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westram 2023-07-11 11:38 Rev.: 19432

* {{{GBT_get_alignment_len}}}
- now also reports error if alignment length is zero
* this case often was unhandled and did easily lead to allocation problems.
- catch error in case of zero alignment length => fixes alloc-size-larger-than-warning (in {{{NT_count_different_chars}}}).
- check + fix callers.

1 lines of code changed in 1 file:

• STAT: ST_ml.cxx (+1 -1)

westram 2022-11-13 15:47 Rev.: 19339

* reintegrates 'refactor' into 'trunk'
- eliminates old interface of {{{GBS_strstruct}}}
- add a few new unittests (editor-config string + some PT-SERVER-functions)
* adds: log:branches/refactor@19300:19338

7 lines of code changed in 1 file:

• STAT: ST_quality.cxx (+7 -8)

westram 2022-03-30 16:31 Rev.: 18978

* remove unused mnemonic parameter to 'create_toggle_field'
- makes no sense anyway: having mnemonic for each toggle is sufficient (hence not implemented).

1 lines of code changed in 1 file:

• STAT: ST_window.cxx (+1 -1)

westram 2022-03-04 15:13 Rev.: 18962

* eliminate unused parameter {{{fallback2default}}} from {{{create_option_menu}}}.

2 lines of code changed in 1 file:

• STAT: ST_window.cxx (+2 -2)

westram 2022-03-04 11:26 Rev.: 18959

* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958

3 lines of code changed in 1 file:

• STAT: Makefile (+3)

westram 2021-09-15 12:52 Rev.: 18730

* remove trailing whitespace from c source.

21 lines of code changed in 5 files:

• STAT: ST_ml.cxx (+10 -10), ST_quality.cxx (+5 -5), ST_window.cxx (+3 -3), st_ml.hxx (+2 -2), st_quality.hxx (+1 -1)

westram 2021-09-15 12:39 Rev.: 18725

* rename {{{CPP_OBJECTS}}} -> {{{OBJECTS}}}.

5 lines of code changed in 1 file:

• STAT: Makefile (+5 -5)

westram 2021-09-15 12:00 Rev.: 18720

* select units using {{{wildcard}}}.

1 lines of code changed in 1 file:

• STAT: Makefile (+1 -4)

westram 2021-08-17 14:15 Rev.: 18665

* change many WARN_TODO triggered warnings into todo markers.

4 lines of code changed in 2 files:

• STAT: ST_ml.cxx (+1 -3), ST_quality.cxx (+3 -7)

westram 2019-04-01 16:41 Rev.: 17724

* partial merge from 'fts' into 'trunk'
- {{{ConfigMapping}}}:
* cleanup
* add missing tests
* fix config bug: trailing backslash at end of values did cause wrong read of data
* adds: log:branches/fts@17718:17723

2 lines of code changed in 1 file:

• STAT: Makefile (+2)

westram 2018-11-01 16:34 Rev.: 17599

* full update from child 'fix' into 'trunk'
* adds: log:branches/fix@17597:17598

24 lines of code changed in 1 file:

• STAT: ST_ml.cxx (+24 -4)

westram 2018-06-15 12:08 Rev.: 17110

* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109

5 lines of code changed in 1 file:

• STAT: ST_ml.cxx (+5 -5)

westram 2018-04-11 15:48 Rev.: 16880

* reintegrates 'multicore' into 'trunk'
- derive sequence classes able to be combined from new class {{{AP_combinableSeq}}}
* elim dummy functions from rest of hierarchy
- implements non-writing combine for add-species (speedup: 25-35%)
- introduce type {{{Mutations}}} => uses long everywhere (before mostly, but not always used float)
- allows use of {{{future}}}s
* nucleotide combine is able to calculate async (disabled via define atm -> {{{NEVER_COMBINE_ASYNC}}}; needs more work on calling algorithm)
* adds: log:branches/multicore@16769:16879

0 lines of code changed in 2 files:

• STAT: MostLikelySeq.hxx (-9), ST_ml.cxx (-22)

westram 2018-02-15 11:51 Rev.: 16861

* reintegrates 'unittest' into 'trunk'
- fixed non-deterministic behavior of add-species:
* 2 sequences in test-DB were identical (changed 1 bp)
* {{{AP_tree_edge}}} cannot be used to store insert-positions (uses pair of {{{AP_tree_nlen}}} instead)
* corrected some undefined behavior (results did depend on compiler version+flags):
- general order of inserts was undefined
- order of initial-insert was undefined (used by complete tree reconstruction)
- bugs fixed:
* not all possible insert-positions were tested
* sometimes species were added at wrong positions
* if multiple species were inserted at the same position, the following optimization
- did modify topology
- now optimizes all multi-inserts globally
- at leaf-positions: includes the leaf (Note: this does not modify the original topology)
* insert order now is "longest sequence first" (was "shortest sequence first")
- fixed unwanted behavior when testing for content of generated files
* adds: log:branches/unittest@16807:16860

