* 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:
* remove CAP2
- antique
- broken since [11839] (at least)
- nobody complained
2 lines of code changed in 5 files:
* fix conditional compilation of {{{findNode}}} and {{{setBranchlens}}}
* silence prototype warning
5 lines of code changed in 3 files:
* {{{-Wno-maybe-uninitialized}}} not known by clang
2 lines of code changed in 1 file:
* 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:
* fix clang warnings
3 lines of code changed in 3 files:
* replace init-by-memset for NA_Alignment
17 lines of code changed in 1 file:
* 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:
* reactivate sanitize=vptr
- failing code was fixed by log:trunk@13769:13772,13778:13779,13782
1 lines of code changed in 1 file:
* 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:
* 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:
* replace init-by-memset for {{{AP_tree_edge}}}
6 lines of code changed in 1 file:
* replace init-by-memset for {{{DI_ENTRY}}}, {{{DI_MATRIX}}} + {{{di_protdist}}}
88 lines of code changed in 4 files:
* 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:
* 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:
* 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:
* replace init-by-memset for {{{export_format}}}
14 lines of code changed in 1 file:
* replace init-by-memset for {{{AWT_species_set_root}}} + {{{AWT_species_set}}}
24 lines of code changed in 2 files:
* replace init-by-memset for {{{ED4_bases_table}}} + {{{ED4_char_table}}}
6 lines of code changed in 2 files:
* replace init-by-memset for {{{gb_cache}}}
21 lines of code changed in 2 files:
* reactivate sanitize=bounds
- failing code was fixed by [13767]
1 lines of code changed in 1 file:
* 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:
* 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:
* add missing dependencies for TOOLS (FILTER, INSDEL, REGEXPR + SEQIO)
- build randomly failed (at rare intervals)
8 lines of code changed in 2 files:
* reactivate/fix sanitize=null
- workaround undefined (but working) NULL-object-method-calls
11 lines of code changed in 4 files:
* fix warnings (maybe uninitialized; new reports by gcc 5.x)
3 lines of code changed in 2 files:
- fix warning (narrowing)
1 lines of code changed in 1 file:
* fix compilation for gcc 4.9.x (broken by [13760])
7 lines of code changed in 1 file:
* 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:
- add gcc 5.1.0
2 lines of code changed in 1 file:
* fixes #649
- skip DB deallocation (if it's memory mapped and not running with leak-sanitizer)
26 lines of code changed in 5 files:
* 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:
* add config manager to PHYL filter settings
* minor layout fixes
48 lines of code changed in 4 files:
* 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:
* 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:
- depends
1 lines of code changed in 1 file:
* stuff/suppress some leaks in ARB_DIST
11 lines of code changed in 3 files:
* delete ED4_ROOT
- fix dtor
- fix some free/delete mismatches
20 lines of code changed in 5 files:
- suppress more
3 lines of code changed in 1 file:
- print enter/leave directory lines
- show 30 biggest leaks by default
6 lines of code changed in 1 file:
- stuff leak
2 lines of code changed in 1 file:
* add convenience target to run arb with sanitizers
* suppress some common leaks
22 lines of code changed in 2 files:
* 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:
* move global buffers into a class
27 lines of code changed in 1 file:
* 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:
* osx compilation was broken by [13740]; attempt to "fix" that
4 lines of code changed in 1 file:
* 32bit crosscompile (on 64bit host) was broken by [13739]. fixed.
