November 2008 Commit Log

Number of Commits:
53
Number of Active Developers:
5
boehnel 2008-11-30 22:21 Rev.: 5622

Adding dynamic buffer


51 lines of code changed in 1 file:

boehnel 2008-11-30 18:21 Rev.: 5621

Adding position dependet mismatches


67 lines of code changed in 3 files:

boehnel 2008-11-29 17:28 Rev.: 5620

Added code to use base pair strength matrix with weighted mismatch
search.


39 lines of code changed in 1 file:

boehnel 2008-11-29 17:11 Rev.: 5619

Fixing comment
Changing calculation of "pg->pg_SpeciesCache->ch_MaxCapacity"

2 lines of code changed in 1 file:

arb_build 2008-11-27 13:26 Rev.: 5618

Auto version upgrade to 4.19 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2008-11-27 13:25 Rev.: 5617

* if multiple equal-scored insertion points are found for a partial sequence, dont create
an error. Instead simply use first and warn about ambiguity.

34 lines of code changed in 1 file:

westram 2008-11-26 17:08 Rev.: 5615


* test for sequence data in alignment (SIGSEGV)
* fixed reporting of non-added species

37 lines of code changed in 1 file:

westram 2008-11-26 17:06 Rev.: 5614

had a case, where stringlen differed from memsize: zero byte is included inside memsize bytes,
i.e. fallback from GB_STRING_SHRT to GB_STRING should work.

0 lines of code changed in 1 file:

westram 2008-11-26 15:34 Rev.: 5613

tab-ex

19 lines of code changed in 1 file:

westram 2008-11-26 12:17 Rev.: 5612


* added documentation
* arb_ludwig calls arb_remote now
* arb_oneach and arb_rwho removed (MBI-specific)

88 lines of code changed in 8 files:

westram 2008-11-25 16:08 Rev.: 5611

* added package installation skript (SH/arb_installubuntu4arb.sh)
* updated arb_INSTALL.txt + arb_UBUNTU.txt

126 lines of code changed in 3 files:

westram 2008-11-25 15:12 Rev.: 5610

added -funit-at-a-time

2 lines of code changed in 1 file:

westram 2008-11-25 13:39 Rev.: 5609

avoid generation of defect intermediate files (happens if lynx is not installed).
These files had to be removed manually, to force regeneration after lynx-installation.

3 lines of code changed in 1 file:

boehnel 2008-11-24 18:14 Rev.: 5608

(long -> int) bugfix for 64-Bit (weighted mismatches didn't work)


2 lines of code changed in 1 file:

boehnel 2008-11-22 17:21 Rev.: 5607

Increased buffer
Added Error handling for to small buffers
Added TODO comment


11 lines of code changed in 1 file:

meierh 2008-11-20 18:51 Rev.: 5606

(Elmar) strlen + 2 weil sowohl die "\0" als auch die "~" brauchen platz

PT_buildtree.cxx
- newtreename = (STRPTR) malloc(strlen(pg->pg_IndexName) + 1);
+ newtreename = (STRPTR) malloc(strlen(pg->pg_IndexName) + 2);

1 lines of code changed in 1 file:

westram 2008-11-20 16:15 Rev.: 5605


Calling

make clean depends

produced wrong dependencies for communication libraries, because the included files are generated.

Now target 'depends' depends on 'com_all', which generates all headers by building the com libs.

6 lines of code changed in 1 file:

westram 2008-11-20 16:07 Rev.: 5604


- argh.. reverted [5603]

58 lines of code changed in 11 files:

westram 2008-11-20 15:55 Rev.: 5603


- dependencies updated

(reverted by [5604])

0 lines of code changed in 11 files:

arb_build 2008-11-20 12:40 Rev.: 5602

Auto version upgrade to 4.18 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2008-11-19 12:58 Rev.: 5601


* AWT_pro_a_nucs_convert returns the length of the translated sequence in new param 'translatedSize'

19 lines of code changed in 4 files:

westram 2008-11-19 12:29 Rev.: 5600


* updated help
* NTREE/ad_transpro.cxx / arb_r2a():
* cleaned up error handling and return points
* localized variables
* use AWT_saveTranslationInfo
* AWT/awt_codon_table.*: renamed params to clearify what table type is used
* AWT/awt_translate.*: added AWT_saveTranslationInfo()

178 lines of code changed in 7 files:

westram 2008-11-17 16:59 Rev.: 5599


* AWT_pro_a_nucs_convert: 2 new parameters (create_start_codon + append_stop_codon)
* Protein-Viewer: show start codon (instead of explicit codon). should maybe be optional

30 lines of code changed in 4 files:

westram 2008-11-17 16:54 Rev.: 5598


- added AWT_is_start_codon, returns code ('M') for start codons, 0 otherwise

32 lines of code changed in 2 files:

westram 2008-11-17 14:56 Rev.: 5597


* changes: - AWT_findTranslationTable -> AWT_getTranslationInfo
retrieves 'transl_table' and 'codon_start'; now
expects both - not sure whether idea is good
- fixed calls to AWT_getTranslationInfo, removed previous code for 'codon_start'
- arb_transdna() now ALWAYS sets field 'codon_start' to '1'

76 lines of code changed in 3 files:

westram 2008-11-17 11:45 Rev.: 5596


* GB_get_physical_memory: using Darwin port from Matt Cottrell
as suggested in Message-Id: <gfh8e5+bk13@eGroups.com>


20 lines of code changed in 1 file:

arb_build 2008-11-14 19:52 Rev.: 5595

Auto version upgrade to 4.17 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2008-11-14 19:52 Rev.: 5594


- auto-skip .old
- auto-include .makefile
- delete old ptpan makefile (get it from svn history if really needed)

3 lines of code changed in 2 files:

westram 2008-11-14 19:30 Rev.: 5593


- skip *~ (backup files)

1 lines of code changed in 1 file:

westram 2008-11-14 19:16 Rev.: 5592


* increased number of NDS entries to 60 (6 pages a 10 entries)
* added page-toggle to NDS window
* implemented viewkey (re-)mapping
* renamed AWT_open_nds_window -> AWT_create_nds_window
* separated xfigs for www and nds window (both used same xfig)
* renamed menu entries for NDS

188 lines of code changed in 7 files:

westram 2008-11-14 19:15 Rev.: 5591


obsolete - removed!

