April 2015 Commit Log

Number of Commits:
123
Number of Active Developers:
2
westram 2015-04-30 15:57 Rev.: 13793


* replace init-by-memset for {{{AW_window}}}, {{{AW_root_Motif}}} + {{{AW_window_Motif}}}
* add ctor for {{{AW_event}}}

91 lines of code changed in 2 files:

westram 2015-04-30 13:47 Rev.: 13791


* remove CAP2
- antique
- broken since [11839] (at least)
- nobody complained

2 lines of code changed in 5 files:

westram 2015-04-30 11:31 Rev.: 13790


* fix conditional compilation of {{{findNode}}} and {{{setBranchlens}}}
* silence prototype warning

5 lines of code changed in 3 files:

westram 2015-04-30 11:17 Rev.: 13789


* {{{-Wno-maybe-uninitialized}}} not known by clang

2 lines of code changed in 1 file:

westram 2015-04-30 10:39 Rev.: 13788


* fix bug introduced with [12975]; {{{count_weighted}}} calculated wrong results:[[BR]]{{{(weights[idx] * (c==0)) ? 1 : 0}}} instead of[[BR]]{{{weights[idx] * ((c==0) ? 1 : 0)}}}[[BR]]'*' binds stronger than '?:'; guided to by clang warning
* replaced {{{(c==0)?1:0}}} by {{{!c}}} where possible and vectorized
* checked vectorization with gcc 4.8.1, 4.9.2 and 5.1.0

17 lines of code changed in 3 files:

westram 2015-04-29 14:34 Rev.: 13787


* fix clang warnings

3 lines of code changed in 3 files:

westram 2015-04-29 14:33 Rev.: 13786


* replace init-by-memset for NA_Alignment

17 lines of code changed in 1 file:

westram 2015-04-29 14:04 Rev.: 13785


* reactivate sanitize=alignment, but disable it for ARBDB and PROBE (ptserver), which both extensively access non-aligned data

22 lines of code changed in 4 files:

westram 2015-04-29 12:32 Rev.: 13783


* reactivate sanitize=vptr
- failing code was fixed by log:trunk@13769:13772,13778:13779,13782

1 lines of code changed in 1 file:

westram 2015-04-29 12:27 Rev.: 13782


* replace init-by-memset for {{{AW_awar}}}, {{{AW_root}}} + {{{AW_selection_list}}}
* remove unused member {{{variable_set_by_toggle_field}}}

61 lines of code changed in 5 files:

westram 2015-04-29 11:32 Rev.: 13780


* expose display if {{{AWAR_DTREE_GREY_LEVEL}}} is changed (only useful in gtk version; harmless in motif)

1 lines of code changed in 1 file:

westram 2015-04-28 16:47 Rev.: 13779


* replace init-by-memset for {{{AP_tree_edge}}}

6 lines of code changed in 1 file:

westram 2015-04-28 16:40 Rev.: 13778


* replace init-by-memset for {{{DI_ENTRY}}}, {{{DI_MATRIX}}} + {{{di_protdist}}}

88 lines of code changed in 4 files:

westram 2015-04-28 13:29 Rev.: 13775


* bail out early if compiling with gcc 4.9.1, DEBUG=0 and SANITIZE!=0 (causes gcc crash)

10 lines of code changed in 1 file:

westram 2015-04-28 13:19 Rev.: 13774


* compilation with gcc 4.9.x++ / NDEBUG / SANITIZE!=0 failed with 'loop vectorization failed' error
- no longer expect loop vectorization when any sanitizer is active

10 lines of code changed in 1 file:

westram 2015-04-28 11:42 Rev.: 13773


* dont warn about deprecated decls
- fix would need new version of Eigen (delay update until compilation really fails)

