March 2009 Commit Log

Number of Commits:
17
Number of Active Developers:
4
baderk 2009-03-31 14:16 Rev.: 5781

Fixed symlink creation

0 lines of code changed in 1 file:

baderk 2009-03-31 13:52 Rev.: 5780

code cleanup

1 lines of code changed in 90 files:

westram 2009-03-30 11:58 Rev.: 5779


- cleanup + var rename

11 lines of code changed in 2 files:

westram 2009-03-30 11:54 Rev.: 5778


- try build twice (maybe also fixes #69)

6 lines of code changed in 1 file:

westram 2009-03-29 10:17 Rev.: 5777

- again removed timestamps

0 lines of code changed in 24 files:

westram 2009-03-29 10:16 Rev.: 5776

- obsolete

0 lines of code changed in 2 files:

westram 2009-03-27 20:44 Rev.: 5775


* made help generator bit more robust
- local link types are no longer detected by extension (*.ps, *pdf) in stylesheets. it is now done once in arb_help2xml.
- '.hlp' extension is no longer suppressed (in xml)
- all local link types may have missing attribute
- arb_help2xml checks for existance of .pdf and .ps now
- warn about all dead links during compilation (and abort on invalid links)
- fixed most broken links in helpfiles

218 lines of code changed in 11 files:

meierh 2009-03-20 11:04 Rev.: 5774

MetaTags PROJECT and PR added as MT_BASIC

3 lines of code changed in 1 file:

westram 2009-03-19 11:56 Rev.: 5773


- If not a valid IUPAC, AWT_decode_iupac() now returns "" (previously " ") for easier testing.

32 lines of code changed in 3 files:

westram 2009-03-19 11:52 Rev.: 5772


- renamed 2 #defines

9 lines of code changed in 4 files:

arb_build 2009-03-18 15:28 Rev.: 5771

Auto version upgrade to 4.27 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-03-18 15:26 Rev.: 5770


* mark long branches:
- removed epsilon value (did not work good)
- long neighbour branches of subtrees with long branches are now marked as well

45 lines of code changed in 4 files:

baderk 2009-03-18 10:17 Rev.: 5769

Added missing dependency (stl algorithm) and removed some unnecessary whitespaces.

7 lines of code changed in 1 file:

westram 2009-03-16 14:11 Rev.: 5768


* rewrote genome importer
* remove redundant 'translation' entries of genes during import
* whole code is using
- 'pos_start' instead of 'pos_begin*'
- 'pos_stop' instead of 'pos_end*'
- 'pos_certain' instead of 'pos_uncertain*'
- 'pos_complement' instead of 'complement'
* convert gene locations in old genome DBs into new format
* added several gene functions to ARBDB
- GEN_create_nonexisting_gene...()
- GEN_find_or_create_gene..()
- GEN_global_gene_identifier()
* added code to handle gene locations into ARBDB (type GEN_position represents every flavour of a Genbank/EMBL feature location)
* added GBT_write_byte()
* rewrote GBT_read_gene_sequence() (adding GBT_read_gene_sequence_and_length)
* changed codon tables according to NCBI code info
- added start codon(s) for code 3, 9, 13
- changed code names
* when importing to a new DB, reset DB type if import fails (before ARB had to be restarted, after one try with wrong genome/non-genome import)

4589 lines of code changed in 72 files:

westram 2009-03-16 12:50 Rev.: 5767


* new switches -keep and -unmark for markSpecies.pl
* improved error handling

125 lines of code changed in 3 files:

arb_build 2009-03-11 14:24 Rev.: 5766

Auto version upgrade to 4.26 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-03-11 14:17 Rev.: 5765


* ARBDB/adlang1.c: - fixed huge memleak introduced in [5726] (occurred on ACI commands 'diff', 'filter' and 'change')
* SOURCE_TOOLS/arb_valgrind: - option -l gave error (wrong quotes)
* WINDOW/AW_nawar.cxx: - memleak
* WINDOW/AW_status.cxx: - memcpy -> memmove (regions overlap)

4 lines of code changed in 4 files:

February 2009 »

Generated by StatSVN 0.7.0