October 2011 Commit Log

Number of Commits:
23
Number of Active Developers:
1
westram 2011-10-22 08:01 Rev.: 8133


* revert yesterdays changes :( ([8129], [8130], [8131] and [8132])
- edit4 is made from glass - touch it and it breaks

(patches were revived with [8607])

232 lines of code changed in 15 files:

westram 2011-10-21 17:29 Rev.: 8132


- removed ED4_base::is_group (unused)

(reverted by [8133], revived by [8607])

38 lines of code changed in 5 files:

westram 2011-10-21 15:03 Rev.: 8131


* EDIT terminals/managers
- dump() now is no longer overloaded
* base classes implement dump_base (and declare dump pure virtual)
* lead classes implement dump (which calls dump_base)
=> always prints real polymorphic type
- dump less info

(reverted by [8133], revived by [8607])

102 lines of code changed in 2 files:

westram 2011-10-21 14:46 Rev.: 8130


* ED4_terminal
- renamed flag -> tflag (it shadowed ED4_base::flag)

(reverted by [8133], revived by [8607])

36 lines of code changed in 8 files:

westram 2011-10-21 14:11 Rev.: 8129


* EDIT4
- fixed several free/delete mismatches
- class hierarchy (do not instanciate base-classes)
* new abstract base class for ED4_group_manager and ED4_root_group_manager (ED4_abstract_group_manager)
* derive ED4_consensus_sequence_terminal from ED4_sequence_terminal_basic

(reverted by [8133], revived by [8607])

64 lines of code changed in 12 files:

westram 2011-10-17 13:34 Rev.: 8104


merge from ptpan_back [8085] [8088] [8091]
* avoid shadow warnings from some TEST_ASSERTions
* patch name shows whether tests were valgrinded
* added template IGNORE_RESULT(), to ignore results tagged with !__ATTR!__USERESULT

104 lines of code changed in 11 files:

westram 2011-10-17 13:29 Rev.: 8103


merge from ptpan_back [8071] [8075] [8076] [8077] [8079]
* moved ARBDB/GB_system -> CORE/GBK_system
* moved basic file related functions from ARBDB to CORE
- GB_time_of_file (no longer automatically evaluates given path)

419 lines of code changed in 69 files:

westram 2011-10-17 13:24 Rev.: 8102


merge from ptpan_back [8070] [8072]
- fix linefeeds in mkptypes

3 lines of code changed in 1 file:

westram 2011-10-17 13:21 Rev.: 8101


merge from ptpan_back [8065] [8066]
* rewrote arb_db_server + added tests

580 lines of code changed in 4 files:

westram 2011-10-17 13:17 Rev.: 8100


merge from ptpan_back [8016] [8017] [8021] [8051] [8067]
* added method to get status of GB_shell object
* removed possibility to execute command via DB-server - always use GB_system instead
* valgrinded external tools called by arb_test

57 lines of code changed in 22 files:

westram 2011-10-17 13:12 Rev.: 8099


merge from ptpan_back [8046] [8047] [8050] [8048] [8057] [8069]
* fixed several problems with unit-tests (race-condition, blocking, broken error messages, valgrinding)

455 lines of code changed in 11 files:

westram 2011-10-17 13:05 Rev.: 8098


merge from ptpan_back [8023] [8030] [8052] [8058] [8062]
* suppress several boost-warnings
* store old SIGSEGV-handler in AISC-servers
* removed chroot (unused and name conflicts with libc)
* fixed abuse of GB_export_errorf
* accept if sighandler is already installed (happens when opening 2 DB-clients from same binary)

39 lines of code changed in 6 files:

westram 2011-10-17 12:45 Rev.: 8097


- missing dependency for PTCLEAN

1 lines of code changed in 1 file:

westram 2011-10-11 08:12 Rev.: 8056


* fixed undefined AWAR_CANIO_BORDERSIZE in canvas_to_xfig
- instead pass value from caller, print dialog uses awar value, xfig-export uses 0.0
* removed 'CANCEL'-buttons from export dialogs
* fixed size of export buttons

62 lines of code changed in 3 files:

westram 2011-10-07 13:39 Rev.: 8041


merge from dev [7990] [7991] [7992] [7993] [7994] [7995] [7996] [7998] [8001] [8003] [8005] [8006] [8007] [8008] [8009] [8011] [8012] [8019]
* added a faked ecoli to ptserver test-db
* added unit-tests for gene-ptserver
* rename ptserver testdb
* ptserver db-cleanup
- size of mapfile for SSUREF108 is reduced by 85% (3,4Gb -> 519Mb)
* ptserver
- refactored
* prefix tree builders
* probe_input_data
- removed ptnd_new_match (dead code)

1885 lines of code changed in 49 files:

westram 2011-10-07 13:26 Rev.: 8040


merge from dev [7975] [8034] [8002] [8004]
- unit tests
* added TEST_ASSERT_MEM_EQUAL
* dump log if tests are disabled (even if warning is not printed)
* do not prototype 'NOTEST_' (used to disable tests)

56 lines of code changed in 5 files:

westram 2011-10-07 13:22 Rev.: 8039


merge from dev [7966] [7968]
* tweaked ARB DB browser

484 lines of code changed in 6 files:

westram 2011-10-07 13:17 Rev.: 8038


merge from dev [7963] [7964] [7965]
- valgrind2grep: fixed symlinks follower
- GBS_shorten_repeated_data
* valgrinded
* shorten smaller repeat counts (down to 5)

40 lines of code changed in 2 files:

westram 2011-10-07 13:14 Rev.: 8037


merge from dev [7958] [7959] [7960] [7961]
* GBT_open (removed unused default parameter)
* error handling fixes
- several functions in ARBDB
- added macro RETURN_ERROR
* shall be used by functions returning errors (opposed to functions exporting errors)
* fails assertion if an error is exported

140 lines of code changed in 22 files:

westram 2011-10-07 12:49 Rev.: 8036


merge from dev [7950] [7951] [7952] [7953] [7954] [7955] [7957]

* replaced weird GBS_find_lib_file (GB_lib_file, GB_property_file, GB_arbtcpdat_path, GB_path_in_ARBLIB, ..)
* changed handling of property-files (removed path prefix '.arb_prop')
* replaced several hardcoded paths
* fixed arb_notify
* fixed crash when showing "lib/message" on startup (outside GB_shell)
* cleaned up error handling in start_macro_recording

246 lines of code changed in 39 files:

westram 2011-10-07 12:33 Rev.: 8035


merge from dev [7940] [7941] [7962]
- do not export error from GB_check_key
- added some NAN guards
- internally increase maxlen by 1 in GBS_strstruct::vnprintf (fixes zero-bytes into buffer)

51 lines of code changed in 5 files:

westram 2011-10-07 09:21 Rev.: 8031


* editing SAI comments was broken by [5851]

9 lines of code changed in 1 file:

westram 2011-10-06 13:25 Rev.: 8028


* missing GB_shell in arb_wetc; fixes
- sequence printing in ARB_EDIT4
- exporting NDS (to printer)

1 lines of code changed in 1 file:

September 2011 »

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