

westram 2008-02-29 13:52 Rev.: 5143

- added several internal dependencies
- wrapped output of %.dummy through logfile (for make -j; experimental)

54 lines of code changed in 1 file:

westram 2008-02-29 13:52 Rev.: 5142

- added -f to ln (to avoid errors)
- remove links directly from find (for make -j)

4 lines of code changed in 1 file:

boehnel 2008-02-28 22:39 Rev.: 5141

removing some compiler warnings

(changes to ED4_cursor.cxx reverted by [5146], changes to AWTC_constructSequence.cxx reverted by [5145])

195 lines of code changed in 23 files:

boehnel 2008-02-28 19:34 Rev.: 5140

fixing compiler warning

1 lines of code changed in 1 file:

boehnel 2008-02-28 19:20 Rev.: 5139

removed some compiler warnings

57 lines of code changed in 7 files:

boehnel 2008-02-28 19:14 Rev.: 5138

"%i -> %zu"

2 lines of code changed in 1 file:

boehnel 2008-02-28 19:13 Rev.: 5137

removed some compiler warnings...

33 lines of code changed in 5 files:

westram 2008-02-28 15:19 Rev.: 5136

- cflags were dropped when ARB_64 was defined

1 lines of code changed in 1 file:

westram 2008-02-28 14:34 Rev.: 5135

- missing quotes

1 lines of code changed in 1 file:

westram 2008-02-28 14:27 Rev.: 5134

- added BUILDHOST_64

1 lines of code changed in 1 file:

westram 2008-02-28 14:27 Rev.: 5133

- first try of 32+64-bit Makefile

67 lines of code changed in 1 file:

westram 2008-02-28 14:14 Rev.: 5132

- double include

0 lines of code changed in 2 files:

westram 2008-02-28 14:14 Rev.: 5131

- include stdio.h

1 lines of code changed in 1 file:

westram 2008-02-28 12:50 Rev.: 5130

- release-assertions in set_mismatches()

3 lines of code changed in 1 file:

westram 2008-02-28 12:18 Rev.: 5129

- depends updated

388 lines of code changed in 52 files:

westram 2008-02-28 12:15 Rev.: 5128

- removed my own strange defines

36 lines of code changed in 6 files:

westram 2008-02-28 12:15 Rev.: 5127

- __ATTR__XXX instead of __attribute__
- removed my own strange defines

12 lines of code changed in 1 file:

westram 2008-02-28 12:14 Rev.: 5126

- prototypes updated

53 lines of code changed in 13 files:

westram 2008-02-28 12:13 Rev.: 5125

- use -G instead of -g to create prototypes

57 lines of code changed in 5 files:

westram 2008-02-28 12:10 Rev.: 5124

- replaced __attribute__ by __ATTR__XXX

75 lines of code changed in 24 files:

westram 2008-02-28 12:07 Rev.: 5123

- use new compiler attributes w/o spamming older compilers with warnings

99 lines of code changed in 1 file:

westram 2008-02-28 12:07 Rev.: 5122

- added attributes.h

7 lines of code changed in 1 file:

westram 2008-02-28 12:06 Rev.: 5121

- added function-type-attribute

2 lines of code changed in 2 files:

westram 2008-02-28 12:06 Rev.: 5120

- forward ARB INCLUDE dir

6 lines of code changed in 3 files:

westram 2008-02-28 11:48 Rev.: 5119

- fixed includes
- __ATTR__XXX instead of __attribute__

16 lines of code changed in 1 file:

westram 2008-02-28 11:47 Rev.: 5118

- stpcpy -> gb_stpcpy

3 lines of code changed in 1 file:

westram 2008-02-28 11:47 Rev.: 5117

- __ATTR__XXX instead of __attribute__
- pre-calculate how much to malloc

6 lines of code changed in 1 file:

westram 2008-02-28 11:47 Rev.: 5116

- new option -G to generate headers using __ATTR__XXX and attributes.h
- raise error if both attribute-methods are mixed up
- print only those filenames into header, from which prototypes are extracted
- in wrapper: check for definition of '__GNUC__' (not 'GNU')

96 lines of code changed in 1 file:

westram 2008-02-28 11:47 Rev.: 5115

- create correct sentinel

1 lines of code changed in 1 file:

boehnel 2008-02-27 23:23 Rev.: 5114

added assertion to test that max_mismatch <= MAX_MISMATCH
There should not only be this assertion but some more testing because in release version, without assertion, the for loop smashes the stack.

