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westram 2023-07-11 12:38 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:

• DIST: DI_matr.cxx (+1 -1)

westram 2022-10-22 19:30 Rev.: 19283

* allow to define a separator used to generate clusternames
- old hardcoded default was '_' (which interferes with groupname conventions)
- new customisable default is '-'
- use custom separator
* in get_upgroup_info().
* for matchrate.
- correctly handle empty separator.
* change other hardcoded characters
- avoid '_' in {{{WHOLE_TREE}}} (now uses {{{<WHOLE TREE>}}}).
- neighter use '/' nor '-' when inserting relative notation (old: {{{3-4/7}}} new {{{3.4[7]}}}).
* part of #832

20 lines of code changed in 3 files:

• DIST: DI_clusters.cxx (+16 -8), DI_foundclusters.cxx (+3 -3), di_foundclusters.hxx (+1 -1)

westram 2022-10-21 16:04 Rev.: 19277

* use {{{MessageSpamFilter}}} when generating groups:
- from callers which may spam arbs message box.
* part of #832

7 lines of code changed in 2 files:

• DIST: DI_clusters.cxx (+6 -1), Makefile (+1)

westram 2022-10-19 17:29 Rev.: 19273

* if keeled group is used to describe cluster
- previously crashed (see #851). fixed by not accessing {{{TreeNode::name}}} directly.
- now gets prefixed with {{{KEELED_INDICATOR}}}.

2 lines of code changed in 1 file:

• DIST: DI_foundclusters.cxx (+2 -1)

westram 2022-08-03 15:52 Rev.: 19206

* reintegrates 'ali' into 'trunk'
* adds: log:branches/ali@19183:19205

13 lines of code changed in 2 files:

• DIST: DI_main.cxx (+4 -3), DI_matr.cxx (+9 -3)

westram 2022-03-04 16:20 Rev.: 18964

* remove parameter {{{fallback2default}}} from
- {{{create_selection_list}}}
- {{{create_list}}}
- {{{awt_create_TREE_selection_list}}}
- {{{awt_create_CONFIG_selection_list}}}
- {{{awt_create_SAI_selection_list}}}
* remove some - now unused - locals.

2 lines of code changed in 2 files:

• DIST: DI_clusters.cxx (+1 -1), DI_matr.cxx (+1 -1)

westram 2022-03-04 16:13 Rev.: 18962

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

8 lines of code changed in 2 files:

• DIST: DI_clusters.cxx (+5 -5), DI_matr.cxx (+3 -3)

westram 2022-03-04 12:26 Rev.: 18959

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

143 lines of code changed in 2 files:

• DIST: DI_matr.cxx (+127 -70), Makefile (+16)

westram 2021-12-20 18:44 Rev.: 18883

* reintegrates 'nds' into 'trunk'
- fixes #841
* adds: log:branches/nds@18843:18882

10 lines of code changed in 1 file:

• DIST: DI_save_matr.cxx (+10 -11)

westram 2021-11-12 14:47 Rev.: 18841

* add progress to {{{neighbourjoining()}}}-phase (this may be really long running)
- add one extra progress to {{{di_calculate_tree_cb()}}} encapsulating matrix-calculation + {{{neighbourjoining()}}}-phase.
- progress inside {{{di_calculate_matrix()}}} now counts 2 steps: loading data + matrix-calculation.

17 lines of code changed in 1 file:

• DIST: DI_matr.cxx (+17 -6)

westram 2021-09-15 13:52 Rev.: 18730

* remove trailing whitespace from c source.

6 lines of code changed in 3 files:

• DIST: DI_clusters.cxx (+3 -3), DI_clustertree.cxx (+2 -2), di_foundclusters.hxx (+1 -1)

westram 2021-09-15 13:48 Rev.: 18729

* eliminate trailing whitespace from Makefiles.

