March 2011 Commit Log

Number of Commits:
58
Number of Active Developers:
1
westram 2011-03-29 14:23 Rev.: 7352


- AISC still broken when compiled with -fstrict-aliasing (undo part of [7348])

5 lines of code changed in 1 file:

westram 2011-03-28 19:42 Rev.: 7348


- compile AISC again with -fstrict-aliasing
- fixed type-punnings

17 lines of code changed in 2 files:

westram 2011-03-28 18:45 Rev.: 7347


- compile with -fstrict-aliasing
- fixed type-punnings (fixes #28)

27 lines of code changed in 3 files:

westram 2011-03-28 17:32 Rev.: 7346


- added -Wextra and -Winit-self

14 lines of code changed in 1 file:

westram 2011-03-28 15:19 Rev.: 7345


- fixed !__ATTR!__FORMAT for member functions
- use STATIC_ATTRIBUTED

4 lines of code changed in 2 files:

westram 2011-03-28 15:06 Rev.: 7344


- possibility to temp.disable some warning types

20 lines of code changed in 1 file:

westram 2011-03-28 14:49 Rev.: 7343


- added -Wlogical-op (detailed check for 4.5.2)

31 lines of code changed in 1 file:

westram 2011-03-28 14:43 Rev.: 7342


- fixed a few warnings

25 lines of code changed in 4 files:

westram 2011-03-27 23:07 Rev.: 7341


- WARN_TODO

4 lines of code changed in 2 files:

westram 2011-03-27 23:05 Rev.: 7340


- added sevaral attribute 'format'

12 lines of code changed in 5 files:

westram 2011-03-27 22:52 Rev.: 7339


- prototypes for CORE were not generated by target 'proto'

4 lines of code changed in 4 files:

westram 2011-03-27 22:43 Rev.: 7338


- marked several functions as 'noreturn'

20 lines of code changed in 17 files:

westram 2011-03-27 18:04 Rev.: 7337


* possibility to toggle the TODO-warnings via config.makefile

212 lines of code changed in 65 files:

westram 2011-03-27 16:22 Rev.: 7336


* ARB_ERROR now complains in DEBUG mode (if not delivered)

2 lines of code changed in 1 file:

westram 2011-03-27 15:04 Rev.: 7335


* renamed intf (global typename from /usr/include/zconf.h)
* fixed several warnings
* put some #warnings into DEVEL_RALF

35 lines of code changed in 13 files:

westram 2011-03-27 13:50 Rev.: 7334


- fixed pass-NULL warnings

39 lines of code changed in 11 files:

westram 2011-03-27 13:04 Rev.: 7333


- if compiling with gcc 4.5.2++, use {{{__attribute__((deprecated("reason")))}}}
- declared deprecation reasons

27 lines of code changed in 9 files:

westram 2011-03-27 12:59 Rev.: 7332


- removed dead code

0 lines of code changed in 3 files:

westram 2011-03-27 11:48 Rev.: 7331


- tested and added gcc 4.5.2

69 lines of code changed in 2 files:

westram 2011-03-26 13:30 Rev.: 7330


merged from dev [7328]

* TEST_path_unfolding failed when lib/pts was a link

5 lines of code changed in 1 file:

westram 2011-03-25 13:58 Rev.: 7319


- RUI / crash when a position > alignmentLength was specified

1 lines of code changed in 1 file:

westram 2011-03-25 09:49 Rev.: 7318


typos

5 lines of code changed in 4 files:

westram 2011-03-24 19:42 Rev.: 7316


merged from dev [7283] [7285] [7297] [7298] [7299] [7305] [7306] [7307] [7308] [7311] [7312] [7313]
* fast aligner
- relative search optionally uses only data from aligned range
- fixed 2 RUIs
- added / changed tests
* !TargetRange
- made independent from target(sequence) to which it is applied
- added copy_corresponding_part() + tests
- added is_restricted() and op == !=
* fixes a bug in next relative search (when no upper limit was given, nothing was found)
* restricts oligo counting to !TargetRange of !FakeFamilyFinder (adapt PT server bahavior)
* !CompactedSubSequence
- fixed expdLength (was wrong if last position contained a base; failed assertion when !CompactedSequence did not contain bases - case seems not to occur during alignment)
- added tests for expdPosition() and compPosition() (documenting new behavior)
- test !CompactedSubSequence to be self-reflexive
- fixed bug in binary search (had no effect on aligner results for examples used in unittests)
* !CompactedSequence
- deny to construct from empty sequence

