August 2011 Commit Log

Number of Commits:
40
Number of Active Developers:
1
westram 2011-08-31 22:10 Rev.: 7916


* removed AWAR_DTREE_REFRESH (-> AWAR_TREE_REFRESH)
* DRYed AWAR_TREE_REFRESH
* loosened coupling between aw_awar.hxx and aw_awar_defs.hxx (former aw_awars.hxx)
- aw_awars.hxx now includes both

158 lines of code changed in 70 files:

westram 2011-08-31 09:57 Rev.: 7915


* fixed ARBDB/CORE-library output handling
- redirect via ARB_redirect_handlers_to() in
* arb_export_tree and
* arb_2_bin (this fixes broken 'arb_repair')
* added test for arb_repair

59 lines of code changed in 7 files:

westram 2011-08-30 17:07 Rev.: 7913


* fix cluster naming
- 'append to name'
* had no effect
* renamed into 'append original'
* appends '{was:ORIGINALNAME}'
- when removing/re-crating clusternames, always consider such "originalname"
* added class ARB_tree_predicate
* fixed ARB_countedTree::relative_position_in
- assertion failed when testing group vs self; now returns 0

151 lines of code changed in 5 files:

westram 2011-08-26 09:37 Rev.: 7900


- fixed target 'savetest'
- headerlibs
- perl2arb (with YAML installed)

4 lines of code changed in 1 file:

westram 2011-08-26 09:22 Rev.: 7899


- fixed build for non OPENGL versions (target 'cma' accidently in wrong section)

1 lines of code changed in 1 file:

westram 2011-08-25 22:56 Rev.: 7898


* removed RNACMA debug code

6 lines of code changed in 4 files:

westram 2011-08-25 22:50 Rev.: 7897


* fixed some warnings

4 lines of code changed in 3 files:

westram 2011-08-25 22:38 Rev.: 7896


* removed disabled-code leftover from changes

2 lines of code changed in 5 files:

westram 2011-08-25 22:30 Rev.: 7895


* added arb_rnacma (correlated mutation analysis) written by Breno Faria
- fixed compilation and runtime errors

1579 lines of code changed in 15 files:

westram 2011-08-25 21:54 Rev.: 7894


* added target 'headerlibs'
* directory 'eigen'
- svn-ignore
- touch after extraction (to avoid multiple extraction)
* fixed arb_LICENSE.txt (help conversion failed)

8 lines of code changed in 3 files:

westram 2011-08-25 19:22 Rev.: 7893


- added parts of 'eigen' headerlib

185 lines of code changed in 6 files:

westram 2011-08-25 15:21 Rev.: 7892


- error handling

1 lines of code changed in 1 file:

westram 2011-08-25 15:02 Rev.: 7891


- revived code removed in [7184] as NT_system_in_xterm_cb()

9 lines of code changed in 3 files:

westram 2011-08-25 11:30 Rev.: 7890


merge from dev [7832] [7836] [7839] [7851]
* remake_after_change
- avoid dupped call to 'ut'
- log premake (incl. stderr)
- auto-premake libdepends
- dump log on failure
* .test depends on .dummy
- allows to build and test library w/o linking it anywhere

25 lines of code changed in 3 files:

westram 2011-08-25 07:51 Rev.: 7888


* added a fake ctor to AW_root (for unit-tests only)
- initializes AWAR subsystem, w/o doing any X-stuff
- use it in TEST_advice_id_awar_handling (failed when unit-test ran via cron)

25 lines of code changed in 4 files:

westram 2011-08-24 18:46 Rev.: 7887


* separated functionality of gap-insertion and toggling gap-type
- '.', '-' and space now always
* insert a gap character in align- or insert-edit-mode and
* overwrite a position with a gap in replace-edit-mode
- above keys+CTRL changes the gaptype of a complete gap-chain (works in edit- and align-mode)
* removed default key-mapping ' '->'-' (handled internally)
- added advice for those who already saved their edit4 properties

143 lines of code changed in 6 files:

westram 2011-08-24 17:53 Rev.: 7886


* aw_xkey_2_awkey:
- return state of CTRL/ALT
- hack for CTRL-SPACE

15 lines of code changed in 1 file:

westram 2011-08-24 16:44 Rev.: 7885


* avoid that one advice may popup multiple times (e.g. when putting the advice into a loop)
- track open advices
- [TDD] generalized tracking of open and disabled advices

99 lines of code changed in 2 files:

westram 2011-08-18 14:13 Rev.: 7871


- fix non-working compiler version checks

4 lines of code changed in 1 file:

westram 2011-08-18 09:11 Rev.: 7868


- do not filter compiler-errors (e.g. unknown options etc.)