3 lines of code changed in 1 file:

westram 2015-04-28 11:34 Rev.: 13772


* replace init-by-memset for {{{export_format}}}

14 lines of code changed in 1 file:

westram 2015-04-28 11:33 Rev.: 13771


* replace init-by-memset for {{{AWT_species_set_root}}} + {{{AWT_species_set}}}

24 lines of code changed in 2 files:

westram 2015-04-28 11:32 Rev.: 13770


* replace init-by-memset for {{{ED4_bases_table}}} + {{{ED4_char_table}}}

6 lines of code changed in 2 files:

westram 2015-04-28 10:43 Rev.: 13769


* replace init-by-memset for {{{gb_cache}}}

21 lines of code changed in 2 files:

westram 2015-04-27 14:53 Rev.: 13768


* reactivate sanitize=bounds
- failing code was fixed by [13767]

1 lines of code changed in 1 file:

westram 2015-04-27 14:42 Rev.: 13767


* introduce class {{{MaxBond}}} (holds max bond strength for std-bases)
* classes {{{MismatchWeights}}} and {{{Splits}}}
- move next to each other (they calculate most similar things)
- derive both from {{{MaxBond}}}
- make sure {{{Splits}}} is only used with std-bases (asan reported out-of-bounds array-access)
* eliminate {{{max_bonds}}} from {{{OutgroupMatcher}}}; use {{{MaxBond}}} from {{{Splits}}} instead
* eliminate {{{ptnd_check_max_bond}}} - use {{{MaxBond}}} instead

95 lines of code changed in 3 files:

westram 2015-04-27 10:59 Rev.: 13766


* undo part of [13760]
- failed to link RNACMA in jenkins/u1404/NDEBUG (uses gcc 4.8.2)
- could not reproduce that failure here (tried with gcc 4.8.1 and 4.8.3)
- rnacma will most likely terminate with runtime error when compiled with gcc 5.1.0 and ASAN

2 lines of code changed in 1 file:

westram 2015-04-27 09:06 Rev.: 13765


* add missing dependencies for TOOLS (FILTER, INSDEL, REGEXPR + SEQIO)
- build randomly failed (at rare intervals)

8 lines of code changed in 2 files:

westram 2015-04-26 15:42 Rev.: 13764


* reactivate/fix sanitize=null
- workaround undefined (but working) NULL-object-method-calls

11 lines of code changed in 4 files:

westram 2015-04-26 14:49 Rev.: 13763


* fix warnings (maybe uninitialized; new reports by gcc 5.x)

3 lines of code changed in 2 files:

westram 2015-04-26 14:41 Rev.: 13762


- fix warning (narrowing)

1 lines of code changed in 1 file:

westram 2015-04-26 14:05 Rev.: 13761


* fix compilation for gcc 4.9.x (broken by [13760])

7 lines of code changed in 1 file:

westram 2015-04-26 13:38 Rev.: 13760


* change link order to avoid runtime error
{{{
ASan runtime does not come first in initial library list
}}}
* (temp) disable failing asan-checks: vptr,alignment,null,bounds (introduced by gcc 5.x)

51 lines of code changed in 7 files:

westram 2015-04-25 14:31 Rev.: 13759


- add gcc 5.1.0

2 lines of code changed in 1 file:

westram 2015-04-25 12:46 Rev.: 13758


* fixes #649
- skip DB deallocation (if it's memory mapped and not running with leak-sanitizer)

26 lines of code changed in 5 files:

westram 2015-04-21 12:18 Rev.: 13755


* reintegrates 'pars' into 'trunk'
- only refactored some code and added a few missing tests
* adds:
- log:branches/pars@13627,13639:13754

120 lines of code changed in 11 files:

westram 2015-04-19 15:17 Rev.: 13754


* add config manager to PHYL filter settings
* minor layout fixes

48 lines of code changed in 4 files:

westram 2015-04-19 14:31 Rev.: 13753


* edit4 key mappings
- added config manager
- use 2-column layout
- replaced magic awar names by define/inline

85 lines of code changed in 5 files:

westram 2015-04-18 18:47 Rev.: 13752


* destroying {{{TreeNode}}}s from {{{TreeRoot}}} leads to pure virtual method call
- reason: class derived from {{{TreeRoot}}} already under deconstruction
- solution: delete from dtor of derived class. fixes #648

