May 2010 Commit Log

Number of Commits:
61
Number of Active Developers:
1
westram 2010-05-31 14:36 Rev.: 6674


* valgrind2grep: - ignore some leaked motif memory (wont fix that (now))
* added aw_uninstall_xkeys() and AW_root::exit_root() to stuff some memleaks

41 lines of code changed in 5 files:

westram 2010-05-31 13:07 Rev.: 6673


* GBS_strstruct
- made a class
- added unit tests

218 lines of code changed in 3 files:

westram 2010-05-28 14:31 Rev.: 6672


* again added old hack-around removed in [6654]
* enabled TRACE_ALLOCS - making unit tests fail for the moment

2 lines of code changed in 2 files:

westram 2010-05-28 14:18 Rev.: 6671


- AllocLogEntry uses void*

6 lines of code changed in 1 file:

westram 2010-05-28 13:51 Rev.: 6670


- allow infinite NTREE clones

1 lines of code changed in 1 file:

westram 2010-05-26 18:45 Rev.: 6669


- don't warn when reporting probe matches to field 'tmp' twice. append instead.

24 lines of code changed in 1 file:

westram 2010-05-26 18:01 Rev.: 6668


* moved match visualization ("GUCACGGCU-=NN=====g=-CAGCAGCCC") from match_string() (aisc:MATCH_STRING) to get_match_overlay()
* removed redundant calculation of wmis/wmismatches (MATCHLIST_WMISMATCHES)
* added rpc hook for get_match_overlay() to PT.aisc (MATCHLIST_OVERLAY)
* removed rpc hook for unused variable is_member (MATCHLIST_IS_MEMBER)

(thx to elmar)

27 lines of code changed in 2 files:

westram 2010-05-26 17:25 Rev.: 6667


* replaced tests in DB-read/write functions by some inlines providing more info
- no longer call GB_internal_error, instead dump backtrace/fail assertion in serious cases
- report(write) or export(read) error otherwise
- did not really replace macros GB_TEST_READ/GB_TEST_WRITE yet (impending conflicts)

63 lines of code changed in 1 file:

westram 2010-05-21 18:44 Rev.: 6666


* AW_root
- ctor initializes AWAR subsystem
- made more clear that AW_root is a singleton
- call dtor atexit; unlink AWARs from prop-DB and free memory (AW_window instances and releated mem still remain)
- close properties DB
- renamed some functions
* AW_awar
- added dtor
* added AWT_create_root (necessary to add properties DB to DB-browser)
* removed AWT_open_properties (done inside AW_root-ctor now)
* EDIT properties
- detect existing properties before constructing AW_root
* removed AW_config_struct

300 lines of code changed in 29 files:

westram 2010-05-21 14:00 Rev.: 6665


- added GB_open_DBs() - returns number of open ARB databases

5 lines of code changed in 2 files:

westram 2010-05-21 13:50 Rev.: 6664


- free remote_hash

1 lines of code changed in 1 file:

westram 2010-05-20 11:33 Rev.: 6663


* allow GB_close in "no transaction" mode (needed to close properties DB)
* free some memory allocated by GBT_open()

6 lines of code changed in 2 files:

westram 2010-05-14 13:42 Rev.: 6662


- exclude directory UNIT_TESTER/tests

1 lines of code changed in 1 file:

westram 2010-05-14 13:31 Rev.: 6661


* gbm_get_mem / gbm_free_mem use void* (like malloc/free)

64 lines of code changed in 15 files:

westram 2010-05-14 13:24 Rev.: 6660


- more fixes to source-list

4 lines of code changed in 1 file:

westram 2010-05-14 12:58 Rev.: 6659


* free()
- removed unneeded casts of argument
- removed unneeded if-clauses

103 lines of code changed in 37 files:

westram 2010-05-14 12:52 Rev.: 6658


- include lib depends to arb_src.tgz

2 lines of code changed in 1 file:

westram 2010-05-14 12:32 Rev.: 6657


- undo part of [6656]

2 lines of code changed in 1 file:

westram 2010-05-14 12:08 Rev.: 6656


- removed unneeded 'struct' keyword
- renamed several structs (especially things like 'blabla_struct')