7 lines of code changed in 1 file:

westram 2011-08-08 09:22 Rev.: 7819


merge from dev [7774] [7778] [7779] [7780] [7781] [7782] [7783] [7784] [7785] [7786] [7787] [7788] [7789] [7790] [7791] [7792] [7793] [7794] [7795] [7796] [7817]
* fixes/improvements to build ARB on multicores
- made dependencies between targets explicit (let make resolve them)
- fixed several failures caused by async calls ('dep_graph', 'up', tests)
- try to make 'perl' 1st ("big target")
* other changes
- ctags (bug in 5.8; tag-order)
- removed obsolete things from Makefiles
- added SOURCE_TOOLS/remake_after_change.pl (call from ARB subdirs, knows what to do)
- tests use own ARB_PID (no clash with running ARB)

1223 lines of code changed in 20 files:

westram 2011-08-08 08:56 Rev.: 7818


merge from dev [7773] [7776] [7797]
* remove indirection via links in directory MAKEBIN
* ignore json/yml for PERL2ARB
* stopper vs compiling RNA3D w/o ARB_OPENGL

31 lines of code changed in 18 files:

westram 2011-08-08 00:22 Rev.: 7815


merge from dev [7766] [7767]
* format each line as single paragraph in section 'OCCURRENCE'
* silently ignore links duplicated by inline-links and do not add them to topics multiple times

43 lines of code changed in 1 file:

westram 2011-08-08 00:19 Rev.: 7814


merge from dev [7760] [7761] [7763] [7764] [7765]
* Gene location editor (GLE)
- rewrote 'Create gene' using GLE
- added 'Edit gene location'
* GEN_position
- GEN_free_position accepts NULL
- GEN_write_position
* improved errors
* check positions to be inside [1 .. length]
* GBS_strstruct (added convenience methods release(), putlong() and putfloat())
* Location creates "complement(join())" if it is "smaller"

666 lines of code changed in 13 files:

westram 2011-08-08 00:14 Rev.: 7813


merge from dev [7753] [7754] [7755] [7762]
* added new target 'build_CTARGET'
- only do CTARGET if sth has been committed to the checked-out branch since the last call of any of the targets (CTARGET needs to be passed to make)

92 lines of code changed in 4 files:

westram 2011-08-08 00:06 Rev.: 7812


merge from dev [7751] [7752]
* updated many old-style typedefs (typedef struct/enum)

432 lines of code changed in 61 files:

westram 2011-08-08 00:01 Rev.: 7811


merge from dev [7748] [7749] [7750]
* comments (C->C++ style)
* fixed umlauts in TREEGEN

1589 lines of code changed in 159 files:

westram 2011-08-07 23:55 Rev.: 7810


merge from dev [7746]
* rename cov targets + add help

7 lines of code changed in 1 file:

westram 2011-08-07 23:51 Rev.: 7809


merge from dev [7742]
* sorted lists

76 lines of code changed in 1 file:

westram 2011-08-07 23:47 Rev.: 7808


merge from dev [7736] [7740] [7741]
* avoid accidental checkins of UNIT_TESTER/Makefile.setup

103 lines of code changed in 10 files:

westram 2011-08-07 20:58 Rev.: 7807


merge from dev [7727] [7729]
* added
- unit-test for Location (EMBL/Genbank)
- Location::as_string()
- added to_Location
* fixes
- accept empty joins
- one leak (on exception)