15 lines of code changed in 5 files:

westram 2015-04-18 18:46 Rev.: 13751


- depends

1 lines of code changed in 1 file:

westram 2015-04-18 16:50 Rev.: 13750


* stuff/suppress some leaks in ARB_DIST

11 lines of code changed in 3 files:

westram 2015-04-18 16:34 Rev.: 13749


* delete ED4_ROOT
- fix dtor
- fix some free/delete mismatches

20 lines of code changed in 5 files:

westram 2015-04-18 16:33 Rev.: 13748


- suppress more

3 lines of code changed in 1 file:

westram 2015-04-18 16:32 Rev.: 13747


- print enter/leave directory lines
- show 30 biggest leaks by default

6 lines of code changed in 1 file:

westram 2015-04-18 15:46 Rev.: 13746


- stuff leak

2 lines of code changed in 1 file:

westram 2015-04-18 15:46 Rev.: 13745


* add convenience target to run arb with sanitizers
* suppress some common leaks

22 lines of code changed in 2 files:

westram 2015-04-18 15:30 Rev.: 13744


* store/restore global buffers when updating db-browser
- if db-browser displays the property-db it receives callbacks on nearly every awar-change
- due to heavy use of global buffers it invalidates them on refresh
- because the property-db is transaction-free, the update occurs from "inside" the awar-change - ARB crashed if the awar-change itself depends on global-buffer contents

14 lines of code changed in 4 files:

westram 2015-04-18 14:11 Rev.: 13743


* move global buffers into a class

27 lines of code changed in 1 file:

westram 2015-04-18 14:09 Rev.: 13742


* use window local macro IDs (menu topics are inserted twice: in 'Species/Database fields admin' and 'Species Info/Fields')

6 lines of code changed in 1 file:

westram 2015-04-18 12:22 Rev.: 13741


* osx compilation was broken by [13740]; attempt to "fix" that

4 lines of code changed in 1 file:

westram 2015-04-18 11:51 Rev.: 13740


* 32bit crosscompile (on 64bit host) was broken by [13739]. fixed.

5 lines of code changed in 2 files:

westram 2015-04-17 16:15 Rev.: 13739


* fix #628
- use main cflags/lflags in PERL2ARB (not cross_cflags/cross_lflags)
- use content of environment variable EXECLIBS to dynalink to asan/ubsan libs
* reactivate test of perlscripts (reverts part of [12998])
* add '-Wno-unused-parameter' for perl module (cant fix macro XS)

8 lines of code changed in 4 files:

westram 2015-04-17 13:37 Rev.: 13738


* fix field selection values; just broke it before commit :/
* correct/touch selected field on field selection update

21 lines of code changed in 1 file:

westram 2015-04-17 13:00 Rev.: 13737


* add config editor allowing to create config subsets

329 lines of code changed in 5 files:

westram 2015-04-16 16:46 Rev.: 13736


* add config manager to PFOLD options

21 lines of code changed in 2 files:

westram 2015-04-16 16:30 Rev.: 13735


* add config manager to helix properties

19 lines of code changed in 2 files:

westram 2015-04-16 16:11 Rev.: 13734


* add config manager to editor options

47 lines of code changed in 2 files:

westram 2015-04-16 15:47 Rev.: 13733


* add config manager to secedit display settings
* fix macro id for bond definition window (failed assertion)

63 lines of code changed in 4 files:

westram 2015-04-16 15:15 Rev.: 13732


* add config manager to 'dot bases'

15 lines of code changed in 3 files:

westram 2015-04-16 14:15 Rev.: 13731


* add config manager to SINA interface

44 lines of code changed in 2 files:

westram 2015-04-16 13:58 Rev.: 13730


* awar code formatting

72 lines of code changed in 1 file:

westram 2015-04-16 13:56 Rev.: 13729


* remove GA_AWAR_LOGLEVEL (no function)

0 lines of code changed in 1 file:

westram 2015-04-16 13:42 Rev.: 13728


* fix macro recording for SINA interface
- toggling normal/advanced did not work (fixed by binding callback to awar)
- always create both config windows (makes sure all macro-ids are registered)

