Directory MERGE/

Lines of Code

Developers

Most Recent Commits

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)

westram 2017-06-08 16:59 Rev.: 16021

* reintegrates 'fix' into 'trunk'
- refactors {{{DbScanner}}} -> OO + shrink 1.4k
- fixes #251 and #506
* adds: log:branches/fix@15975,15982:16020

9 lines of code changed in 2 files:

• MERGE: MG_extendeds.cxx (+3 -4), MG_species.cxx (+6 -3)

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

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

26 lines of code changed in 5 files:

• MERGE: MG_adapt_ali.cxx (+4 -4), MG_checkfield.cxx (+2 -2), MG_species.cxx (+7 -8), MG_trees.cxx (+2 -2), Makefile (+11)

westram 2016-07-27 10:30 Rev.: 15094

* reintegrates 'fix' into 'trunk'
* adds: log:branches/fix@15066,15073:15076,15082,15086:15093

2 lines of code changed in 1 file:

• MERGE: MG_main.cxx (+2 -1)

westram 2016-07-14 13:45 Rev.: 15053

* merge most WINDOW patches from 'color' into 'trunk'
- color-ranges (completes implementation of #682)
* new types (cyclic, planar and spatial)
* can display as canvas-overlay
* setup in separate window
* allow external access via ID (query, activate)
* adds: log:branches/color@14984,14986:14987,14989,14993,15000,15005:15006,15008,15011,15036

1 lines of code changed in 1 file:

• MERGE: Makefile (+1)

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

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

212 lines of code changed in 6 files:

• MERGE: MG_checkfield.cxx (+130 -103), MG_extendeds.cxx (+2 -2), MG_gene_species.cxx (+2 -2), MG_names.cxx (+4 -10), MG_species.cxx (+72 -64), Makefile (+2)

westram 2016-04-18 10:51 Rev.: 14741

* mark more unwanted widget-callbacks (#559)

1 lines of code changed in 1 file:

• MERGE: MG_names.cxx (+1 -1)

westram 2016-01-23 06:20 Rev.: 14674

* rename {{{GB_write_as_string}}} -> {{{GB_write_autoconv_string}}}

1 lines of code changed in 1 file:

• MERGE: MG_checkfield.cxx (+1 -1)

westram 2015-11-27 19:31 Rev.: 14556

* reintegrates 'dbsave' into 'trunk'
- implements #665
* adds: log:branches/dbsave@14521:14555

41 lines of code changed in 2 files:

• MERGE: MG_main.cxx (+40 -71), Makefile (+1)

westram 2015-11-11 09:42 Rev.: 14488

* remove duplicate CLOSE/CANCEL buttons (they only suggest window is modal, while it isnt)

6 lines of code changed in 1 file:

• MERGE: MG_main.cxx (+6 -13)

westram 2015-11-08 13:01 Rev.: 14480

* use typed callbacks in config-manager

5 lines of code changed in 1 file:

• MERGE: MG_gene_species.cxx (+5 -4)

westram 2015-11-04 09:57 Rev.: 14453

* do not cast AW_POPDOWN

25 lines of code changed in 9 files:

• MERGE: MG_alignment.cxx (+2 -1), MG_checkfield.cxx (+1 -1), MG_configs.cxx (+3 -2), MG_extendeds.cxx (+3 -2), MG_main.cxx (+8 -5), MG_names.cxx (+2 -1), MG_preserves.cxx (+2 -1), MG_species.cxx (+2 -1), MG_trees.cxx (+2 -1)

westram 2015-09-02 16:31 Rev.: 14256

* reintegrates 'config' into 'trunk' (implements #607)
* adds: log:branches/config@14199:14255

1 lines of code changed in 1 file:

• MERGE: MG_configs.cxx (+1 -1)

westram 2015-09-01 16:57 Rev.: 14239

* add GB_USERFLAG_WASMARKED
* rename {{{GB_set_user_flag}}} -> {{{GB_raise_user_flag}}}
* add {{{GB_write_user_flag}}}

1 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+1 -1)

westram 2015-08-28 11:58 Rev.: 14228

* {{{GBT_names_erase}}} -> {{{CharPtrArray::safe_remove}}}

1 lines of code changed in 1 file:

• MERGE: MG_preserves.cxx (+1 -1)

westram 2015-08-28 11:21 Rev.: 14227

* elim 3 of 4 {{{GBT_names_...}}} functions

9 lines of code changed in 1 file:

• MERGE: MG_preserves.cxx (+9 -9)

westram 2015-08-28 09:12 Rev.: 14225

* {{{GBT_join_names}}} -> {{{GBT_join_strings}}}

1 lines of code changed in 1 file:

• MERGE: MG_preserves.cxx (+1 -1)

westram 2015-08-26 11:24 Rev.: 14203

- DRY digit calculation

1 lines of code changed in 1 file:

• MERGE: MG_adapt_ali.cxx (+1 -1)

westram 2015-08-05 12:53 Rev.: 14128

* add missing help to merge tool (field transfer/merge; tagging)
* fix layout of some windows

23 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+23 -24)

westram 2015-08-01 12:15 Rev.: 14126

* update help about saving databases

3 lines of code changed in 1 file:

• MERGE: MG_main.cxx (+3 -1)

westram 2015-07-18 12:47 Rev.: 14049

* documentation
- editor-configurations vs property-configurations
* warn about likelihood of confusion
* rename hlp files (to make clear which is talked about)
- add "Save properties" in EDIT4
- add "Show only differences to selected" in EDIT4

3 lines of code changed in 2 files:

• MERGE: MG_configs.cxx (+2 -2), MG_main.cxx (+1 -1)

westram 2015-04-21 12:18 Rev.: 13755

* reintegrates 'pars' into 'trunk'
- only refactored some code and added a few missing tests
* adds:
- log:branches/pars@13627,13639:13754

2 lines of code changed in 1 file:

• MERGE: MG_preserves.cxx (+2 -2)

westram 2015-04-04 13:17 Rev.: 13668

* 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)

11 lines of code changed in 1 file:

• MERGE: MG_gene_species.cxx (+11 -5)

(301 more)