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westram 2022-11-26 10:49 Rev.: 19349

* fix mnemonics:
- in 'Tree' menu:
* p: was used for 'Print tree' + 'Compare topology...'
* o: 'Sync tree scrolling..' -> 'Compare topology...'
* e: 'Beautify tree' -> 'Sync tree scrolling..'
* u: 'Mark duplicates' -> 'Beautify tree'
* k: now used for 'Mark duplicates'
* removed 'Select tree' (also bound to tree button).
* T: used for 'Tree admin' now (was 'Select tree')
* i: used for (genome-only) 'Relink tree to organisms' (was 'Tree admin')
- in 'Sequence' menu:
* S: was used for 'Split sequences' + 'Align Sequences'.
* l: now used for 'Align sequences'.
- in species transfer of merge tool.
- in properties menu of 'ARB gene map'.
- in properties menu of 'PROBE and SAI' (most changed).

1 lines of code changed in 1 file:

• MERGE: MG_species.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

44 lines of code changed in 3 files:

• MERGE: MG_adapt_ali.cxx (+32 -25), MG_checkfield.cxx (+11 -8), Makefile (+1)

westram 2022-09-02 13:35 Rev.: 19248

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

1 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+1 -1)

westram 2022-08-03 14:52 Rev.: 19206

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

1 lines of code changed in 1 file:

• MERGE: MG_alignment.cxx (+1 -1)

westram 2022-07-21 13:01 Rev.: 19167

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

3 lines of code changed in 2 files:

• MERGE: MG_alignment.cxx (+1 -1), MG_species.cxx (+2 -2)

westram 2022-07-09 09:17 Rev.: 19143

* handle results from add-new-changekey functions.
- while refreshing keys: only warn.
* generally fix error handling in {{{MG_copy_and_check_alignments}}}.

24 lines of code changed in 2 files:

• MERGE: MG_alignment.cxx (+23 -13), MG_species.cxx (+1 -1)

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

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

1 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+1 -1)

westram 2022-06-20 11:12 Rev.: 19063

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

1 lines of code changed in 1 file:

• MERGE: MG_preserves.cxx (+1 -1)

westram 2022-03-30 16:36 Rev.: 18979

* fix use of empty labels:
- {{{AW_window::label}}} no longer
* accepts empty labels.
* allows to overwrite existing labels (assume this happens by mistake).
- {{{create_toggle_field}}}:
* assert label is used (in flavor with label-parameter)
* remove empty and NULp labels passed (from callers).

1 lines of code changed in 1 file:

• MERGE: MG_gene_species.cxx (+1 -1)

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:

• MERGE: MG_gene_species.cxx (+1 -1)

westram 2022-03-04 15:20 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.

10 lines of code changed in 5 files:

• MERGE: MG_configs.cxx (+2 -2), MG_extendeds.cxx (+2 -2), MG_gene_species.cxx (+1 -1), MG_preserves.cxx (+3 -3), MG_trees.cxx (+2 -2)

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

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

3 lines of code changed in 2 files:

• MERGE: MG_species.cxx (+2 -2), MG_trees.cxx (+1 -1)

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

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

11 lines of code changed in 1 file:

• MERGE: Makefile (+11)

westram 2021-11-05 14:15 Rev.: 18827

* cleanup merge selectors.

20 lines of code changed in 2 files:

• MERGE: MG_extendeds.cxx (+8 -20), MG_species.cxx (+12 -18)

westram 2021-11-05 11:35 Rev.: 18826

* add SAI selectors for both databases
- fixes crash when opening SAI transfer

64 lines of code changed in 1 file:

• MERGE: MG_extendeds.cxx (+64 -2)

westram 2021-11-05 11:33 Rev.: 18825

* merging via FTS into new database did not copy alignment information. fixed.

2 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+2)

westram 2021-10-07 18:18 Rev.: 18754

* define {{{ItemSelector}}} for SAIs (lacks changekey functionality, i.e. does not fit into a search&query).
* mark places where species-selector is misused for SAIs.

