Directory GDEHELP/MENUS/

Lines of Code

Developers

Most Recent Commits

westram 2022-08-12 17:40 Rev.: 19234

* reintegrates 'gde' into 'trunk'
* adds: log:branches/gde@19228:19233

378 lines of code changed in 4 files:

• GDEHELP/MENUS: raxml.menu (del), raxml7.menu (new 172), raxml8.menu (new 107), sativa.menu (new 99)

westram 2022-03-21 13:24 Rev.: 18969

* fix vertical alignment of inputfield-labels (works for multiline labels).
* reintroduce a multiline label in fasttree window (had been removed with [18838] due to misalignment)
* change some debug dumps.

1 lines of code changed in 1 file:

• GDEHELP/MENUS: fasttree.menu (+1 -1)

westram 2021-12-17 15:35 Rev.: 18865

* add minimal documentation for
- probcons and
- muscle.

2 lines of code changed in 1 file:

• GDEHELP/MENUS: align.menu (+2)

westram 2021-12-17 15:34 Rev.: 18864

* remove 'Start a slave ARB on a foreign host' (obsolete).

0 lines of code changed in 1 file:

• GDEHELP/MENUS: start_arb.menu (del)

westram 2021-12-17 15:32 Rev.: 18863

* document 'Import fields from calc-sheet'.
* link to 'Export fields (to calc-sheet using NDS)'.
* add another pointer, where to add helpfiles for GDE menus.

1 lines of code changed in 1 file:

• GDEHELP/MENUS: import.menu (+1)

westram 2021-11-14 12:18 Rev.: 18842

* allow conditional build of OPENMP version of {{{FastTree}}}
- tweak preprocessor: allow to {{{#define}}} via CLI.
- globally define whether OPENMP shall be used
* export to submakefiles.
* disable under OSX
- capability to build OPENMP binary depends on compiler
- LLVM/Clang 3.7 required
- forward {{{USE_OPENMP}}} into preprocessor.
- in fasttree.menu: when not defined {{{USE_OPENMP}}} -> skip MP option from GUI + hardcode binary.
- conditionally build OPENMP binary depending on {{{USE_OPENMP}}}.

15 lines of code changed in 1 file:

• GDEHELP/MENUS: fasttree.menu (+15 -6)

westram 2021-11-10 14:46 Rev.: 18840

* also build OPENMP version of {{{FastTree}}}
- add selector for single/multi processor version to GUI.
- store used version in tree comment.
- svn/git-ignore MP binary

8 lines of code changed in 1 file:

• GDEHELP/MENUS: fasttree.menu (+8 -2)

westram 2021-11-10 14:32 Rev.: 18838

* minor fixes to fasttree GUI:
- only use single line in description (otherwise parts are not visible).
- fix duplicated itemmeta.

2 lines of code changed in 1 file:

• GDEHELP/MENUS: fasttree.menu (+2 -2)

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

64 lines of code changed in 1 file:

• GDEHELP/MENUS: fasttree.menu (+64 -18)

westram 2021-11-07 19:39 Rev.: 18836

* define items for "RAxML 7" using #defines
- fixes bogus warning about missing itemhelp for "RAxML 7 (DNA)" [18831]
- show sequence type in tree comments (uses NUC/PRO)
- use nucleotide/protein in menu entries (resets properties *sic*)
* rename controlling define

15 lines of code changed in 1 file:

• GDEHELP/MENUS: raxml.menu (+15 -8)

westram 2021-11-07 19:33 Rev.: 18835

* define items for "PHYML-20130708" using #defines
- fixes bogus warning about missing itemhelp for "PHYML-20130708 (DNA)" [18831]
- use nucleotide/protein in menu entries (resets properties *sic*)
- change STYPE stored in tree comment to NUC/PRO
* rename controlling define

17 lines of code changed in 1 file:

• GDEHELP/MENUS: phyml_20130708.menu (+17 -10)

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

* whitespace + typo.

3 lines of code changed in 2 files:

• GDEHELP/MENUS: raxml.menu (+2 -2), warning.menu (+1 -1)

westram 2021-11-04 15:54 Rev.: 18824

* add help for fasttree (copied start of text from homepage and link there).

1 lines of code changed in 1 file:

• GDEHELP/MENUS: fasttree.menu (+1)

westram 2021-11-04 15:08 Rev.: 18823

* split menufile for treepuzzle, mrbayes and fasttree.
* add separators for readability.