8 lines of code changed in 1 file:

boehnel 2008-02-27 23:20 Rev.: 5113

changed fix value to sizeof(...) (for 64bit)

2 lines of code changed in 1 file:

boehnel 2008-02-27 18:18 Rev.: 5112

"if (max_malloc >= nettomemsize) break;" -> "if (max_malloc/1024 >= nettomemsize) break;"
(max_malloc is in bytes, nettomemsize already is in kb)

1 lines of code changed in 1 file:

boehnel 2008-02-27 17:23 Rev.: 5111

assertion only in 64 bit.... sorry

2 lines of code changed in 1 file:

westram 2008-02-27 17:02 Rev.: 5110

- use %zi for size_t argument

1 lines of code changed in 1 file:

westram 2008-02-27 16:48 Rev.: 5109

- cast parameter for %li to (long), to work in 32bit version as well

1 lines of code changed in 1 file:

boehnel 2008-02-27 16:44 Rev.: 5108

added "ASSERT_PRINT_AND_CRASH"

6 lines of code changed in 1 file:

boehnel 2008-02-27 16:38 Rev.: 5107

"int -> long" and added an assertion

5 lines of code changed in 1 file:

boehnel 2008-02-27 16:36 Rev.: 5106

"%u -> %lu" and "%i -> %li"

3 lines of code changed in 1 file:

boehnel 2008-02-27 16:35 Rev.: 5105

"%i -> %li"

1 lines of code changed in 1 file:

boehnel 2008-02-27 16:34 Rev.: 5104

"int -> long"

1 lines of code changed in 1 file:

westram 2008-02-27 13:38 Rev.: 5103

- added uint32_t

1 lines of code changed in 1 file:

westram 2008-02-27 13:37 Rev.: 5102

- typo

1 lines of code changed in 1 file:

westram 2008-02-27 13:37 Rev.: 5101

- MG_create_field_content:
. error if origin organism/gene not found
. added assertions if no result and no error
. use enum for method-parameter

24 lines of code changed in 1 file:

westram 2008-02-27 13:37 Rev.: 5100

- updated

2 lines of code changed in 1 file:

westram 2008-02-27 13:37 Rev.: 5099

- include stdint.h (for uint32_t)
- crctab now uint32_t

5 lines of code changed in 1 file:

westram 2008-02-27 13:37 Rev.: 5098

- include stdint.h (for uint32_t)

3 lines of code changed in 1 file:

westram 2008-02-27 13:37 Rev.: 5097

- GB[S]_checksum returns uint32_t

3 lines of code changed in 1 file:

westram 2008-02-27 13:37 Rev.: 5096

- stop allocating when nettomemsize is reached

10 lines of code changed in 1 file:

boehnel 2008-02-26 20:48 Rev.: 5095

"0 -> NULL"

1 lines of code changed in 1 file:

boehnel 2008-02-26 19:42 Rev.: 5094

"int -> long"

2 lines of code changed in 1 file:

boehnel 2008-02-26 19:19 Rev.: 5093

"__attribute__((format(printf,2,3)))"

1 lines of code changed in 1 file:

boehnel 2008-02-26 19:15 Rev.: 5092

"__attribute__((format(printf, 1, 2)))"

2 lines of code changed in 1 file:

boehnel 2008-02-26 18:57 Rev.: 5091

"%i -> %ui"