0 lines of code changed in 2 files:

westram 2008-11-14 14:42 Rev.: 5590


cleanup obsolete code

3 lines of code changed in 1 file:

westram 2008-11-14 13:32 Rev.: 5589


* removed initialization-calls for removed global variable 'awt_pro_a_nucs'
* Added replacement class AWT_translator (some instances are cached internally)
* protein code_nr is now explicitely passed to AWT_pro_a_nucs_convert(), fixed all calls
This makes AWT_pro_a_nucs_convert independent from AWAR_PROTEIN_TYPE and no longer
requires to initialize any global before using it.
* warnings about missing 'transl_table' / 'codon_start' now uses '1..n',
instead of internal index '0..n-1'
* Translate sequences:
* fixed counting of species w/o 'transl_table' or 'codon_start'.
Did as well count species which had no data in selected alignment.
* fallback for 'transl_table' now is table selected in translation window (was always 0)
* print number of taxa without data (in handled alignment)

359 lines of code changed in 9 files:

westram 2008-11-13 14:56 Rev.: 5588


- pass const hash to GBS_read_hash

3 lines of code changed in 2 files:

westram 2008-11-13 14:35 Rev.: 5587


* MERGE/MG_main.cxx: - calling 'arb_ntree db1.arb db2.arb' with a not-existing 'db2.arb'
showed a message that ARB is creating a new DB, but it did not progress.

30 lines of code changed in 2 files:

boehnel 2008-11-12 19:38 Rev.: 5586

Disabling DOUBLEDELTALEAVES and DOUBLEDELTAOPTIONAL by default, because
of (yet) undiscovered bugs


2 lines of code changed in 1 file:

boehnel 2008-11-12 19:36 Rev.: 5585

Enabling and adjustin Visual feedback


3 lines of code changed in 1 file:

boehnel 2008-11-12 18:30 Rev.: 5584

added some asserts


5 lines of code changed in 1 file:

meierh 2008-11-12 13:18 Rev.: 5583

ticket #140 removed "\\" from the path to "arb_who". --> "check server"
works!

1 lines of code changed in 1 file:

westram 2008-11-11 13:16 Rev.: 5582


GB_get_physical_memory:

* compile error for darwin (to force port)
* print warning, if default memsize is assumed
* increased default memsize to 512 Mb

32 lines of code changed in 1 file:

boehnel 2008-11-11 10:54 Rev.: 5581

long -> int Bugfix (Segfaults)


5 lines of code changed in 1 file:

westram 2008-11-07 19:08 Rev.: 5580


* PT_main.cxx: - 'memory reservation for nmap' now done AFTER deciding whether
we need to rebuild ptserver.
Effects:
. if index already existed, memory was allocated twice (once in
initial arb_pt_server, and once in recursively called arb_pt_server which
is building the index)
. if no index existed, memory was allocated not at all (it rather crashed
before change [5576:5577])
. if index was up-to-date, it should have worked around the out-of-memory bug
@elmar: could you please check, whether the current version worksaround as well?

19 lines of code changed in 1 file:

baderk 2008-11-06 16:04 Rev.: 5578

free() undefined. Added stdlib.h.

1 lines of code changed in 1 file:

baderk 2008-11-06 16:02 Rev.: 5577

Removed defines and added file size (file exists) check before malloc (see [5561]).

9 lines of code changed in 1 file:

baderk 2008-11-04 18:35 Rev.: 5576

Added IF DEFINED DEVEL_RALF as long as patch [5561] prevents pt-server from building.

4 lines of code changed in 1 file:

baderk 2008-11-04 18:11 Rev.: 5575

Added gcc version 4.3.2

1 lines of code changed in 1 file:

baderk 2008-11-04 18:10 Rev.: 5574

Revert to previous revision (dirty code removed).

2 lines of code changed in 1 file:

baderk 2008-11-04 17:47 Rev.: 5573

Fixes broken pt-server building caused by patch #5561. Quick and dirty... Please test it!

2 lines of code changed in 1 file:

boehnel 2008-11-03 21:35 Rev.: 5572

Adding support for large DBs with ptpan


56 lines of code changed in 1 file:

baderk 2008-11-03 19:44 Rev.: 5571

Fixed XPM Button sizes (odd dimensions cause segfaults)

109 lines of code changed in 4 files:

meierh 2008-11-03 18:25 Rev.: 5570

fixed buffer overflow

1 lines of code changed in 1 file:

westram 2008-11-03 12:35 Rev.: 5569


- fixed buffer overflows (thx elmar)

2 lines of code changed in 2 files:

boehnel 2008-11-02 19:01 Rev.: 5568

Adding support for large dbs in ptpan

102 lines of code changed in 1 file:

October 2008 »

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