Directory ARB_GDE/

Directory Created:
2000-11-23 11:41
Total Files:
16
Deleted Files:
2
Lines of Code:
4059

[root]/ARB_GDE

Lines of Code

ARB_GDE/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 617 (100.0%) 17428 (100.0%) 28.2
westram 591 (95.8%) 11736 (67.3%) 19.8
oldcode 13 (2.1%) 5480 (31.4%) 421.5
meierh 1 (0.2%) 171 (1.0%) 171.0
epruesse 9 (1.5%) 38 (0.2%) 4.2
boehnel 2 (0.3%) 3 (0.0%) 1.5
baderk 1 (0.2%) 0 (0.0%) 0.0

Most Recent Commits

westram 2022-03-30 17:39 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 17:29 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 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.

3 lines of code changed in 1 file:

  • ARB_GDE: GDE.cxx (+3 -3)
westram 2022-03-04 16:13 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 12:26 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 13:46 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 17:04 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 20:53 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 20:22 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 20:17 Rev.: 18830


* whitespace + typo.

1 lines of code changed in 1 file:

  • ARB_GDE: GDE_menu.h (+1 -1)
westram 2021-10-10 09:33 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 13:52 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 13:48 Rev.: 18729


* eliminate trailing whitespace from Makefiles.

1 lines of code changed in 1 file:

  • ARB_GDE: Makefile (+1 -1)
westram 2021-09-15 13:41 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 13:39 Rev.: 18725


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

5 lines of code changed in 1 file:

  • ARB_GDE: Makefile (+5 -5)
westram 2021-09-15 13:00 Rev.: 18720


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

2 lines of code changed in 1 file:

  • ARB_GDE: Makefile (+2 -11)
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

1 lines of code changed in 1 file:

  • ARB_GDE: GDE.cxx (+1 -1)
westram 2019-07-17 16:22 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 19:32 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 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:

  • ARB_GDE: Makefile (+2)
westram 2018-10-24 15:58 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 18:43 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 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

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 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]

6 lines of code changed in 1 file:

  • ARB_GDE: GDE_ParseMenu.cxx (+6 -3)
westram 2017-11-28 19:22 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 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

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 15:23 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 13:42 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 15:37 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 16:23 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 11:05 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 13:19 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 16:13 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 12:35 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 18:14 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 10:57 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 20:12 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 18:37 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)
westram 2015-09-10 12:17 Rev.: 14281


* GDE commands failed to read sequence filter settings
- was broken by [14118]

11 lines of code changed in 3 files:

  • ARB_GDE: GDE.cxx (+4 -4), GDE_awars.h (+6 -3), GDE_event.cxx (+1 -1)
westram 2015-07-31 16:15 Rev.: 14118


* added {{{awt_create_filter_awars}}}
- made all awars 'tmp' (saving them did not work)

7 lines of code changed in 2 files:

  • ARB_GDE: GDE.cxx (+7 -9), GDE_awars.h (-7)

(270 more)

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