2 lines of code changed in 1 file:

• MERGE: MG_extendeds.cxx (+2 -2)

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

* remove trailing whitespace from c source.

13 lines of code changed in 3 files:

• MERGE: MG_main.cxx (+1 -1), MG_preserves.cxx (+3 -3), MG_trees.cxx (+9 -9)

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

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

5 lines of code changed in 1 file:

• MERGE: Makefile (+5 -5)

westram 2021-05-08 14:19 Rev.: 18647

* reduced optimisation for TEST_remapping() and TEST_shaded_values().

10 lines of code changed in 1 file:

• MERGE: MG_adapt_ali.cxx (+10 -10)

westram 2020-10-05 15:24 Rev.: 18599

* fix parameters of {{{GBT_rename_alignment}}} + {{{gbt_rename_alignment_of_item}}}
- rename.
- change to bool.
- callers use bool.

1 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+1 -1)

westram 2020-03-04 10:08 Rev.: 18359

* add new FTS transfer mode to merge-tool (implements #825)
- allows to skip transport of sequence alignment data (i.e. allows plain metadata updates)
* update+fix documentation

41 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+41 -20)

westram 2019-10-08 16:51 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

41 lines of code changed in 5 files:

• MERGE: MG_adapt_ali.cxx (+1 -1), MG_checkfield.cxx (+1 -1), MG_gene_species.cxx (+2 -2), MG_preserves.cxx (+2 -2), MG_species.cxx (+35 -26)

westram 2019-09-17 14:46 Rev.: 18092

* full update from child 'fts' into 'trunk'
- implements #562
* adds:
- [18091/branches/fts]
- log:branches/gui@17754:17924,17926:18090

600 lines of code changed in 5 files:

• MERGE: MG_adapt_ali.cxx (+46 -42), MG_adapt_ali.hxx (+13 -2), MG_alignment.cxx (+1 -1), MG_species.cxx (+537 -250), Makefile (+3)

westram 2019-09-17 14:13 Rev.: 18088

* reintegrates 'fts' into 'trunk'
* adds:
- log:branches/fts@17653,17655:17717,17724:18087
- [17925/branches/gui]

1 lines of code changed in 1 file:

• MERGE: needs_libs (+1)

westram 2019-07-17 15:27 Rev.: 17982

* reduced use of GB_change_my_security:
- use GB_securityLevel instead of manually fiddling around with GB_change_my_security.
- inspected and accepted leftover uses (see comments).

1 lines of code changed in 1 file:

• MERGE: MG_main.cxx (+1 -1)

westram 2019-07-17 15:22 Rev.: 17980

* use security objects instead of manually calling GB_push/pop_my_security.
* eliminate GB_push/pop_my_security.
* fix scoping using a TA object.

8 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+8 -10)

westram 2019-05-10 12:57 Rev.: 17877

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

1 lines of code changed in 1 file:

• MERGE: MG_checkfield.cxx (+1 -1)

westram 2019-04-29 13:44 Rev.: 17836

* reintegrates 'clone' into 'trunk'
* adds: log:branches/clone@17813:17835

10 lines of code changed in 5 files:

• MERGE: MG_alignment.cxx (+1 -1), MG_configs.cxx (+1 -1), MG_extendeds.cxx (+1 -1), MG_species.cxx (+6 -6), MG_trees.cxx (+1 -1)

westram 2019-04-05 18:32 Rev.: 17748

* remove hardcoded 'markCreated==true' from
- GBT_find_or_create_species_rel_species_data and
- GBT_find_or_create_species.
* hardcode 'markCreated==false' in GBT_find_or_create_SAI.
- changes result DB.
- increase diff buf size (result DB has loooong lines).