1 lines of code changed in 1 file:

• DIST: Makefile (+1 -1)

westram 2021-09-15 13:39 Rev.: 18725

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

6 lines of code changed in 1 file:

• DIST: Makefile (+6 -5)

westram 2021-09-15 13:00 Rev.: 18720

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

1 lines of code changed in 1 file:

• DIST: Makefile (+1 -11)

westram 2021-09-07 10:37 Rev.: 18704

* reintegrates 'tree' into 'trunk'
* adds: log:branches/tree@18666:18703

3 lines of code changed in 2 files:

• DIST: DI_save_matr.cxx (+2 -3), Makefile (+1)

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

* change many WARN_TODO triggered warnings into todo markers.

1 lines of code changed in 1 file:

• DIST: DI_view_matrix.cxx (+1 -3)

westram 2020-11-10 17:24 Rev.: 18634

* reintegrates 'root' into 'trunk'
- implements #449
* adds: log:branches/root@18451:18633

10 lines of code changed in 2 files:

• DIST: DI_matr.cxx (+3 -1), Makefile (+7)

westram 2020-03-03 13:23 Rev.: 18352

* full update from child 'fix' into 'trunk'
* adds: log:branches/fix@18339:18351

100 lines of code changed in 6 files:

• DIST: DI_main.cxx (+13 -15), DI_matr.cxx (+52 -48), DI_view_matrix.cxx (+7 -8), Makefile (-2), di_view_matrix.hxx (+28 -25), dist.hxx (del)

westram 2019-10-08 17:51 Rev.: 18159

* full update from child 'fix' into 'trunk'
- fix item name accessors ({{{GBT_get_name}}} + {{{GBT_get_name_or_description}}})
- add {{{null2empty}}}
* adds: log:branches/fix@18140:18158

3 lines of code changed in 2 files:

• DIST: DI_clusters.cxx (+2 -3), DI_matr.cxx (+1 -1)

westram 2019-05-10 13:57 Rev.: 17877

* reintegrates 'gcc' into 'trunk'
* adds: log:branches/gcc@17850:17876

1 lines of code changed in 1 file:

• DIST: DI_protdist.cxx (+1 -1)

westram 2019-04-01 17:41 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:

• DIST: Makefile (+2)

westram 2018-10-17 11:00 Rev.: 17478

* reintegrates 'svalues' into 'trunk'
- implements #614
* adds: log:branches/svalues@17357:17419,17428:17464,17469,17471:17477

4 lines of code changed in 1 file:

• DIST: DI_matr.cxx (+4 -1)

westram 2018-07-23 16:52 Rev.: 17262

* partial merge from 'group' into 'trunk'
- fixes to arb_progress
* adds:
- log:branches/group@17191:17218,17220:17260
- log:branches/progress@17195:17216,17218:17259

4 lines of code changed in 2 files:

• DIST: DI_clustertree.cxx (+1 -1), DI_matr.cxx (+3 -3)

westram 2018-07-13 13:12 Rev.: 17192

* DRY

5 lines of code changed in 1 file:

• DIST: DI_protdist.cxx (+5 -5)

westram 2018-07-13 13:05 Rev.: 17191

* use {{{hypot}}}

23 lines of code changed in 1 file:

• DIST: DI_protdist.cxx (+23 -17)

westram 2018-07-10 16:48 Rev.: 17178

* reintegrates 'gcc' into 'trunk'
- complete arb port to gcc 8.1
- fixes NDEBUG-related issues (not handled by [16986])
* adds: log:branches/gcc@17164:17177

11 lines of code changed in 2 files:

• DIST: DI_matr.cxx (+3 -1), DI_protdist.cxx (+8 -8)

westram 2018-06-15 13:08 Rev.: 17110

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

25 lines of code changed in 6 files:

• DIST: DI_clusters.cxx (+10 -8), DI_clustertree.cxx (+8 -8), DI_compress_matrix.cxx (+1 -1), DI_foundclusters.cxx (+3 -3), DI_matr.cxx (+2 -2), di_matr.hxx (+1 -1)

westram 2018-05-04 18:06 Rev.: 16986

* reintegrates 'gcc' into 'trunk'
- ports arb to gcc 8.1 (fixing warnings)
* adds: log:branches/gcc@16965:16985

Update: continued by [17178]

3 lines of code changed in 1 file:

• DIST: di_protdist.hxx (+3 -3)

westram 2018-05-02 11:32 Rev.: 16961

* partial merge from 'fix' into 'trunk'
- refactored {{{AW_device}}} text output
* reduces calls to strlen (using {{{SizedCstr}}})
* eliminated/modernized several parameters/functions (esp. in {{{TextOverlayCallback}}}s)
* adds: log:branches/fix@16939:16960

1 lines of code changed in 1 file:

• DIST: Makefile (+1)

westram 2018-04-30 18:27 Rev.: 16936

* reintegrates 'cleanup' into 'trunk'
- performs #762 (shrink 3.7 k)
* adds: log:branches/cleanup@16924:16935

0 lines of code changed in 1 file:

• DIST: DI_matr.cxx (-2)

westram 2018-04-11 16:48 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

10 lines of code changed in 2 files:

• DIST: DI_clustertree.cxx (+9 -8), di_clustertree.hxx (+1)

westram 2017-11-28 19:22 Rev.: 16766

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

113 lines of code changed in 4 files:

• DIST: DI_clusters.cxx (+1 -1), DI_matr.cxx (+1 -1), DI_protdist.cxx (+18 -27), DI_save_matr.cxx (+93 -95)

westram 2017-11-28 18:09 Rev.: 16763

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

169 lines of code changed in 13 files:

• DIST: DI_clusters.cxx (+17 -17), DI_clustertree.cxx (+10 -10), DI_compress_matrix.cxx (+7 -7), DI_foundclusters.cxx (+14 -14), DI_main.cxx (+1 -1), DI_matr.cxx (+65 -65), DI_protdist.cxx (+11 -11), DI_save_matr.cxx (+2 -2), DI_view_matrix.cxx (+17 -17), di_clustertree.hxx (+17 -17), di_foundclusters.hxx (+2 -2), di_matr.hxx (+4 -4), di_view_matrix.hxx (+2 -2)

westram 2017-11-28 12:32 Rev.: 16761

* remove set but unused variable (distance cancel chars not used in "auto-detect correction"; could be passed to auto-detector)

2 lines of code changed in 1 file:

• DIST: DI_matr.cxx (+2 -2)

westram 2017-11-19 16:19 Rev.: 16683

* full update from child 'gcc' into 'trunk'
- more warning fixes
- fix bug in prettyprint
* adds: log:branches/gcc@16668:16682

2 lines of code changed in 1 file:

• DIST: DI_view_matrix.cxx (+2 -1)

westram 2017-01-04 18:06 Rev.: 15513

* reintegrates 'warnings' into 'trunk'
- activate additional warnings (gcc 5.x++)
- Cxx11-forward final (classes+methods)
- fix tag problems caused by using preprocessor
* adds: log:branches/warnings@15486:15489,15491:15501,15506:15512

4 lines of code changed in 2 files:

• DIST: DI_clusters.cxx (+2 -2), di_clustertree.hxx (+2 -2)

westram 2016-08-30 14:26 Rev.: 15256

* replace redundant data {{{AW_font_limits::height}}} with {{{get_height()}}}

2 lines of code changed in 1 file:

• DIST: DI_view_matrix.cxx (+2 -2)

westram 2016-08-30 12:30 Rev.: 15254

* depends for [15253]

1 lines of code changed in 1 file:

• DIST: Makefile (+1)

westram 2016-08-17 20:39 Rev.: 15198

* remove {{{virtual}}} if {{{OVERRIDE}}} is present
- OVERRIDE implies 'implicit virtual' (if code compiles as C++11 <- tested on build server!)

2 lines of code changed in 2 files:

• DIST: DI_clusters.cxx (+1 -1), di_clustertree.hxx (+1 -1)

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

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

40 lines of code changed in 8 files:

• DIST: DI_clusters.cxx (+2 -2), DI_compress_matrix.cxx (+4 -4), DI_foundclusters.cxx (+1 -1), DI_matr.cxx (+10 -11), DI_protdist.cxx (+11 -9), DI_save_matr.cxx (+1 -1), Makefile (+10), di_matr.hxx (+1 -1)

(341 more)