February 2007 Commit Log

Number of Commits:

24

Number of Active Developers:

2

westram 2007-02-22 12:48 #24 Rev.: 4330

- incremented nameserver db version to 3
- initiate dups-checker for db-versions below 3
- slightly changed print-out of dups-checker
- use hash to avoid repeated "name-exists"-tests to speed up
renaming DBs where many similar names occur (e.g. 'Uncultured bacteria')
- now creates up to 16.4 million different short names for species with
same (or similar) full name (limit was approx. 100000 before)

70 lines of code changed in 1 file:

• NAMES: names.cxx (+70 -17)

westram 2007-02-22 12:48 #23 Rev.: 4329

- doubled hash-size for dups/zombie detection

1 lines of code changed in 1 file:

• ARBDB: adtools.c (+1 -1)

westram 2007-02-21 13:33 #22 Rev.: 4328

- hotkey fix

1 lines of code changed in 1 file:

• MERGE: MG_main.cxx (+1 -1)

westram 2007-02-21 13:30 #21 Rev.: 4327

- call MG_export_fields for pseudo species only

14 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+14 -5)

westram 2007-02-21 13:29 #20 Rev.: 4326

- expect a pseudo species in MG_export_fields

5 lines of code changed in 1 file:

• MERGE: MG_gene_species.cxx (+5 -3)

westram 2007-02-20 13:09 #19 Rev.: 4325

- print error about all duplicate species + advice

12 lines of code changed in 1 file:

• ARBDB: adtools.c (+12 -6)

baderk 2007-02-16 17:19 #18 Rev.: 4324

A lookup table is used during the consensus computation to speed up the iupac-code weighting.

252 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_GroupData.cxx (+237 -302), SQ_GroupData.h (+15 -9)

westram 2007-02-13 13:54 #17 Rev.: 4323

- removed CHIP-interface (now directly integrated in CHIP-DESIGNER)

1 lines of code changed in 11 files:

• Makefile (+1 -2)
• CHIP: Makefile (del), ca_mark.cxx (del), ca_mark.hxx (del), ca_probe.cxx (del), ca_probe.hxx (del), chip.hxx (del), chip_main.cxx (del), probe_functions.cxx (del), probe_functions.hxx (del), test.cxx (del)

baderk 2007-02-12 13:13 #16 Rev.: 4322

Runtime optimization of the sequence quality function (work still in progress)

116 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_GroupData.cxx (+113 -69), SQ_GroupData.h (+3 -2)

westram 2007-02-08 16:01 #15 Rev.: 4321

- skip .log

1 lines of code changed in 1 file:

• util: arb_srclst.pl (+1)

baderk 2007-02-08 15:50 #14 Rev.: 4320

Reformatted sourcecode (TABs removed)

292 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_GroupData.cxx (+167 -151), SQ_GroupData.h (+125 -105)

westram 2007-02-08 15:47 #13 Rev.: 4319

- cleaned up some targets
- added target 'release_quick' (skips rebuild)

8 lines of code changed in 1 file:

• Makefile (+8 -18)

baderk 2007-02-08 14:09 #12 Rev.: 4318

gcc version 4.1.2 added

1 lines of code changed in 1 file:

• Makefile (+1 -1)

westram 2007-02-08 13:03 #11 Rev.: 4317

- updated

2 lines of code changed in 1 file:

• ARBDB: ad_t_prot.h (+2)

westram 2007-02-08 13:03 #10 Rev.: 4316

- 'transfer listed species' was completely broken:
. only tried to replace organisms (not all species)
. instead of deleting existing organism, it deleted ALL organisms
(no idea how that bug was able to exist undetected for 6 months)

10 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+10 -8)

westram 2007-02-08 13:03 #9 Rev.: 4315

- added species hash functions
- changed error message occurring during rename, when a real duplicate
species is in database

28 lines of code changed in 1 file:

• ARBDB: adtools.c (+28 -3)

westram 2007-02-08 13:01 #8 Rev.: 4314

- GEN_is_organism denies to work with non-genome-db

4 lines of code changed in 1 file:

• ARBDB: adGene.c (+4 -4)

westram 2007-02-07 13:50 #7 Rev.: 4313

- fixed call of nt_exit
- removed debug quick exit

5 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+5 -9)

westram 2007-02-01 16:59 #6 Rev.: 4312

- exclude '#*#'
- more comments
- precompiled expressions
- match tracing

123 lines of code changed in 1 file:

• util: arb_srclst.pl (+123 -93)

westram 2007-02-01 14:02 #5 Rev.: 4311

- openGL
- 64bit note

14 lines of code changed in 1 file:

• arb_INSTALL.txt (+14)

westram 2007-02-01 13:57 #4 Rev.: 4310

- libGLEW version upgrade

7 lines of code changed in 4 files:

• lib/addlibs: install_libs.sh (+2 -1), libGLEW.readme (+3 -3), libGLEW.so.1.2.4 (del), libGLEW.so.1.3.5 (new 2)

westram 2007-02-01 11:08 #3 Rev.: 4309

- debug-only variable

9 lines of code changed in 1 file:

• WINDOW: AW_xfont.cxx (+9 -2)

westram 2007-02-01 11:08 #2 Rev.: 4308

- debug-only variable

5 lines of code changed in 1 file:

• SL/FILE_BUFFER: FileBuffer.cxx (+5 -2)

westram 2007-02-01 11:08 #1 Rev.: 4307

- warning fix

5 lines of code changed in 1 file:

• AWT: AWT_input_mask.cxx (+5 -6)

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