14 lines of code changed in 2 files:

westram 2015-04-16 12:50 Rev.: 13727


* use typed callbacks in SINA interface

9 lines of code changed in 3 files:

westram 2015-04-16 12:33 Rev.: 13726


* use different window-IDs for normal and advanced SINA window

1 lines of code changed in 1 file:

westram 2015-04-15 16:37 Rev.: 13725


* add config manager to integrated aligners

54 lines of code changed in 6 files:

westram 2015-04-15 15:35 Rev.: 13723


* compile fix [sic]

1 lines of code changed in 1 file:

westram 2015-04-15 14:25 Rev.: 13722


* minor layout fixes for fast-aligner window (avoids some overlapping elements in gtk)

12 lines of code changed in 2 files:

westram 2015-04-15 13:30 Rev.: 13720


* label handling
- comparing address of input char* stopped working (no idea why). caused #615
- use small helper class in RES_LABEL_CONVERT

66 lines of code changed in 3 files:

westram 2015-04-15 08:45 Rev.: 13719


* add config managers to 'next relative searches'

44 lines of code changed in 4 files:

westram 2015-04-15 08:37 Rev.: 13718


* config-manager
- do not handle unknown entries in configs as errors. Just print warnings showing details about restored and unknown entries.
- {{{AWT_config::write_to_awars}}} cannot fail anymore
- test and handle config parse-errors

59 lines of code changed in 2 files:

westram 2015-04-13 16:34 Rev.: 13717


* use typed callbacks in item interfaces

169 lines of code changed in 8 files:

westram 2015-04-13 15:21 Rev.: 13716


* add config manager to 'modify fields'

25 lines of code changed in 2 files:

westram 2015-04-13 14:41 Rev.: 13715


* add config manager to tree export

61 lines of code changed in 4 files:

westram 2015-04-13 14:04 Rev.: 13714


* add config manager to branch analysis

41 lines of code changed in 3 files:

westram 2015-04-13 11:34 Rev.: 13713


* use typed callbacks for config-manager-setup

34 lines of code changed in 8 files:

westram 2015-04-13 10:48 Rev.: 13712


* add config manager to probe match

42 lines of code changed in 4 files:

westram 2015-04-13 10:46 Rev.: 13711


* refactored bond awarname generation

17 lines of code changed in 1 file:

westram 2015-04-12 14:19 Rev.: 13710


* add compatible config managers to
- consensus definition (EDIT4) and
- consensus SAI (NTREE)

204 lines of code changed in 9 files:

westram 2015-04-12 13:53 Rev.: 13709


* replace magic awar names by defines

60 lines of code changed in 1 file:

arb_build 2015-04-12 12:16 Rev.: 13708

fix 32bit-compilation for gcc 4.3.3 (gcc 4.4.3 did only warn)

1 lines of code changed in 1 file:

westram 2015-04-11 12:48 Rev.: 13707


* chimera check: implement missing removal of report-entries

82 lines of code changed in 4 files:

westram 2015-04-11 10:29 Rev.: 13706


* add config-manager to chimera check

32 lines of code changed in 3 files:

westram 2015-04-11 10:10 Rev.: 13705


* add config-manager to sequence quality

27 lines of code changed in 3 files:

westram 2015-04-10 13:13 Rev.: 13704


* add config-managers to all GDE windows
- automatically handles any 'arg' defined in .menu files (if argtype != 'filename')
- changed layout (of all 3 gde .figs) to allow to place button for config-manager
- added warnings to gde_menus.hlp (which changes affect configs)

137 lines of code changed in 7 files:

westram 2015-04-10 12:30 Rev.: 13703


* config-manager crashed in 'Store', 'Restore' and 'Factory defaults', if config definition contains a missing awar (now just warns)

25 lines of code changed in 1 file:

westram 2015-04-10 10:04 Rev.: 13702


* avoid copy of {{{GmenuItemArg}}}; use ''const'' ref

7 lines of code changed in 2 files:

westram 2015-04-10 09:53 Rev.: 13701


* formatting; locals

20 lines of code changed in 1 file:

westram 2015-04-10 08:44 Rev.: 13700


* delete range-list on error
* do not show errors about missing SAI {{{''}}}

6 lines of code changed in 1 file:

westram 2015-04-10 08:32 Rev.: 13699


* insert/delete by SAI
- added config manager + predefined configs
- switch values of !SaiContains (reinit AWAR_INSDEL_CONTAINS by rename)
- AWAR_INSDEL_AFFECTED now temp