2 lines of code changed in 1 file:

boehnel 2008-02-26 18:55 Rev.: 5090

"%i -> %li"

1 lines of code changed in 1 file:

boehnel 2008-02-26 18:52 Rev.: 5089

"int -> long"

3 lines of code changed in 1 file:

boehnel 2008-02-26 18:45 Rev.: 5088

"__attribute__ ((sentinel))"

12 lines of code changed in 4 files:

boehnel 2008-02-26 18:11 Rev.: 5087

"%i -> %lu"

1 lines of code changed in 1 file:

boehnel 2008-02-26 18:08 Rev.: 5086

"__attribute__ ((sentinel))"....

1 lines of code changed in 1 file:

boehnel 2008-02-26 17:59 Rev.: 5085

"%d -> %ld"

4 lines of code changed in 1 file:

boehnel 2008-02-26 17:50 Rev.: 5084

"%u -> %lu"

5 lines of code changed in 1 file:

boehnel 2008-02-25 20:28 Rev.: 5083

mmap doesn't return zero on error but MAP_FAILED (equals (void *) -1)
...also added the errno variable in output

2 lines of code changed in 1 file:

baderk 2008-02-25 17:12 Rev.: 5082

Some minor fixes to get 'probe design' at least running.
The 'probe design' code (e.g. gb_main) disgusting at some places...

4 lines of code changed in 2 files:

boehnel 2008-02-24 21:39 Rev.: 5081

adding "__attribute__ ((sentinel))" - But it doesn't help anything I think, because not ending the function call with a "NULL"
only gives a warning, not an error. And who would see that warning in a make?

1 lines of code changed in 1 file:

boehnel 2008-02-24 21:30 Rev.: 5080

adding "__attribute__ ((sentinel))" - But it doesn't help anything I think, because not ending the function call with a "NULL"
only gives a warning, not an error. And who would see that warning in a make?

2 lines of code changed in 1 file:

boehnel 2008-02-24 21:27 Rev.: 5079

adding "__attribute__ ((sentinel))" - But it doesn't help anything I think, because not ending the function call with a "NULL" only gives a warning, not an error. And who would see that warning in a make?

15 lines of code changed in 2 files:

westram 2008-02-21 11:11 Rev.: 5078

- beautified

161 lines of code changed in 1 file:

westram 2008-02-21 10:43 Rev.: 5077

- typo

11 lines of code changed in 8 files:

westram 2008-02-21 10:42 Rev.: 5076

- updated

0 lines of code changed in 1 file:

westram 2008-02-21 10:42 Rev.: 5075

- avoid dup entry for GB_usleep in prototypes

10 lines of code changed in 1 file:

westram 2008-02-20 15:23 Rev.: 5074

- GB_get_physical_memory now tests allocatable memory (thx to Elmar)

34 lines of code changed in 1 file:

westram 2008-02-20 14:59 Rev.: 5073

- fixed hotkey

1 lines of code changed in 1 file:

westram 2008-02-20 14:59 Rev.: 5072

- ask for destination DB-type

13 lines of code changed in 1 file:

westram 2008-02-15 19:20 Rev.: 5071

- depends updated

52 lines of code changed in 2 files:

westram 2008-02-15 19:19 Rev.: 5070

- fixed include wrapper
- cleanup

23 lines of code changed in 1 file:

westram 2008-02-15 19:19 Rev.: 5069

- auto-generate prototypes

13 lines of code changed in 1 file:

westram 2008-02-15 19:19 Rev.: 5068

- indented etc.
- fixed include wrapper

142 lines of code changed in 1 file:

westram 2008-02-15 19:19 Rev.: 5067

- removed prototypes (now generated into GDE_proto.h)
- fixed include wrapper
- added GapCompression-type

28 lines of code changed in 1 file:

westram 2008-02-15 19:19 Rev.: 5066

- made local functions static
- fixed call to ReadArbdb2()

