Directory ARB_GDE/

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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:

• ARB_GDE: GDE_arbdb_io.cxx (+1 -1)

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

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

21 lines of code changed in 2 files:

• ARB_GDE: GDE.cxx (+17 -12), GDE_arbdb_io.cxx (+4 -1)

westram 2022-03-30 16:39 Rev.: 18980

* {{{create_toggle_field}}}:
- change one flavor: allow to pass label AND orientation.
- directly pass labels (instead of explicit calls to {{{AW_window::label}}})

4 lines of code changed in 1 file:

• ARB_GDE: GDE.cxx (+4 -6)

westram 2022-03-30 16:29 Rev.: 18977

* use {{{AW_orientation}}} to specify orientation of radio button.

1 lines of code changed in 1 file:

• ARB_GDE: GDE.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.

3 lines of code changed in 1 file:

• ARB_GDE: GDE.cxx (+3 -3)

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

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

2 lines of code changed in 1 file:

• ARB_GDE: GDE.cxx (+2 -2)

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

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

7 lines of code changed in 1 file:

• ARB_GDE: Makefile (+7)

westram 2022-02-09 12:46 Rev.: 18931

* define unique IDs for jobs running via GDE:
- provide in menu-code via {{{$AGDE_JOBID}}}.
- use as window-logname => allows to relate separate parts of jobs in arb log.

42 lines of code changed in 1 file:

• ARB_GDE: GDE_event.cxx (+42 -20)

westram 2021-12-17 16:04 Rev.: 18866

* fix failing unit-test (was broken by [18864])
* [hack] force rebuild+exec of unittest after menu changes.
* explain motivation for menu unittest.

11 lines of code changed in 2 files:

• ARB_GDE: GDE_ParseMenu.cxx (+8 -3), Makefile (+3)

westram 2021-11-07 19:53 Rev.: 18837

* add {{{FastTree}}} for protein.
- mention STYPE in tree comment.
* customize {{{FastTree}}}:
- allow to configure rate categories.
- NJ
* also provide -slow mode.
* provide weighted NJ
- allow to configure bootstraps.
* rename controlling define

1 lines of code changed in 1 file:

• ARB_GDE: GDE_ParseMenu.cxx (+1 -1)

westram 2021-11-07 19:22 Rev.: 18831

* improve GDE-menu robustness
- warn if 'item' lacks an 'itemhelp' entry.
- fail if 'itemhelp' lacks .hlp name.
- bail out if 'item' contains duplicated 'itemhelp' or 'itemmeta' (menu parser)
* currently results in the following warnings:
{{{
MENUS/import.menu:15: Warning: item 'Import fields from calc-sheet' lacks an 'itemhelp' entry!
MENUS/align.menu:1: Warning: item 'ProbCons' lacks an 'itemhelp' entry!
MENUS/align.menu:50: Warning: item 'Muscle' lacks an 'itemhelp' entry!
MENUS/phyml_20130708.menu:24: Warning: item 'PHYML-20130708 (DNA)' lacks an 'itemhelp' entry!
MENUS/raxml.menu:18: Warning: item 'RAxML 7 (DNA)' lacks an 'itemhelp' entry!
MENUS/start_arb.menu:1: Warning: item 'Start a slave ARB on a foreign host ...' lacks an 'itemhelp' entry!
}}}

Edit: fixed by [18863:18865]

2 lines of code changed in 1 file:

• ARB_GDE: GDE_ParseMenu.cxx (+2)

westram 2021-11-07 19:17 Rev.: 18830

* whitespace + typo.

1 lines of code changed in 1 file:

• ARB_GDE: GDE_menu.h (+1 -1)

westram 2021-10-10 08:33 Rev.: 18781

* reintegrates 'help' into 'trunk'
- relocate help sources
* adds: log:branches/help@18763:18780

1 lines of code changed in 1 file:

• ARB_GDE: GDE_ParseMenu.cxx (+1 -1)

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

* remove trailing whitespace from c source.

2 lines of code changed in 2 files:

• ARB_GDE: GDE_arbdb_io.cxx (+1 -1), gde.hxx (+1 -1)

westram 2021-09-15 12:48 Rev.: 18729

* eliminate trailing whitespace from Makefiles.

1 lines of code changed in 1 file:

• ARB_GDE: Makefile (+1 -1)

westram 2021-09-15 12:41 Rev.: 18726

* use {{{SOURCES}}} where list of source files is needed.

4 lines of code changed in 1 file:

• ARB_GDE: Makefile (+4 -4)

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

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

5 lines of code changed in 1 file:

• ARB_GDE: Makefile (+5 -5)

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

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

2 lines of code changed in 1 file:

• ARB_GDE: Makefile (+2 -11)

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

1 lines of code changed in 1 file:

• ARB_GDE: GDE.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.

2 lines of code changed in 1 file:

• ARB_GDE: GDE_event.cxx (+2 -4)

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).