1 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+1 -1)

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:

• MERGE: Makefile (+2)

westram 2018-10-24 14:58 Rev.: 17534

* partial merge from 'fix' into 'trunk'
- globally define what are "gaps"
- kept behavioral changes to a minimum:
* defaults for (user-defined) gap-definition in EDIT4 changed
* EDIT sequence search also uses user-defined gaps
* adds: log:branches/fix@17529:17533

5 lines of code changed in 3 files:

• MERGE: MG_adapt_ali.cxx (+3 -1), MG_preserves.cxx (+1 -1), Makefile (+1)

westram 2018-07-23 15:52 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

3 lines of code changed in 2 files:

• MERGE: MG_checkfield.cxx (+2 -2), merge.hxx (+1 -1)

westram 2018-07-10 15:48 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

1 lines of code changed in 1 file:

• MERGE: MG_checkfield.cxx (+1 -1)

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

118 lines of code changed in 10 files:

• MERGE: MG_adapt_ali.cxx (+24 -24), MG_alignment.cxx (+2 -2), MG_checkfield.cxx (+10 -10), MG_configs.cxx (+1 -1), MG_extendeds.cxx (+2 -2), MG_gene_species.cxx (+18 -18), MG_main.cxx (+11 -11), MG_names.cxx (+6 -6), MG_species.cxx (+38 -38), MG_trees.cxx (+6 -6)

westram 2017-11-17 12:54 Rev.: 16668

* full update from child 'gcc' into 'trunk'
- fix/suppress (new) compiler warnings
- skip vectorizer notes
* adds: log:branches/gcc@16656:16667

2 lines of code changed in 2 files:

• MERGE: MG_species.cxx (+1), MG_trees.cxx (+1 -1)

westram 2017-11-14 14:36 Rev.: 16653

* reintegrates 'gcc' into 'trunk' (fixes defect part of #752)
- allow compilation with gcc 7.x series (accepting 2 clang-test-results for gcc 7.x)
- vectorization:
* in {{{SL/CONSENSUS/chartable.cxx}}} works again with gcc 7.x (broken for 6.x series)
- checker: added syntax to exclude a range of versions
* check new 7.x vectorizations + fix vectorization-counts
* adds: log:branches/gcc@16578:16635,16649:16652

1 lines of code changed in 1 file:

• MERGE: MG_preserves.cxx (+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

5 lines of code changed in 3 files:

• MERGE: MG_adapt_ali.cxx (+3 -3), MG_checkfield.cxx (+1 -1), MG_preserves.cxx (+1 -1)

westram 2017-10-08 14:54 Rev.: 16508

* reintegrates 'macros' into 'trunk'
- introduce generic input prompt (related #179)
- use it instead of locally generated windows:
* species (rename + create)
* alignment (rename, copy + create)
* experiments (rename, copy + create)
* genes (rename, copy + extract)
* mergetool (rename SAI + configs)
* SAIviz color translation (copy + create)
- fixed bugs in mergetool ([16503],[16504])
* adds: log:branches/macros@16484:16507

99 lines of code changed in 6 files:

• MERGE: MG_alignment.cxx (+9 -14), MG_configs.cxx (+40 -71), MG_extendeds.cxx (+32 -63), MG_species.cxx (+6 -6), Makefile (+2), merge.hxx (+10 -8)

westram 2017-09-18 14:23 Rev.: 16374

* reintegrates 'aci' into 'trunk'
- refactored wide parts of ACI code (incl. SRT+REG)
* added more test
* ACI tracing
- more complete and readable
- automatically turned off when done with expression
* improved error messages (esp. diagnostics)
* documentation (updated, added missing)
* fixed a bunch of bugs (incl. SEGV and deadlock)
* ACI now runs inside execution environment
- ACI language may be extended with custom commands (implements #756)
* added ACI extension for group-batch-rename
* adds:
- log:branches/aci@16170:16373
- log:branches/addtest@16193:16316

8 lines of code changed in 2 files:

• MERGE: MG_gene_species.cxx (+7 -2), Makefile (+1)

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