1349 lines of code changed in 88 files:

westram 2010-05-13 16:43 Rev.: 6655


* struct GBS_strstruct -> GBS_strstruct

71 lines of code changed in 12 files:

westram 2010-05-13 16:30 Rev.: 6654


* This patch stuffs all memory leaks in ARBDB (as far as covered by unit-tests) for DEBUG and NDEBUG version!
* ARBDB global data (aka 'gb_local')
- track number of opened/closed DBs
- GBK_install_SIGSEGV_handler only once in GB_init_gb()
- when closing last DB -> call GB_exit_gb() freeing more memory (also called atexit, including assertion failing if a DB is still open)
- added class ARBDB_memory_manager (just calls gbm_init_mem + gbm_flush_mem)
- GB_exit_gb flushes ARBDB_memory_manager (if all blocks were freed by gbm_free_mem, everything will be flushed)
* fixed a few more static buffer leaks
* gb_make_entry - alloc correct blocksizes for GB_STRING and GB_LINK
* fixed a hack in gb_read_bin_rek_V2
- was increasing size of memory block to avoid illegal memory access in decompress (introduced in [1003]; may occur again)
- due to mismatch in size between gbm_get_mem and gbm_free_mem memory was never flushed even if all blocks have been freed
* fixed memleak in gb_read_bin_rek_V2
- when loading mapfile, previously created 'gb_main' was not freed
* added allocation logger to admalloc.cxx (inactive - use TRACE_ALLOCS to activate it)
- traces all allocs/frees of ARBDB managed memory
- detects wrong usage (double free, size and index mismatch) and shows were the block was allocated
- added new backtrace functions helpful for debugging (store stack-backtraces and print them later)

403 lines of code changed in 13 files:

westram 2010-05-13 15:20 Rev.: 6653


- skip scoped symbols (xx::yy) - e.g. static variables inside functions

3 lines of code changed in 1 file:

westram 2010-05-12 17:35 Rev.: 6652


- use smart pointers for several static buffers (freeing more reachable memleaks)

57 lines of code changed in 3 files:

westram 2010-05-12 17:30 Rev.: 6651


- rewrote arb_tcp.dat-handling (fixing memleaks)

82 lines of code changed in 1 file:

westram 2010-05-12 13:19 Rev.: 6650


- fixed memleak caused by hash-statistics (DEBUG only)

33 lines of code changed in 1 file:

westram 2010-05-12 11:53 Rev.: 6649


* GB_close crashed for DBs with mapfiles since [6648]
- on mapfile-load relink new DB main-entry to dummy-father
- use ARBDB memory management for DB indices (was always wrong, but no problem since they were never freed)

11 lines of code changed in 3 files:

westram 2010-05-11 14:16 Rev.: 6648


* stuffed all direct memory leaks in GB_open/GB_close
- call gbcm_logout for main-user
- free dates
- gb_delete_main_entry -> gb_delete_dummy_father
- free key data
- free command hash
- splitted up gb_delete_entry into GBDATA- and GBCONTAINER-version
- destroy DB indices when destroying GBCONTAINER

200 lines of code changed in 9 files:

westram 2010-05-11 08:19 Rev.: 6647


- field conversion errors were reported for wrong species

2 lines of code changed in 1 file:

westram 2010-05-10 18:42 Rev.: 6646


* DB cache
- didn't cache anything since ages (gb_cache_entry.clock was always zero, i.e. always out-of-date). Was already broken in [2].
- increased max. cache memory from 25Mb to 50Mb
- increased max. cache entries from 8192 to 16384
- destroy cache on GB_close (fixes biggest and most useless ARBDB memleak)
- changed cache indices to uint16_t (reducing each cache entry by 8 byte (16 byte;64bit)).
- rewrote complete cache code removing much duplicated code
- added debug code to calc cache stats
* increased max. undo memory from 10Mb to 20Mb

294 lines of code changed in 8 files:

westram 2010-05-10 18:41 Rev.: 6645


- fix error handling

2 lines of code changed in 1 file:

westram 2010-05-10 17:04 Rev.: 6644


- disabled several debug prints

17 lines of code changed in 1 file:

westram 2010-05-10 16:55 Rev.: 6643


- compile error

0 lines of code changed in 1 file:

westram 2010-05-10 16:26 Rev.: 6642


- disabled some DEBUG code

2 lines of code changed in 1 file:

westram 2010-05-10 16:25 Rev.: 6641


* fast_aligner
- fill start of alignBuffer with gaps when aligning partial sequence only (w/o this insertion of result from clustalV produced checksum errors)
- avoid possible error-overwrite

17 lines of code changed in 1 file:

westram 2010-05-07 20:22 Rev.: 6640


* removed unused parameters/parameter names
* made several functions static
* removed useless struct keywords

105 lines of code changed in 12 files:

westram 2010-05-07 19:42 Rev.: 6639


* GB_change_my_security
- removed constant result
- removed unused parameter 'passwd'

15 lines of code changed in 8 files:

westram 2010-05-07 17:47 Rev.: 6638


* replaced more duplicated code

15 lines of code changed in 1 file:

westram 2010-05-07 17:37 Rev.: 6637


* replaced duplicated code

21 lines of code changed in 1 file:

westram 2010-05-07 17:29 Rev.: 6636


* replaced defines by enum GBCM_ServerResult
- fixed functions

84 lines of code changed in 5 files:

westram 2010-05-06 18:16 Rev.: 6635


* removed unused parameter names (fixing unused warnings)