499 lines of code changed in 9 files:

westram 2011-03-24 19:24 Rev.: 7315


- depends / prototypes updated - completes [7314]

0 lines of code changed in 2 files:

westram 2011-03-24 19:20 Rev.: 7314


merged from dev [7300] [7301] [7309] [7310]

* move to CORE
- GBS_strstruct + old interface functions
- GB_strpartdup + GB_strndup
* templates to generate handy test-results
* removed dead code (constructSequence)

550 lines of code changed in 85 files:

westram 2011-03-23 19:22 Rev.: 7304


* nameserver
- always use 'ZZZ' or 'ZZZZZ' if out of prefix/suffix or advice missing
- when fullname started with non-alpha character, wrong advices were used
- fixed one bug introduced in [7303]

24 lines of code changed in 1 file:

westram 2011-03-23 18:44 Rev.: 7303


- nameserver
- fallback to 'Zzz'
- also generate short prefixes like 'C3p' (adds 260 previously unused prefixes)

23 lines of code changed in 1 file:

westram 2011-03-23 18:15 Rev.: 7302


- nameserver
- when failing to generate short prefix (3 chars) for first part of full_name, fall-back to 'Xxx' (instead of crashing)
- stuffed leak in check_for_case_error()

2 lines of code changed in 1 file:

westram 2011-03-19 13:10 Rev.: 7293


merged from dev [7282] [7284] [7286] [7287]

* fix ARB macros
* other minor things

8 lines of code changed in 4 files:

westram 2011-03-16 17:08 Rev.: 7279


- dependency

1 lines of code changed in 1 file:

westram 2011-03-16 16:46 Rev.: 7276


merged from dev [7263] [7269] [7270] [7273]

* multi probe wtf
* rounding prob in arb_export_rates (32/64bit)
* EDIT4 / jump to neg. positions

57 lines of code changed in 10 files:

westram 2011-03-16 16:42 Rev.: 7275


merged from dev [7265] [7266] [7267] [7268]
* when grouping locations of designed probes ('A=' 'A+' 'A-')
- use 'YZa-z'
- avoid overflow (prints '? ' now)

125 lines of code changed in 3 files:

westram 2011-03-16 16:25 Rev.: 7274


merged from dev [7262] [7264]

- fixed some typos (affecting probe design via 'arb_probe')

22 lines of code changed in 2 files:

westram 2011-03-16 13:04 Rev.: 7272


merged from dev [7244] [7250] [7251] [7252] [7253] [7254] [7255] [7257] [7258] [7259] [7260] [7261] [7271]
* extracted conversion logic of absolute <-> relative position into !BasePosition
- refactored BI_ecoli_ref and ED4_base_position (using !BasePosition)
- corrected input range of abs_2_rel ([0..N-1] -> [0..N])
* clean up chaos caused by different semantics of positions (biological[1..N] vs informational[0..N-1])
- commented (hopefully) all AWARs and variables which use biological positions
- made semantic changes explicit by using bio2info() and info2bio()
* positions passed to/reported by PTserver are now biological positions. Affects
- probe design (absolute position, ecoli range restriction)
- probe match (absolute position, ecoli position (bugfix see below)).
- !ProbeMatchParser does not change semantics
* fix several bugs
- ED4_jump_to_cursor_position limited position to screen before converting from relative to absolute position
- SEC_root::paintEcoliPositions added 1 to relative pos (instead of including position at cursor)
- ecoli position in probe match/PTserver (did not include ecoli-base at match position)
- ecoli range restriction in probe design/PTserver (check was broken, see [7261])
- base position for consensus terminals

743 lines of code changed in 50 files:

westram 2011-03-11 13:06 Rev.: 7248


merged from dev [7242] [7243] [7245]

* next-relative search in NTREE may be restricted to a target range

415 lines of code changed in 12 files:

westram 2011-03-11 12:58 Rev.: 7247


merged from dev [7225] [7226] [7233] [7229] [7230] [7231] [7232] [7234] [7235] [7236] [7237] [7238] [7239] [7240] [7241]

* made test-results from familysearch more easy to handle
* pt_server
- refactored postree-traversal
- refactored PT_read_chain (-> PT_forwhole_chain)
- fixed 3 logical bugs in next-relatives-search (see r7230 and r7232)
- added several warnings about dupped code/logic
- added PT_withall_tips
- moved debug code into separate file and renamed functions
- probe_tree.hxx -> probe_tree.h


1084 lines of code changed in 16 files:

westram 2011-03-11 12:31 Rev.: 7246


merged from dev [7227] [7228]

* extended !SmartPtr
* compile fix for coverage

52 lines of code changed in 14 files:

westram 2011-03-05 12:33 Rev.: 7223


- include arb_valgrind_logged into source

1 lines of code changed in 1 file:

westram 2011-03-04 16:36 Rev.: 7221


- fixed RUI and unclosed socket (error case)

8 lines of code changed in 2 files:

westram 2011-03-04 16:34 Rev.: 7220


- changed test timeout for valgrinded system calls

8 lines of code changed in 2 files:

westram 2011-03-04 16:30 Rev.: 7219


- more static leaks

27 lines of code changed in 3 files:

westram 2011-03-04 12:50 Rev.: 7218


- static leak

13 lines of code changed in 1 file:

westram 2011-03-04 11:26 Rev.: 7217


- calcSequenceChecksum (KISS, leak)

2 lines of code changed in 1 file:

westram 2011-03-04 11:04 Rev.: 7216


- fixed static leaks

22 lines of code changed in 3 files:

westram 2011-03-04 10:42 Rev.: 7215


* DRYed aisc_get_hostname() + aisc_client_get_hostname() + GB_get_hostname() -> arb_gethostname()
- stuffs static leak
* GB_host_is_local() ignores case

29 lines of code changed in 11 files:

westram 2011-03-04 10:40 Rev.: 7214


- static leak

5 lines of code changed in 1 file:

westram 2011-03-04 09:09 Rev.: 7213


- run build process in valgrind

5 lines of code changed in 1 file:

westram 2011-03-04 09:07 Rev.: 7212


- stuffed a few leaks

16 lines of code changed in 4 files:

westram 2011-03-03 20:38 Rev.: 7211


- fixed some RUIs

14 lines of code changed in 1 file:

westram 2011-03-03 20:30 Rev.: 7210


- changed valgrind options
- less leak resolution
- track file descriptors
- valgrind static init code

10 lines of code changed in 1 file:

westram 2011-03-03 20:25 Rev.: 7209


- changed meaning of VALGRIND flag in Makefile.setup
- fixed broken target 'valgrind' in UNIT_TESTER/Makefile.test (broken by [7202]; directory named like target)

32 lines of code changed in 5 files:

westram 2011-03-03 20:03 Rev.: 7208


- added arb_gethostbyname() to CORE lib
- replaced all calls to gethostbyname()
- force rebuilding .depends in XXX_COM

81 lines of code changed in 9 files:

westram 2011-03-03 13:48 Rev.: 7207


- do not warn about slow tests when external call has been valgrinded

2 lines of code changed in 1 file:

westram 2011-03-03 13:47 Rev.: 7206


- compile flag to restrict valgrinding to selected external calls
- touch w/o system

16 lines of code changed in 1 file:

westram 2011-03-03 13:41 Rev.: 7205


- wrong delete operator
- fixed RUI in PT_exit (destroy_PT_main uses psg)

2 lines of code changed in 1 file:

westram 2011-03-03 13:39 Rev.: 7204


- close unbound socket

4 lines of code changed in 1 file:

westram 2011-03-03 12:56 Rev.: 7203


- replaced magics for shutdown()

5 lines of code changed in 3 files:

westram 2011-03-02 14:38 Rev.: 7202


- call ptserver and several external tools (launched from TOOLS/arb_test.cxx) via valgrind, if valgrinding is requested inside unit tests

349 lines of code changed in 15 files:

February 2011 »

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