153 lines of code changed in 1 file:

westram 2008-02-15 19:19 Rev.: 5065

- changed name of AWAR_GDE_COMPRESSION (to enforce new default for all users)

2 lines of code changed in 1 file:

westram 2008-02-15 19:18 Rev.: 5064

- code cleanup
- made local functions static
- fixed parameter types for ReadArbdb + ReadArbdb2

15 lines of code changed in 1 file:

westram 2008-02-15 19:18 Rev.: 5063

- made local functions static
- allow '\n' in labels

18 lines of code changed in 1 file:

westram 2008-02-15 19:18 Rev.: 5062

- code cleanup
- made local functions static

717 lines of code changed in 1 file:

westram 2008-02-15 19:18 Rev.: 5061

- made local functions static

210 lines of code changed in 2 files:

westram 2008-02-15 19:18 Rev.: 5060

- code cleanup
- made local functions static
- compression: toggle->option-menu, added option "columns w/o info"
- fixed width calculation for labels containing '\n'

33 lines of code changed in 1 file:

westram 2008-02-15 19:18 Rev.: 5059

- added GDE_proto.h (generated)

1 lines of code changed in 1 file:

westram 2008-02-14 20:20 Rev.: 5058

- added protein data (and some other non-release things)

4 lines of code changed in 1 file:

westram 2008-02-14 17:10 Rev.: 5057

- added override-toggle position

9 lines of code changed in 1 file:

westram 2008-02-14 17:10 Rev.: 5056

- announce correct DB to DB browser (was dest instead of source)
- call MG_start_cb2() with 'dest_is_new'==true

2 lines of code changed in 1 file:

westram 2008-02-14 17:10 Rev.: 5055

- untabified
- new param 'dest_is_new' for MG_start_cb2()
- fixed include wrapper

9 lines of code changed in 1 file:

westram 2008-02-14 17:10 Rev.: 5054

- moved actual merge code for species into MG_transfer_one_species(),
which test, whether merging is possible
- rewrote MG_transfer_selected_species() and MG_transfer_species_list()
using MG_transfer_one_species()

132 lines of code changed in 1 file:

westram 2008-02-14 17:10 Rev.: 5053

- added an override-toggle (allows to merge w/o renaming species)

18 lines of code changed in 1 file:

westram 2008-02-14 17:10 Rev.: 5052

- new parameter for MG_start_cb2(): dest_is_new
if true -> initialize genome-DB-flag according to source DB
- dont raise error at startup (if DB-type mismatches), cause some
merges are possible between genome- and non-genome-DBs (e.g. trees, configs,
pseudo-species from genome->non-genome)

10 lines of code changed in 1 file:

westram 2008-02-14 17:10 Rev.: 5051

- MG_export_fields() works (again?) w/o given error_suppressor

6 lines of code changed in 1 file:

westram 2008-02-14 17:10 Rev.: 5050

- help for override-toggle

7 lines of code changed in 1 file:

westram 2008-02-14 17:10 Rev.: 5049

- mark_organisms_with_marked_genes(): crashed if DB contained pseudo-species

2 lines of code changed in 1 file:

westram 2008-02-14 17:09 Rev.: 5048

- shorten output-length of field in search result to 1000 chars

3 lines of code changed in 1 file:

baderk 2008-02-12 18:19 Rev.: 5047

Taken back previous patch 'disabled maximize/resize' feature for AW_window_simple dialogs. Resize remains disabled for messageboxes.

3 lines of code changed in 1 file:

westram 2008-02-12 12:16 Rev.: 5046

- fig for GDE windows w/o sequence export

21 lines of code changed in 1 file:

westram 2008-02-12 12:00 Rev.: 5045

- untabified, indented and fixed {}'s

265 lines of code changed in 1 file:

murban 2008-02-08 20:13 Rev.: 5044

added functions for protein structure comparison; added import filters and perl script for dssp files; added menu entry in EDIT4 for choosing the active protein structure SAI

1042 lines of code changed in 21 files:

January 2008 »

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