201 lines of code changed in 3 files:

westram 2011-08-07 19:15 Rev.: 7806


merge from dev [7720] [7721] [7722] [7723] [7724] [7725] [7726] [7747]
* !ItemSelector
- is now const by default (org struct is called !MutableItemSelector)
- now passed/stored as reference
- hide !MutableItemSelectors using access functions (so only const !ItemSelectors can be passed around)
* !BoundItemSel
- color_mark_data was in fact a !BoundItemSel
- !BoundItemSel is now const by default (org struct is called !MutableBoundItemSel)
* renames
- !DbScanner -> GB_DbScanner
- db_scanner_data -> !DbScanner
* fixes
- skip query if querying empty set (e.g. db w/o experiments)
- assertion failure on multiple instances of field admin menu entries (genes + experiments)
- gene-info shows selected gene when opened 1st time
- error no longer exported in experiment create
- deleting current item and then selecting a new one failed to remove callback on keydata
* added TODOs for genes/experiment UI/ItemSelectors

890 lines of code changed in 42 files:

westram 2011-08-07 19:07 Rev.: 7805


merge from dev [7719]
* reduce nested access

136 lines of code changed in 1 file:

westram 2011-08-07 19:00 Rev.: 7804


merge from dev [7711] [7712] [7714] [7715] [7717] [7718]
* DBUI
- removed NT_ prefixes
- removed ad_ prefixes
* DB_QUERY
- typed and renamed variables/parameters storing !DbQuery
- callbacks (fixed casts and names)
- remove unused result and unused parameter from awt_query_update_list (now !DbQuery_update_list)
- removed awt-prefixes
- public interface in namespace QUERY
* ITEMS
- several renames (awt-prefix,...)

1261 lines of code changed in 51 files:

westram 2011-08-07 18:06 Rev.: 7803


merge from dev [7716] [7732] [7733] [7734] [7735]
* script to add+remove svn ignores recursively
- ignore *.gcno
- do not ignore *.gcda
- no longer ignore 'Makefile.bak' - instead ignore '*.bak'
- no longer ignore '!ChangeLog' in subdirs

182 lines of code changed in 1 file:

westram 2011-08-07 18:03 Rev.: 7802


merge from dev [7713] [7728] [7730] [7731]
* force LANG=C for compilation to get rid of unicode-compiler-output
* show column in compiler messages
* coverage
- cleanup coverage files after unit-tests
- highlight coverage <90%
- if COVERAGE=1
* run tests synchronous
* cleanup coverage results after each test
- DRY gcov2msg.pl

24 lines of code changed in 2 files:

westram 2011-08-07 17:41 Rev.: 7801


merge from dev [7710]
* resolve some nesting in library dependencies
- allows unit tests in GENOM and GENOM_IMPORT

357 lines of code changed in 112 files:

westram 2011-08-07 17:22 Rev.: 7800


merge from dev [7687] [7692] [7693] [7694] [7695] [7697] [7706] [7707] [7708]
* replaced 'char**' (heap-array of heap-char*) by new class !StrArray
- added several tests for !StrArray
- removed function flavours using element result parameter (e.g. GBT_get_tree_names_and_count)
* split !StrArray into !StrArray (heap), !ConstStrArray (just pointers) and base class (!CharPtrArray)
- use !ConstStrArray in several cases (e.g. config, tree and alignment names)
* GBT_split_string
- changed allocation: dups source and does destructive split (similar to strtok)
- returns !ConstStrArray instead of char**
- added destructive versions (GBT_splitNdestroy_string)
* refactored parsePositions / parseCSV using !ConstStrArray

952 lines of code changed in 46 files:

westram 2011-08-07 17:11 Rev.: 7799


merge from dev [7703] [7704] [7705]
* splitted ARB_init_global_awars to support late binding of global awars (needed in ARB_NTREE)
* focus policy (toggles between current and old behavior before [5548])
* use toggle_toggle
* made !RefSelector Noncopyable
* fixed postcompile filter for classes nested in namespaces

95 lines of code changed in 11 files:

westram 2011-08-07 17:07 Rev.: 7798


* merge from dev [7772]
- increased unittest timeouts

4 lines of code changed in 1 file:

July 2011 »

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