February 2009 Commit Log

Number of Commits:

28

Number of Active Developers:

3

arb_build 2009-02-27 18:46 #28 Rev.: 5764

Auto version upgrade to 4.25 by devel@arb-home.de

2 lines of code changed in 1 file:

• SOURCE_TOOLS: version_info (+2 -2)

westram 2009-02-27 18:46 #27 Rev.: 5763

* rewrote parts of insert/delete columns
- handles secondary structure properly (still problems if secedit is opened while inserting)
- uses only one alloced buffer (not one for each insertion)
* several functions went static
* replaced some GB_STRDUP's

365 lines of code changed in 4 files:

• ARBDB: ad_t_lpro.h (-4), ad_t_prot.h (-1), adtools.c (+360 -240)
• NTREE: NT_ins_col.cxx (+5 -1)

westram 2009-02-27 18:42 #26 Rev.: 5762

- call ED4_pfold_set_SAI from ED4_alignment_length_changed only if alignment is AA (otherwise some AWARs are not defined)

5 lines of code changed in 1 file:

• EDIT4: ED4_root.cxx (+5 -3)

westram 2009-02-27 18:41 #25 Rev.: 5761

- keep going on target 'up'

4 lines of code changed in 1 file:

• Makefile (+4 -1)

westram 2009-02-27 18:34 #24 Rev.: 5760

- GDE sequence export did not work since [5695]

5 lines of code changed in 1 file:

• ARB_GDE: GDE_event.cxx (+5 -5)

westram 2009-02-27 18:31 #23 Rev.: 5759

- tree reader failed on DNAPARS treefile (added LF to beginning of name)

2 lines of code changed in 1 file:

• ARBDB: adtools.c (+2 -1)

westram 2009-02-26 17:46 #22 Rev.: 5758

- use GB_warning instead of printing to stderr (shows up in message-window when called from GUI). See also [5756] and [5751]

3 lines of code changed in 2 files:

• ARBDB: ad_lpro.h (-1), ad_save_load.c (+3 -3)

arb_build 2009-02-25 13:12 #21 Rev.: 5757

Auto version upgrade to 4.24 by devel@arb-home.de

2 lines of code changed in 1 file:

• SOURCE_TOOLS: version_info (+2 -2)

westram 2009-02-25 13:11 #20 Rev.: 5756

- make clear data was lost

1 lines of code changed in 1 file:

• ARBDB: ad_save_load.c (+1 -1)

westram 2009-02-25 12:31 #19 Rev.: 5755

* ARBDB/arbdb.c: - const fix
- comments
* PHYLO/PH_main.cxx: - delete->free
* ARBDB/adcompr.c: - removed useless assertion

20 lines of code changed in 3 files:

• ARBDB: adcompr.c (+1 -1), arbdb.c (+18 -9)
• PHYLO: PH_main.cxx (+1 -1)

westram 2009-02-25 12:31 #18 Rev.: 5754

* ARBDB/arb_assert.h: - no backtrace ifdef ASSERT_CRASH
* ARBDB/adstring.c: - avoid duplicated backtrace in GB_internal_error (DEBUG mode)

12 lines of code changed in 2 files:

• ARBDB: adstring.c (+6 -2), arb_assert.h (+6 -5)

westram 2009-02-25 12:30 #17 Rev.: 5753

- inserted 2 {} to avoid local variables to be interpreted by code-generator

16 lines of code changed in 1 file:

• PERL2ARB: ARB.xs.default (+16 -14)

westram 2009-02-25 12:29 #16 Rev.: 5752

* ARBDB/adindex.c: - rewrote gb_index_check_out():
. removed useless result
. report more details on failure
. reduced variable scopes

39 lines of code changed in 2 files:

• ARBDB: ad_lpro.h (+1 -1), adindex.c (+38 -40)

westram 2009-02-25 12:29 #15 Rev.: 5751

* ARBDB/ad_save_load.c: - when saving to ASCII-DB: overwrite broken DB string entries
(where GB_read_string returns NULL) with a error message
and report error to console.
* ARBDB/adTest.c: - changed message for zero DB entries (broken entries)

5 lines of code changed in 2 files:

• ARBDB: adTest.c (+1 -1), ad_save_load.c (+4)

arb_build 2009-02-09 20:28 #14 Rev.: 5750

Auto version upgrade to 4.23 by devel@arb-home.de

2 lines of code changed in 1 file:

• SOURCE_TOOLS: version_info (+2 -2)

westram 2009-02-09 20:16 #13 Rev.: 5749

* filtered 2 motif bugs from valgrind output

10 lines of code changed in 1 file:

• SOURCE_TOOLS: valgrind2grep (+10 -3)

westram 2009-02-09 20:14 #12 Rev.: 5748

* smoothed estimated time in progress bar

63 lines of code changed in 1 file:

• WINDOW: AW_status.cxx (+63 -19)

westram 2009-02-09 20:13 #11 Rev.: 5747

* added argument to ARB_SIGSEGV (print backtrace or not?)

8 lines of code changed in 2 files:

• ARBDB: adstring.c (+2 -2), arb_assert.h (+6 -6)

westram 2009-02-09 20:12 #10 Rev.: 5746

* avoid buffer overflow (limit size of big input streams in error message)

41 lines of code changed in 1 file:

• ARBDB: adquery.c (+41 -5)

westram 2009-02-09 20:11 #9 Rev.: 5745

* fixed BIT arguments (parsing error)

33 lines of code changed in 1 file:

• ARBDB: adlang1.c (+33 -39)

boehnel 2009-02-09 16:54 #8 Rev.: 5744

* bugfixes for Probe Design
* adding Epsilon for floating point comparision

5 lines of code changed in 1 file:

• ptpan: PT_new_design.cxx (+5 -6)

boehnel 2009-02-09 14:57 #7 Rev.: 5743

* changed debug output
* fixed indentation

15 lines of code changed in 1 file:

• ptpan: PT_new_design.cxx (+15 -11)

boehnel 2009-02-02 01:03 #6 Rev.: 5742

* Bugfix to get probe design work

4 lines of code changed in 1 file:

• ptpan: PT_new_design.cxx (+4 -1)

boehnel 2009-02-02 01:03 #5 Rev.: 5741

* adding GB_init_gb() (needed for PT_new_design)

2 lines of code changed in 1 file:

• ptpan: PT_main.cxx (+2)

boehnel 2009-02-02 01:01 #4 Rev.: 5740

* make proto (adding PP_buildPosWeight, PP_convertBondMatrix)

2 lines of code changed in 1 file:

• ptpan: pt_prototypes.h (+2)

boehnel 2009-02-02 01:00 #3 Rev.: 5739

* removing "static" of functions PP_buildPosWeight and PP_convertBondMatrix
* adding debug output
* moving debug output

26 lines of code changed in 1 file:

• ptpan: PT_match.cxx (+26 -20)

boehnel 2009-02-02 00:55 #2 Rev.: 5738

changing "gb_init_gb" -> "GB_init_gb" to make it global visible (needed for ptpan, new design)

3 lines of code changed in 4 files:

• ARBDB: ad_load.c (+1 -1), ad_lpro.h (-1), ad_prot.h (+1), arbdb.c (+1 -1)

boehnel 2009-02-02 00:54 #1 Rev.: 5737

Bugfix for 64 bit

1 lines of code changed in 1 file:

• PROBE: probe_tree.hxx (+1 -1)

January 2009 »