5 lines of code changed in 2 files:
* 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:
* 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:
* add config editor allowing to create config subsets
329 lines of code changed in 5 files:
* add config manager to PFOLD options
21 lines of code changed in 2 files:
* add config manager to helix properties
19 lines of code changed in 2 files:
* add config manager to editor options
47 lines of code changed in 2 files:
* add config manager to secedit display settings
* fix macro id for bond definition window (failed assertion)
63 lines of code changed in 4 files:
* add config manager to 'dot bases'
15 lines of code changed in 3 files:
* add config manager to SINA interface
44 lines of code changed in 2 files:
* awar code formatting
72 lines of code changed in 1 file:
* remove GA_AWAR_LOGLEVEL (no function)
0 lines of code changed in 1 file:
* 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:
* use typed callbacks in SINA interface
9 lines of code changed in 3 files:
* use different window-IDs for normal and advanced SINA window
1 lines of code changed in 1 file:
* add config manager to integrated aligners
54 lines of code changed in 6 files:
* compile fix [sic]
1 lines of code changed in 1 file:
* minor layout fixes for fast-aligner window (avoids some overlapping elements in gtk)
12 lines of code changed in 2 files:
* 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:
* add config managers to 'next relative searches'
44 lines of code changed in 4 files:
* 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:
* use typed callbacks in item interfaces
169 lines of code changed in 8 files:
* add config manager to 'modify fields'
25 lines of code changed in 2 files:
* add config manager to tree export
61 lines of code changed in 4 files:
* add config manager to branch analysis
41 lines of code changed in 3 files:
* use typed callbacks for config-manager-setup
34 lines of code changed in 8 files:
* add config manager to probe match
42 lines of code changed in 4 files:
* refactored bond awarname generation
17 lines of code changed in 1 file:
* add compatible config managers to
- consensus definition (EDIT4) and
- consensus SAI (NTREE)
204 lines of code changed in 9 files:
* replace magic awar names by defines
60 lines of code changed in 1 file:
fix 32bit-compilation for gcc 4.3.3 (gcc 4.4.3 did only warn)
1 lines of code changed in 1 file:
* chimera check: implement missing removal of report-entries
82 lines of code changed in 4 files:
* add config-manager to chimera check
32 lines of code changed in 3 files:
* add config-manager to sequence quality
27 lines of code changed in 3 files:
* 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:
* 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:
* avoid copy of {{{GmenuItemArg}}}; use ''const'' ref
7 lines of code changed in 2 files:
* formatting; locals
20 lines of code changed in 1 file:
* delete range-list on error
* do not show errors about missing SAI {{{''}}}
6 lines of code changed in 1 file:
* 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:
* filled empty help for 'Insert delete/using SAI'
43 lines of code changed in 1 file:
* auto-redisplay and auto-remake of displayed help-file (DEBUG only)
58 lines of code changed in 1 file:
* fix formats (32bit)
* fix NULL conversion
5 lines of code changed in 3 files:
* fix 32bit compilation broken by [13691]
13 lines of code changed in 1 file:
* 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:
* 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:
* 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:
* 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:
* visualize SAIs:
- correct help (menu references)
- add some predefined color definitions
37 lines of code changed in 2 files:
* add two predefined configs to parsimony optimizer settings
15 lines of code changed in 1 file:
* allow to define hardcoded configs
114 lines of code changed in 3 files:
* prefix 'cfg_' only in {{{set/get_config}}}
* do not export io error (just return it)
29 lines of code changed in 1 file:
* 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:
* refuse to store/restore config w/o name (stored entry was 'cfg_')
29 lines of code changed in 1 file:
* save/load config-manager comments to/from file
29 lines of code changed in 1 file:
- plain code move
49 lines of code changed in 1 file:
* store awars in AWT_configuration (no more special handling of VISIBLE_COMMENT)
30 lines of code changed in 1 file:
* replace magics
37 lines of code changed in 1 file:
* all awars in config-manager use "" as default (-> hardcode)
8 lines of code changed in 1 file:
* gtk layout fix
1 lines of code changed in 1 file:
* allows to comment configurations (config-manager)
112 lines of code changed in 4 files:
* fix layout of config-manager buttons (in gtk)
4 lines of code changed in 1 file:
* layout fixes; teaser
10 lines of code changed in 1 file:
* doc 'Factory defaults'
* sync with button names/order
6 lines of code changed in 1 file:
* awar_pointer is only allowed to keep {{{GBDATA*}}}
2 lines of code changed in 2 files:
* 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:
- adds {{{AW_awar::reset_to_default()}}}
13 lines of code changed in 2 files:
- doc menu entry changed with [13657]
1 lines of code changed in 1 file:
* 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:
* 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:
* 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:
* 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:
- fix progress counter
1 lines of code changed in 1 file:
* cleanup TREEDISP interface (names)
23 lines of code changed in 5 files:
- minor layout fixes
8 lines of code changed in 1 file:
* 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:
* fixes #645
* adds:
- log:branches/addtest@13650:13653
110 lines of code changed in 3 files: