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westram 2025-01-30 13:19 Rev.: 19500

* rename {{{GBT_create_alignment}}} -> {{{GBT_create_new_alignment}}}.
* restore old {{{GBT_create_alignment}}} flavor used before r19146 for binary compatibility.

14 lines of code changed in 2 files:

• ARBDB: ad_t_prot.h (+2 -1), adali.cxx (+12 -2)

westram 2023-07-13 18:34 Rev.: 19437

* fix bogus warning
{{{
adTest.cxx:154: warning: '%s' directive argument is null [-Wformat-overflow=]
adTest.cxx:154: warning: '%s' directive argument is null [-Wformat-overflow=]
}}}

1 lines of code changed in 1 file:

• ARBDB: adTest.cxx (+1)

westram 2023-07-13 17:44 Rev.: 19435

* fix NDEBUG builds for gcc 10.1 - 10.5
- allow to use 10.4 + 10.5
- expect 18 vectorizations starting with gcc 10.1
- suppress bogus warning
- similar to [19434]

1 lines of code changed in 1 file:

• ARBDB: adoptimize.cxx (+1 -1)

westram 2023-07-13 16:34 Rev.: 19434

* fixes for gcc 10.3:
- suppress known bogus warning
- set vectorization count to 18

1 lines of code changed in 1 file:

• ARBDB: adoptimize.cxx (+1 -1)

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.

9 lines of code changed in 2 files:

• ARBDB: adali.cxx (+7 -2), adseqcompr.cxx (+2 -2)

westram 2023-07-11 12:35 Rev.: 19431

* fix NDEBUG warnings (gcc 10.2)
- by simplifying {{{GB_transaction}}} dtor (completely separates asserting from not-asserting code)
- format-overflow-warning.

5 lines of code changed in 1 file:

• ARBDB: arbdbpp.cxx (+5 -3)

westram 2023-07-11 11:04 Rev.: 19430

* un-inline {{{CharPtrArray::remove}}} to get rid of vectorizer warning.
* note strange vectorization count for gcc 10.2.0

1 lines of code changed in 1 file:

• ARBDB: adoptimize.cxx (+1 -1)

westram 2023-06-28 09:02 Rev.: 19415

* fix {{{ARB_edge::iteration_count()}}}:
- did report ''negative'' counts for broken trees (see previous commit)
- added tests; fixed behavior: now returns zero in these cases.
* accept zero as increment amount to {{{arb_progress::inc_by()}}}.

9 lines of code changed in 2 files:

• ARBDB: TreeNode.cxx (+8), TreeNode.h (+1 -1)

westram 2023-06-28 08:56 Rev.: 19414

* warn when invalid trees exist (e.g. relicts from old bug, caused by deleting all species).

6 lines of code changed in 1 file:

• ARBDB: adtree.cxx (+6 -1)

westram 2023-05-31 09:21 Rev.: 19365

* string splitters:
- unittests for {{{GBT_split_string}}}:
* add tests for dropEmptyTokens.
* document special behavior for empty string.
- define enum {{{SplitMode}}}. use enum instead of bool param for GBT_splitNdestroy_string + GBT_split_string.

1 lines of code changed in 1 file:

• ARBDB: adlang1.cxx (+1 -1)

westram 2022-11-13 19:29 Rev.: 19346

* reintegrates 'refactor' into 'trunk'
- polish {{{GBS_strstruct}}}
* adds: log:branches/refactor@19339:19345

11 lines of code changed in 6 files:

• ARBDB: aditem.cxx (+1 -1), adlang1.cxx (+1 -1), adname.cxx (+1 -1), adsocket.cxx (+1 -1), adstring.cxx (+6 -6), gb_aci.cxx (+1 -1)

westram 2022-11-13 16:47 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

220 lines of code changed in 12 files:

• ARBDB: adGene.cxx (+17 -27), ad_config.cxx (+7 -10), ad_config.h (+5 -2), adali.cxx (+5), adhash.cxx (+9 -12), adindex.cxx (+27 -24), aditem.cxx (+6 -7), adlang1.cxx (+80 -80), adname.cxx (+5 -7), adsocket.cxx (+10 -10), adstring.cxx (+46 -58), gb_aci.cxx (+3 -3)

westram 2022-10-22 19:24 Rev.: 19282

* reject groupnames which would be misinterpreted as bootstrap values
- misinterpretation would happen during re-import after export

22 lines of code changed in 1 file:

• ARBDB: adtree.cxx (+22)

westram 2022-10-22 19:19 Rev.: 19281

* pull-out {{{parse_treelabel()}}} from {{{setBranchName_acceptingBootstrap()}}}.

38 lines of code changed in 1 file:

• ARBDB: TreeNode.h (+38)

westram 2022-10-22 19:14 Rev.: 19279

* use + add wrapped concatenators to {{{GBS_strstruct}}}

1 lines of code changed in 1 file:

• ARBDB: adstring.cxx (+1 -3)

westram 2022-10-21 16:08 Rev.: 19278

* warn about..
- {{{;}}} in group names (conflicts with taxonomy).
- group names containing underscores (reserved for group overlaps).
- group names ending with {{{~NUM}}} (reserved for splitted groups).

24 lines of code changed in 1 file:

• ARBDB: adtree.cxx (+24 -4)

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

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

5 lines of code changed in 2 files:

• ARBDB: Makefile (+1), adtree.cxx (+4)

westram 2022-10-19 17:24 Rev.: 19272

* define + use KEELED_INDICATOR instead of hardcoding '!'\\=> related code is now easy to find.

8 lines of code changed in 3 files:

• ARBDB: TreeNode.h (+2), adlang1.cxx (+3 -2), adtree.cxx (+3 -3)

westram 2022-09-02 14:38 Rev.: 19249

* revive old version of {{{GBT_add_new_changekey}}} (=interface before [19140]).
- mark as deprecated
- implement via {{{GBT_add_new_species_changekey}}}
- fixes binary compatibility for sina 1.3 binary (still used on ubuntu 10.04)

11 lines of code changed in 2 files:

• ARBDB: adChangeKey.cxx (+10), ad_t_prot.h (+1)

westram 2022-09-02 14:35 Rev.: 19248

* rename {{{GBT_add_new_changekey}}} -> {{{GBT_add_new_species_changekey}}}.

3 lines of code changed in 2 files:

• ARBDB: adChangeKey.cxx (+2 -2), ad_t_prot.h (+1 -1)

westram 2022-09-01 16:19 Rev.: 19245

* reintegrates 'sina' into 'trunk'
- build/deliver sina together with arb
* adds: log:branches/sina@18984:19043,19046:19069,19072:19244

8 lines of code changed in 4 files:

• ARBDB: adali.cxx (+1 -1), adoptimize.cxx (+1 -1), adseqcompr.cxx (+3 -3), adtcp.cxx (+3 -1)

westram 2022-08-06 19:25 Rev.: 19222

* reintegrates 'split' into 'trunk'
- completes #846
* adds: log:branches/split@19169:19221

24 lines of code changed in 1 file:

• ARBDB: adali.cxx (+24 -19)

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

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

138 lines of code changed in 5 files:

• ARBDB: Makefile (+1), ad_t_prot.h (+2), adali.cxx (+128 -25), adlang1.cxx (+6 -4), adseqcompr.cxx (+1 -2)

westram 2022-07-21 14:01 Rev.: 19167

* reintegrates 'split' into 'trunk'
* adds: log:branches/split@19102:19166

178 lines of code changed in 10 files:

• ARBDB: adChangeKey.cxx (+9), ad_config.cxx (+1 -4), ad_t_prot.h (+5 -2), adali.cxx (+119 -34), adfile.cxx (+1 -3), adtcp.cxx (+8 -14), adtools.cxx (+5 -7), adtree.cxx (+1 -6), arbdb.h (+8 -1), arbdbpp.cxx (+21 -4)

westram 2022-07-09 10:15 Rev.: 19142

* correct recursive call used to create hierarchical key-prefixes:
- did use wrong keypath for ALL BUT species.

1 lines of code changed in 1 file:

• ARBDB: adChangeKey.cxx (+1 -1)

westram 2022-07-09 10:14 Rev.: 19141

* javadoc {{{GBT_add_new_changekey_to_keypath}}}.

7 lines of code changed in 1 file:

• ARBDB: adChangeKey.cxx (+7)

westram 2022-07-09 10:12 Rev.: 19140

* in "add new changekey"-functions:
- change type of param 'type' (int -> GB_TYPES)
- fix callers where needed.

10 lines of code changed in 2 files:

• ARBDB: adChangeKey.cxx (+6 -6), ad_t_prot.h (+4 -4)

westram 2022-07-01 14:26 Rev.: 19105

* allow 1 or 3 vectorizations
* fixes linux RELEASE build

2 lines of code changed in 1 file:

• ARBDB: adoptimize.cxx (+2 -2)

westram 2022-06-29 14:54 Rev.: 19100

* reintegrates 'split' into 'trunk'
- implemented beta version of alignment splitter
* adds: log:branches/split@19077:19099

3 lines of code changed in 2 files:

• ARBDB: ad_t_prot.h (+1 -1), adali.cxx (+2 -2)

westram 2022-06-20 12:40 Rev.: 19069

* fix vectorize-checks for gcc 5.4

2 lines of code changed in 2 files:

• ARBDB: adcompr.cxx (+1 -1), adoptimize.cxx (+1 -1)

westram 2022-06-20 12:18 Rev.: 19067

* fix vectorize-checks for gcc 5.5

2 lines of code changed in 2 files:

• ARBDB: adcompr.cxx (+1 -1), adoptimize.cxx (+1 -1)

westram 2022-06-20 12:17 Rev.: 19066

* fix vectorize-checks for gcc 7.x-series

1 lines of code changed in 1 file:

• ARBDB: adoptimize.cxx (+1 -1)

westram 2022-06-20 12:15 Rev.: 19065

* fix vectorize-checks for gcc 8.x-series

4 lines of code changed in 2 files:

• ARBDB: adoptimize.cxx (+1 -1), adseqcompr.cxx (+3 -3)

westram 2022-06-20 12:14 Rev.: 19064

* fix vectorize-checks for gcc 9.x-series

5 lines of code changed in 3 files:

• ARBDB: adcompr.cxx (+1 -1), adoptimize.cxx (+1 -1), adseqcompr.cxx (+3 -3)

westram 2022-06-20 12:12 Rev.: 19063

* fixed LOOP_VECTORIZED expressions that used '*'-count (for gcc 10.x-series).

6 lines of code changed in 3 files:

• ARBDB: adcompr.cxx (+1 -1), adoptimize.cxx (+2 -2), adseqcompr.cxx (+3 -3)

westram 2022-03-23 11:25 Rev.: 18971

* include {{{rpc/types.h}}} under OSX only (fixes compilation under SuSE Leap 15.3).

Notes:
* originally introduced with [14000]
* merged to trunk with [14007]

7 lines of code changed in 1 file:

• ARBDB: arbdb.cxx (+7 -1)

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

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

35 lines of code changed in 1 file:

• ARBDB: Makefile (+35)

westram 2022-03-01 15:38 Rev.: 18939

* add {{{GB_test_delete_possible}}}:
- tests TA + returns security error.
- use it in {{{GB_delete}}} + {{{GB_set_temporary}}}.
* test user has security to delete tree **before** copying the tree (which may take some time).

43 lines of code changed in 4 files:

• ARBDB: ad_prot.h (+1), ad_save_load.cxx (+1 -1), adtree.cxx (+10 -2), arbdb.cxx (+31 -29)

westram 2022-02-28 14:53 Rev.: 18936

* when called with flag==3 now count marked species in
- GBT_mark_all+GBT_mark_all_that
- mark_species_in_tree+mark_species_in_tree_that
* add count feature to all mark menus + submenus
- generate reports for different set of counted species.
- show top-area hint only once per arb session.

25 lines of code changed in 2 files:

• ARBDB: ad_t_prot.h (+2 -2), aditem.cxx (+23 -4)

westram 2022-01-29 15:33 Rev.: 18907

* partial merge from 'stable' into 'trunk'
* adds: log:branches/stable@18903:18906

2 lines of code changed in 2 files:

• ARBDB: ad_prot.h (+1 -1), arbdb.cxx (+1 -1)

(1408 more)