48 lines of code changed in 3 files:

westram 2015-04-09 15:10 Rev.: 13698


* filled empty help for 'Insert delete/using SAI'

43 lines of code changed in 1 file:

westram 2015-04-09 14:25 Rev.: 13696


* auto-redisplay and auto-remake of displayed help-file (DEBUG only)

58 lines of code changed in 1 file:

westram 2015-04-09 09:15 Rev.: 13695


* fix formats (32bit)
* fix NULL conversion

5 lines of code changed in 3 files:

westram 2015-04-09 09:14 Rev.: 13694


* fix 32bit compilation broken by [13691]

13 lines of code changed in 1 file:

westram 2015-04-09 08:52 Rev.: 13693


* rename species
- changed some progress titles
- progress for commit phase does not include pseudo-species part for non-genome-dbs

29 lines of code changed in 3 files:

westram 2015-04-08 17:30 Rev.: 13692


* use full progress bar for rename-phase (and a second one for changes to trees, configs, etc.)

1 lines of code changed in 1 file:

westram 2015-04-08 16:35 Rev.: 13691


* fixes #646
- nameserver restarted name-modification for identical prefixes (but different suffixes)
- remember counters for all prefix-lengths in hash -> fixes above problem
* added a third method to generate names:
- use 1-letter-prefix (a-z) plus 7-letter-suffix (base36-encoded)
- this will allow to produce all possible short-names (2037468266496 = 1.8 !TeraNames)
* terminate nameserver with fatal error if (ever) reached
- names generated with this method will start with a lower case letter
* misleading warning ("Failed to make a short-name")
- removed from NDEBUG
- now says "Failed to find a unique short prefix for word"

93 lines of code changed in 1 file:

westram 2015-04-07 17:47 Rev.: 13690


* NDS
- optionally uses only visible definitions -> allows to switch between 6 sets of max. 10 defined entries
- default is to display all 60 entries (as done before)

73 lines of code changed in 4 files:

westram 2015-04-07 12:04 Rev.: 13689


* visualize SAIs:
- correct help (menu references)
- add some predefined color definitions

37 lines of code changed in 2 files:

westram 2015-04-07 11:13 Rev.: 13688


* add two predefined configs to parsimony optimizer settings

15 lines of code changed in 1 file:

westram 2015-04-07 11:04 Rev.: 13687


* allow to define hardcoded configs

114 lines of code changed in 3 files:

westram 2015-04-07 09:50 Rev.: 13686


* prefix 'cfg_' only in {{{set/get_config}}}
* do not export io error (just return it)

29 lines of code changed in 1 file:

westram 2015-04-07 08:02 Rev.: 13685


* erase deleted configs from properties
- do not misuse awars to access stored config values (awars cannot be easily deleted)

60 lines of code changed in 3 files:

westram 2015-04-05 14:40 Rev.: 13684


* refuse to store/restore config w/o name (stored entry was 'cfg_')

29 lines of code changed in 1 file:

westram 2015-04-05 14:14 Rev.: 13683


* save/load config-manager comments to/from file

29 lines of code changed in 1 file:

westram 2015-04-05 13:56 Rev.: 13682


- plain code move

49 lines of code changed in 1 file:

westram 2015-04-05 13:41 Rev.: 13681


* store awars in AWT_configuration (no more special handling of VISIBLE_COMMENT)

30 lines of code changed in 1 file:

westram 2015-04-05 13:12 Rev.: 13680


* replace magics

37 lines of code changed in 1 file:

westram 2015-04-05 13:00 Rev.: 13679


* all awars in config-manager use "" as default (-> hardcode)

8 lines of code changed in 1 file:

westram 2015-04-05 12:28 Rev.: 13678


* gtk layout fix

1 lines of code changed in 1 file:

westram 2015-04-05 12:22 Rev.: 13677


* allows to comment configurations (config-manager)