16 lines of code changed in 1 file:

westram 2010-05-06 18:09 Rev.: 6634


* ARBDB memory management
- gbm_put_memblk/gbm_get_memblk went static
- renamed gbm_get_mem_impl/gbm_free_mem_impl to avoid auto-prototyping
- replaced macros handling MEMORY_TEST=0/1 by inline-functions to get rid of unused-warnings
* removed some unused code

18 lines of code changed in 5 files:

westram 2010-05-06 17:35 Rev.: 6633


- unused warnings (removed parameters/parameternames)

16 lines of code changed in 6 files:

westram 2010-05-06 17:33 Rev.: 6632


- rename

2 lines of code changed in 2 files:

westram 2010-05-06 17:28 Rev.: 6631


- automatically name unnamed parameters in xsub-wrappers

8 lines of code changed in 1 file:

westram 2010-05-06 11:50 Rev.: 6630


- gb_save_mapfile returns GB_ERROR instead of exporting it

4 lines of code changed in 3 files:

westram 2010-05-06 11:05 Rev.: 6629


* fixed DB-main-index handling
- use GB_random() instead of time() to choose a random index
- release indices when destroying DB-main
- release index if error occurs while logging into DB
* gb_save_mapfile()
- release temporary DB-main-index used during save
- now it's possible to save a DB with mapfile and to load it afterwards w/o getting an index conflict
- single return
- removed gotos
* rewrote GB_save_as(), GB_save_quick_as(), GB_save_quick() and gb_check_saveable()
- single return
- removed gotos
- fixed error handling
- if saving mapfile fails, fallback to simple binary save
- quicksave did not return error if quicksaving was disabled. Instead silently no quicksave occurred! (related to stable patch [6519])
* several fixes of error-handling in
- gb_create_reference
- gb_add_reference
- renameQuicksaves
- GB_create_directory
* unit tests
- test save/load of mapfile (NDEBUG or MEMORY_TEST=0 only)
- fixed wrong use of TEST_ASSERT_RESULT!__NOERROREXPORTED; complete tested call needs to be passed as argument - not just result of call; otherwise it will only warn about exported error instead of creating a test failure.

427 lines of code changed in 5 files:

westram 2010-05-04 17:13 Rev.: 6628


- depends + prototypes updated

2 lines of code changed in 2 files:

westram 2010-05-04 17:13 Rev.: 6627


- quicksave *.a99 was never used

42 lines of code changed in 1 file:

westram 2010-05-04 17:06 Rev.: 6626


- unit tests for save/load DB

229 lines of code changed in 1 file:

westram 2010-05-04 17:00 Rev.: 6625


* DBs for unit-testing

106 lines of code changed in 3 files:

westram 2010-05-04 16:59 Rev.: 6624


* some unit-test assertions for error handling

129 lines of code changed in 1 file:

westram 2010-05-04 16:50 Rev.: 6623


* was not able to load ASCII-DB, if one string entry starts with '%'

27 lines of code changed in 1 file:

westram 2010-05-03 16:52 Rev.: 6622


* if DB contained no tree, NDS list view was unscrollable
- reason: AWT_graphic_tree::check_update() returned error if no tree-root found. fixed

1 lines of code changed in 1 file:

westram 2010-05-03 15:59 Rev.: 6621


- debug output

1 lines of code changed in 1 file:

westram 2010-05-03 14:53 Rev.: 6620


- determine hash-size from tree-size (reverts hack [6619])

1 lines of code changed in 1 file:

westram 2010-05-03 14:41 Rev.: 6619


- ~~fixed useless hash-size-warning (occurs with many zombies)~~

(reverted by [6620])

2 lines of code changed in 1 file:

westram 2010-05-03 14:20 Rev.: 6618


* If properties were saved with 'Rotate molecule'=true, the meaning of the toggle was inverted.
- now molecule starts rotating instantly after startup
* removed useless static variable 'Spinning' (was just a duplicate of 'RNA3D->bAutoRotate')

21 lines of code changed in 1 file:

westram 2010-05-02 16:12 Rev.: 6617


- fix_depends.pl didn't work if $ARBHOME contained '+' or similar

2 lines of code changed in 1 file:

westram 2010-05-02 14:24 Rev.: 6616


* restored previous version (checkin by mistake)

0 lines of code changed in 1 file:

westram 2010-05-02 14:19 Rev.: 6615


* when installing SIGPIPE handlers, also accept SIG_IGN as old handler

18 lines of code changed in 6 files:

westram 2010-05-02 13:15 Rev.: 6614


- swapped argument order of ASSERT_RESULT()

13 lines of code changed in 5 files:

April 2010 »

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