6 lines of code changed in 2 files:

• STAT: MostLikelySeq.hxx (+1), ST_ml.cxx (+5 -1)

westram 2017-11-28 18:22 Rev.: 16766

* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

1 lines of code changed in 1 file:

• STAT: ST_ml.cxx (+1 -2)

westram 2017-11-28 17:09 Rev.: 16763

* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

48 lines of code changed in 5 files:

• STAT: MostLikelySeq.hxx (+1 -1), ST_ml.cxx (+30 -30), ST_quality.cxx (+9 -9), ST_window.cxx (+7 -7), st_ml.hxx (+1 -1)

westram 2017-11-06 13:54 Rev.: 16628

* reintegrates 'vectorize' into 'trunk'
- fixes #700
* documented vectorization-checks
* fine-grained check based on gcc-version
- drops old gcc-versions (<4.4.3)
- new attribute {{{__ATTR__DONT_VECTORIZE}}}
* disabled vectorization of {{{POS_TREE2::init_static()}}} for newer gcc-versions (generated code fails tests)
- added a bunch of new vectorization-checks (probably irrelevant to overall performance)
* adds: log:branches/vectorize@15531:16585,16595:16627

3 lines of code changed in 1 file:

• STAT: ST_ml.cxx (+3 -3)

westram 2017-06-29 14:18 Rev.: 16043

* reintegrates 'fix' into 'trunk'
- valgrind fixes
* generally repaired valgrinding (external tools)
* {{{group_scaling}}} was not initialized correct (RUI)
- DRYed code to run external tools from unittests
* adds: log:branches/fix@16037:16042

1 lines of code changed in 1 file:

• STAT: ST_ml.cxx (+1 -1)

westram 2016-08-11 10:05 Rev.: 15176

* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

8 lines of code changed in 2 files:

• STAT: Makefile (+3), ST_ml.cxx (+5 -5)

westram 2016-07-14 14:15 Rev.: 15054

* reintegrates 'color' into 'trunk'
- implements #443 (+parts of #444)
* adds: log:branches/color@14920:14921,14923:14928,14930:14939,14941:14951,14954:14956,14958:14959,14961:14964,14968,14970:14981,14985,14988,14990:14992,14994:14999,15001:15004,15007,15009,15012:15026,15028:15035,15037:15039,15041:15053

0 lines of code changed in 1 file:

• STAT: Makefile (-2)

westram 2016-04-29 17:02 Rev.: 14786

* reintegrates 'gde' into 'trunk'
- fixes #695
* adds: log:branches/gde@14670:14675,14682:14785

53 lines of code changed in 3 files:

• STAT: Makefile (+3), ST_quality.cxx (+2 -1), ST_window.cxx (+48 -18)

westram 2015-11-04 10:23 Rev.: 14455

* {{{AW_CB0}}} -> {{{WindowCallbackSimple}}}

5 lines of code changed in 3 files:

• STAT: ST_window.cxx (+1 -1), st_ml.hxx (+3 -3), st_window.hxx (+1 -1)

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

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

7 lines of code changed in 2 files:

• STAT: ST_window.cxx (+4), st_window.hxx (+3 -1)

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

* chimera check: implement missing removal of report-entries

73 lines of code changed in 3 files:

• STAT: Makefile (+4), ST_quality.cxx (+6 -6), ST_window.cxx (+63 -25)

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

* add config-manager to chimera check

18 lines of code changed in 2 files:

• STAT: Makefile (+1), ST_window.cxx (+17)

westram 2015-03-29 11:47 Rev.: 13625

* reintegrates 'pars' into 'trunk'
- fixes #528, #609, #620, #631, #633, #640, #641
- implements #619, #627
* adds:
- log:branches/addtest@13123:13260,13523:13551,13570
- log:branches/check@13365:13375,13450:13457
- log:branches/check2@13458:13465
- log:branches/fix@13522:13588
- log:branches/fixres@13270:13277,13279:13293,13295:13326
- log:branches/pars@12938:13280,13282:13325,13327:13387,13389:13527,13530:13624