112 lines of code changed in 4 files:

westram 2015-04-04 15:52 Rev.: 13676


* fix layout of config-manager buttons (in gtk)

4 lines of code changed in 1 file:

westram 2015-04-04 15:05 Rev.: 13674


* layout fixes; teaser

10 lines of code changed in 1 file:

westram 2015-04-04 14:45 Rev.: 13673


* doc 'Factory defaults'
* sync with button names/order

6 lines of code changed in 1 file:

westram 2015-04-04 14:12 Rev.: 13670


* awar_pointer is only allowed to keep {{{GBDATA*}}}

2 lines of code changed in 2 files:

westram 2015-04-04 13:17 Rev.: 13668


* adds 'Factory defaults' to config-manager
- default behavior is to reset all awars handled by config-manager to their default values
- can be customized to any action. This is now used
* in NDS (where AWARs have just empty/zero defaults). Uses modified {{{create_nds_vars()}}} to restore defaults.
* in gene species transfer definitions (where some of the stored awars contain a set of translation rules)

149 lines of code changed in 8 files:

westram 2015-04-04 12:04 Rev.: 13667


- adds {{{AW_awar::reset_to_default()}}}

13 lines of code changed in 2 files:

westram 2015-04-04 09:47 Rev.: 13666


- doc menu entry changed with [13657]

1 lines of code changed in 1 file:

westram 2015-04-03 16:51 Rev.: 13665


* added less custom ways to install config-managers:
- using fixed mapping ({{{AWT_config_mapping_def}}})
- using a setup-callback for {{{AWT_config_definition}}}
* replaced all config-managers by less custom versions where possible. Exceptions:
- NDS (does some custom conversion from older data-format)
- merge-tool/gene-species (uses user-defined definitions-sets)

72 lines of code changed in 11 files:

westram 2015-04-03 14:59 Rev.: 13664


* avoid pitfall when doing {{{restore CONFIG1, select CONFIG2 and press SAVE}}}
- old behavior: CONFIG2 was overwritten with settings from CONFIG1; saved file also contained settings from CONFIG1 (both unintended, happened silently)
- new behavior: restores CONFIG2 and saves settings into file

2 lines of code changed in 2 files:

westram 2015-04-03 14:30 Rev.: 13663


* config-restore failed to restore under some conditions:
- if AWAR1 is restored prior to AWAR2 and changing the value of AWAR2 causes AWAR1 to adapt its value => AWAR1 did not contain stored value
* added hack against that problem:
- if {{{current==stored}}} => do nothing
- if afterwards {{{current!=stored}}} => restore again (repeat until no further change or retried 10x)
- warns about failed restore

31 lines of code changed in 1 file:

westram 2015-04-03 12:27 Rev.: 13662


* replace manual/widget-bound by awar-bound update-callbacks (motivation: eliminate custom call in {{{primer_design_restore_config}}})
* display memory estimation non-editable
* allow explicit primer length (no reason to insist on a length-range>1)

56 lines of code changed in 1 file:

westram 2015-04-03 12:20 Rev.: 13661


- fix progress counter

1 lines of code changed in 1 file:

westram 2015-04-02 11:20 Rev.: 13659


* cleanup TREEDISP interface (names)

23 lines of code changed in 5 files:

westram 2015-04-02 10:58 Rev.: 13658


- minor layout fixes

8 lines of code changed in 1 file:

westram 2015-04-02 10:31 Rev.: 13657


* fix 'Tree options'
- move code into SL/TREEDISP
- DRY window (use same code from ARB_NTREE and ARB_PARSIMONY). Provides missing options + config-manager in ARB_PARSIMONY.
- DRY/fix callback-bindings. Fixes missing tree refreshes in ARB_PARSIMONY.
- sync 'Properties' menus

163 lines of code changed in 6 files:

westram 2015-04-01 14:19 Rev.: 13654


* fixes #645
* adds:
- log:branches/addtest@13650:13653

110 lines of code changed in 3 files:

March 2015 »

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