September 2011 Commit Log

Number of Commits:
19
Number of Active Developers:
2
westram 2011-09-30 21:10 Rev.: 7997


- fix savetest 4 trunk

1 lines of code changed in 1 file:

westram 2011-09-30 08:58 Rev.: 7987


* support new probe match params introduced in [7986] from ARB_NT (fixes #241)
- Separate expert windows for probe match/design
- create_probe_design_variables
* renamed property-db params to make clear which awars go to props/db
* AWAR_PROBE_ADMIN_PT_SERVER now saved in DB
- added help for new parameters; fixed help of probe-design-expert; put bonds into own helpfile

335 lines of code changed in 7 files:

westram 2011-09-29 18:43 Rev.: 7986


* PT-SERVER
- allow to specify amount+limit where N is accept
- moved hardcoded PT_MAX_MATCHES into AISC interface as parameter (with same limit)
* added links to information related to MAGIC_NUMBER
- maintain a list of previously used MAGIC_NUMBERs
* AISC parameters
- removed unused parameter MATCH_MAX_SPECIES
- added new parameters MATCH_MAX_HITS, MATCH_N_ACCEPT, MATCH_N_LIMIT
* defaulted them to previously hardcoded limits
* parametrized set_table_for_PT_N_mis() using MATCH_N_ACCEPT + MATCH_N_LIMIT
* protect vs illegal index into psg.N_mismatches
* arb_probe
- fixed commandline parser (no longer modifies passed argv)
- added new parameters matchacceptN, matchlimitN + matchmaxresults
- added some unit tests
* testing N-matches (in match-string and/or seqdata)
* testing truncation of results

342 lines of code changed in 11 files:

baderk 2011-09-27 15:44 Rev.: 7980

Increased the hardcoded upper limit for number of PT-Server matches to 1024k.

1 lines of code changed in 1 file:

westram 2011-09-21 13:21 Rev.: 7971


- perl script to collect information from gene-field and store it into organism-field

156 lines of code changed in 2 files:

westram 2011-09-13 15:39 Rev.: 7937


- ptserver
- disabled debug messages
- use arb_progress

13 lines of code changed in 3 files:

westram 2011-09-13 15:30 Rev.: 7936


- GBS_readable_size() accepts prev hardcoded unit_suffix

12 lines of code changed in 3 files:

westram 2011-09-12 08:53 Rev.: 7935


- removed outdated ptpan

17 lines of code changed in 29 files:

westram 2011-09-01 15:59 Rev.: 7933


merge from dev_elmar [7700] [7701] [7702]
* fix "icount == count + data_missing"
* fix PT server crashes with 2 million sequences
* reduce spam in NDEBUG mode for large PT server tree

11 lines of code changed in 3 files:

westram 2011-09-01 15:25 Rev.: 7931


merge from dev [7905] [7908] [7927]
* added !__ATTR!__DEPRECATED_FUNCTION.. (helps to declare ctors deprecated)
* silenced several warnings
- new flavors for attributes USERESULT / DEPRECATED (toggle with WARN_TODO from config.makefile)
- some TODOs
* fix broken attribute; introduced by [7585]
Note: [7908] merged partially only (cb.h skipped!)

54 lines of code changed in 19 files:

westram 2011-09-01 15:18 Rev.: 7930


merge from dev [7875]
* expect gcc 4.3 or higher

24 lines of code changed in 4 files:

westram 2011-09-01 15:13 Rev.: 7929


merge from dev [7844] [7855] [7865] [7869] [7910] [7911]
* misc minor patches affecting:
- diff2grep
- remake_after_change
- COMPILE_ASSERT
- warning fixes
* dont export error from move_group_info

39 lines of code changed in 6 files:

westram 2011-09-01 15:05 Rev.: 7928


merge from dev [7864] [7904]
* 'make proto' no longer updates (all done automatically)
- AISC_COM prototypes
- AISC prototypes

0 lines of code changed in 1 file:

westram 2011-09-01 14:26 Rev.: 7926


merge from dev [7823] [7829] [7831] [7835] [7840] [7846] [7860] [7867] [7924]
* silenced unit tests
- only print test log
* for failed tests
* tests with warnings if WARN_LEVEL==1
* when running with COVERAGE=1
* unit test suite now reports failure if valgrind reports errors
* again increase timeout for slow tests (now 20 seconds)
* changes to TEST_..-macros
- moved TEST_ASSERT_CONTAINS to test_unit.h
- TEST_ASSERT_RESULT!__NOERROREXPORTED: dump exported error if any
- moved code to compare error messages (or parts of) to TEST_ASSERT_NORESULT!__ERROREXPORTED_CHECKERROR
- added TEST_FAILS_INSIDE_VALGRIND

Note: [7846] not merged completely (adquery.cxx skipped)

73 lines of code changed in 7 files:

westram 2011-09-01 14:11 Rev.: 7925


merge from dev [7821] [7822] [7923]
* fix build with COVERAGE (broken by [7785])
- fix compilation with coverage for RNACMA
- link RNACMA.a only if needed
* sort coverage by chunk-size
* added file-based filter (commented out)

34 lines of code changed in 3 files:

westram 2011-09-01 13:12 Rev.: 7922


- improved error message on dbfield-type-mismatch

38 lines of code changed in 1 file:

westram 2011-09-01 10:36 Rev.: 7919


- keep & ignore latest_iwhite.patch

2 lines of code changed in 1 file:

westram 2011-09-01 10:23 Rev.: 7918


* explicit counters for different tree modifications (!GroupChanges)
* removed member 'tree_modified' (now uses !GroupChanges)

75 lines of code changed in 1 file:

westram 2011-09-01 09:25 Rev.: 7917


* cluster-name suffix now configurable
- show example name for selected cluster
- help file updated
* cleaned up all those "name"-functions
- changed names to make different tasks clear
* fixed alignment of cluster list formatting (wrong for small float values)
* ENTER in max.dist or clustersize starts calculation

326 lines of code changed in 5 files:

August 2011 »

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