19 lines of code changed in 4 files:

• STAT: Makefile (+1 -1), MostLikelySeq.hxx (+8), ST_ml.cxx (+9 -6), st_ml.hxx (+1 -2)

westram 2015-01-23 14:19 Rev.: 13443

* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

1 lines of code changed in 1 file:

• STAT: Makefile (+1 -1)

epruesse 2014-09-02 16:51 Rev.: 12815

fix common typos reported by lintian
- splitted -> split (irregular verb)
- ressources -> resources
- explicitely -> explicitly

1 lines of code changed in 1 file:

• STAT: st_quality.hxx (+1 -1)

westram 2014-05-12 15:16 Rev.: 12210

* create_selection_list_on_itemfields
- add and pass down new parameter 'fallback2default'

1 lines of code changed in 1 file:

• STAT: ST_window.cxx (+1 -9)

westram 2014-05-12 14:22 Rev.: 12205

* inlined default param for create_option_menu

2 lines of code changed in 1 file:

• STAT: ST_window.cxx (+2 -2)

westram 2014-04-30 13:36 Rev.: 12138

* reintegrates 'fix' into 'trunk'
- fixes #522
* adds:
- log:branches/fix@12058:12137

49 lines of code changed in 1 file:

• STAT: ST_ml.cxx (+49 -33)

westram 2014-04-27 13:24 Rev.: 12101

* chimera check
- renamed code, help, fig, macro id (to distinguish from 'sequence quality tool')
- try to document how it works

5 lines of code changed in 2 files:

• STAT: ST_window.cxx (+4 -4), st_window.hxx (+1 -1)

westram 2014-04-16 15:13 Rev.: 12043

* reintegrates 'fix' into 'trunk' (fixes #519)
- this patch wasn't really straightforward, instead each change caused new unexpected side effects. It's quite likely that i didn't detect all of them.
* adds:
- log:branches/fix@12023,12027:12042

37 lines of code changed in 1 file:

• STAT: ST_ml.cxx (+37 -33)

westram 2013-12-26 12:48 Rev.: 11401

* reintegrates 'tree' into 'trunk':
- consensus trees:
* support for merging partial trees ("worked" before, but results were crap; implements #65)
* generated trees are automatically re-rooted and -ordered
* always list source trees in consensus-tree-comment; show info about partial trees
* fixed progress bar
- made GBT_TREE a base class of other tree classes (implements #31)
- save tree properties in properties (not in DB)
- new functions 'Remove zombies/marked from ALL trees'
- tree load/save: layout fixes
- unit tests
* added tests for basic tree modifications (PARSIMONY)
- performance:
* compute_tree updates tree information in one traversal
* tree generators are now capable to generate any type of tree (w/o needing to copy it once)
- bugfixes:
* NNI (of marked species) was also always performed for colored species
* centered beautify-order is stable now
* improved 'search optimal root'
* adds:
- log:branches/tree@10500:10534,10542:11182,11184:11186,11188:11400
- log:branches/treeTests@11198:11335

7 lines of code changed in 2 files:

• STAT: Makefile (+1), ST_ml.cxx (+6 -6)

westram 2013-11-29 10:18 Rev.: 11262

* typed callback for
- uses of COLSTAT_create_selection_window()
- inside STAT

7 lines of code changed in 1 file:

• STAT: ST_window.cxx (+7 -9)

westram 2013-11-29 09:32 Rev.: 11261

* use awt_create_select_filter_win() as typed callback
* removed superfluous struct keyword
* renamed some variables ('cd'-ex)

1 lines of code changed in 1 file:

• STAT: ST_window.cxx (+1 -1)

westram 2013-11-02 20:28 Rev.: 11048

* use typed DB callbacks (rest)

6 lines of code changed in 1 file:

• STAT: ST_ml.cxx (+6 -8)

westram 2013-11-02 16:41 Rev.: 11034

* depends for [11033]

3 lines of code changed in 1 file:

• STAT: Makefile (+3)

westram 2013-11-01 14:50 Rev.: 11023

* publish DB callback interface separately from rest of DB interface

3 lines of code changed in 2 files:

• STAT: Makefile (+2), ST_ml.cxx (+1)

westram 2013-10-31 15:40 Rev.: 11002

* 'class { public' -> struct

2 lines of code changed in 1 file:

• STAT: st_quality.hxx (+2 -4)

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