2 lines of code changed in 1 file:

• ARB_GDE: GDE_event.cxx (+2 -2)

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:

• ARB_GDE: 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

8 lines of code changed in 3 files:

• ARB_GDE: GDE_arbdb_io.cxx (+3 -2), GDE_event.cxx (+3 -2), Makefile (+2)

westram 2018-09-20 17:43 Rev.: 17396

* reintegrates 'fix' into 'trunk'
- elim dead code
- use const hash loop
* adds: log:branches/fix@17380,17388:17395

55 lines of code changed in 3 files:

• ARB_GDE: GDE_FileIO.cxx (+21 -20), GDE_ParseMenu.cxx (+34 -32), GDE_proto.h (-2)

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

77 lines of code changed in 7 files:

• ARB_GDE: GDE_FileIO.cxx (+2 -2), GDE_Genbank.cxx (+5 -5), GDE_ParseMenu.cxx (+9 -5), GDE_arbdb_io.cxx (+3 -3), GDE_def.h (+21 -5), GDE_event.cxx (+36 -45), Makefile (+1)

westram 2018-05-04 17:06 Rev.: 16986

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

Update: continued by [17178]

6 lines of code changed in 1 file:

• ARB_GDE: GDE_ParseMenu.cxx (+6 -3)

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

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

151 lines of code changed in 5 files:

• ARB_GDE: GDE_FileIO.cxx (+30 -47), GDE_Genbank.cxx (+62 -95), GDE_HGLfile.cxx (+50 -108), GDE_arbdb_io.cxx (+1 -2), GDE_event.cxx (+8 -13)

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

105 lines of code changed in 7 files:

• ARB_GDE: GDE.cxx (+11 -11), GDE_FileIO.cxx (+18 -18), GDE_Genbank.cxx (+19 -15), GDE_HGLfile.cxx (+3 -3), GDE_ParseMenu.cxx (+24 -24), GDE_arbdb_io.cxx (+8 -8), GDE_event.cxx (+22 -22)

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

4 lines of code changed in 2 files:

• ARB_GDE: GDE_ParseMenu.cxx (+2 -2), GDE_event.cxx (+2 -2)

westram 2017-08-23 12:42 Rev.: 16237

* fix spelling for 'occurrence'

5 lines of code changed in 1 file:

• ARB_GDE: GDE_ParseMenu.cxx (+5 -5)

westram 2016-12-06 14:37 Rev.: 15398

* partial merge from 'mladd' into 'trunk'
- GDE fixes
* adds: log:branches/mladd@15395,15397

6 lines of code changed in 1 file:

• ARB_GDE: GDE.cxx (+6 -6)

westram 2016-09-27 15:23 Rev.: 15279

* reintegrates 'errhandle' into 'trunk'
* adds: log:branches/errhandle@15275:15278

5 lines of code changed in 1 file:

• ARB_GDE: GDE_ParseMenu.cxx (+5 -4)

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

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

95 lines of code changed in 9 files:

• ARB_GDE: GDE.cxx (+1 -1), GDE_FileIO.cxx (+7 -52), GDE_Genbank.cxx (+15 -27), GDE_HGLfile.cxx (+3 -4), GDE_ParseMenu.cxx (+36 -55), GDE_arbdb_io.cxx (+15 -17), GDE_event.cxx (+10 -10), GDE_proto.h (+1 -3), Makefile (+7)

westram 2016-07-14 12:19 Rev.: 15050

* merge [15027] from 'color' into 'trunk'

2 lines of code changed in 1 file:

• ARB_GDE: GDE.cxx (+2 -2)

westram 2015-12-16 15:13 Rev.: 14622

* reintegrates 'ui' into 'trunk'
- implements #656
- adds instant update for
* next neighbour search
* branch analysis (mark functions)
* arb-phylo (filter setup)
* adds: log:branches/ui@14588:14621

10 lines of code changed in 1 file:

• ARB_GDE: GDE.cxx (+10 -43)

westram 2015-11-05 11:35 Rev.: 14474

* use typed callbacks for SAI-selectionbox-filter

2 lines of code changed in 1 file:

• ARB_GDE: GDE.cxx (+2 -2)

westram 2015-11-04 17:14 Rev.: 14473

* remove unused AW_CL from {{{GDE_init}}}

6 lines of code changed in 5 files:

• ARB_GDE: GDE.cxx (+2 -3), GDE_arbdb_io.cxx (+1 -2), GDE_menu.h (-1), GDE_proto.h (+1 -1), gde.hxx (+2 -3)

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

* do not cast AW_POPDOWN

2 lines of code changed in 1 file:

• ARB_GDE: GDE.cxx (+2 -2)

westram 2015-10-28 19:12 Rev.: 14435

* fix macro ids for GDE items (broken by [14433])

32 lines of code changed in 4 files:

• ARB_GDE: GDE.cxx (+7 -3), GDE_ParseMenu.cxx (+1), GDE_menu.h (+8 -3), Makefile (+16)

westram 2015-10-28 17:37 Rev.: 14433

* use typed callbacks in ARB_GDE

21 lines of code changed in 3 files:

• ARB_GDE: GDE.cxx (+19 -26), GDE_event.cxx (+1 -1), GDE_proto.h (+1 -1)

(272 more)