161 lines of code changed in 3 files:

• GDEHELP/MENUS: fasttree.menu (new 36), mrbayes.menu (new 125), puzzle.menu (-164)

westram 2018-10-17 10:00 Rev.: 17478

* reintegrates 'svalues' into 'trunk'
- implements #614
* adds: log:branches/svalues@17357:17419,17428:17464,17469,17471:17477

7 lines of code changed in 1 file:

• GDEHELP/MENUS: phyml_20130708.menu (+7 -7)

westram 2018-09-06 08:19 Rev.: 17355

* fix {{{Conversion warnings occurred in Action}}} for fasttree
- "MODEL" used as variable name and as part of resulting tree-comment
- (side-effect: resets saved properties of model to default value)

3 lines of code changed in 1 file:

• GDEHELP/MENUS: puzzle.menu (+3 -3)

westram 2017-10-27 15:33 Rev.: 16575

* mention raxml versions numbers (in help and menus)

2 lines of code changed in 1 file:

• GDEHELP/MENUS: raxml.menu (+2 -2)

westram 2017-10-03 17:26 Rev.: 16469

* reintegrates 'textedit' into 'trunk'
- fixes #586
* editor now always started asynchronously
* uses inotify to track file changes
- ~~also use inotify to track directory updates (in order to update file selections when needed)~~\\(./) by [16515] ff.; merged by [16551]
* adds: log:branches/textedit@16448:16468

11 lines of code changed in 7 files:

• GDEHELP/MENUS: desoete.menu (+1 -1), phylip_dist.menu (+3 -3), phylip_help.menu (+1 -1), phylip_ml.menu (+1 -1), phylip_pars.menu (+2 -2), phyml.menu (+2 -2), phyml_20130708.menu (+1 -1)

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

6 lines of code changed in 2 files:

• GDEHELP/MENUS: align.menu (+5 -3), puzzle.menu (+1 -1)

westram 2015-04-30 13:47 Rev.: 13791

* remove CAP2
- antique
- broken since [11839] (at least)
- nobody complained

0 lines of code changed in 1 file:

• GDEHELP/MENUS: align.menu (-32)

westram 2015-03-25 10:28 Rev.: 13603

* un-"plenk"

9 lines of code changed in 4 files:

• GDEHELP/MENUS: phylip_ml.menu (+1 -1), phylip_pars.menu (+2 -2), pretty_print.menu (+5 -5), start_arb.menu (+1 -1)

westram 2014-09-23 14:05 Rev.: 12931

* fix label ('#...' means gfx)

1 lines of code changed in 1 file:

• GDEHELP/MENUS: raxml.menu (+1 -1)

westram 2014-09-04 16:28 Rev.: 12834

* reintegrates 'fix' into 'trunk'
- fixing #504
* adds:
- log:branches/fix@12806,12812:12818,12820:12822,12828:12833

9 lines of code changed in 1 file:

• GDEHELP/MENUS: align.menu (+9)

westram 2014-03-24 20:30 Rev.: 11886

* reintegrates 'cleanup' into 'trunk'
* adds:
- log:branches/cleanup@11876:11885

0 lines of code changed in 12 files:

• GDEHELP/MENUS: desoete.menu (-1), dnamlrates.menu (-1), fastdnaml.menu (-1), inc_fastdnaml.menu (-1), phylip_dist.menu (-2), phylip_dist_org.menu (-1), phylip_ml.menu (-1), phylip_pars.menu (-2), phyml.menu (-2), phyml_20130708.menu (-1), puzzle.menu (-1), raxml.menu (-1)

westram 2014-03-24 17:57 Rev.: 11874

* reintegrates 'customize' into 'trunk'
- implements #484
- clean up worst things in GDE to allow use of custom menu-files
* adds:
- log:branches/customize@11828:11840,11844:11873

20 lines of code changed in 10 files:

• GDEHELP/MENUS: align.menu (+7), desoete.menu (+1), export.menu (+1), import.menu (-2), phylip_dist.menu (+2), phylip_dist_org.menu (+1), pretty_print.menu (+1), puzzle.menu (+4), start_arb.menu (-1), warning.menu (+3 -2)

westram 2014-02-21 11:44 Rev.: 11649

- fix test for "no tree selected" in arb_raxml
- passing an empty tree to RAxML caused it to run forever under some circumstances
- added comments at "no tree selected"-tests

2 lines of code changed in 1 file:

• GDEHELP/MENUS: phyml_20130708.menu (+2)

westram 2014-02-20 15:55 Rev.: 11643

* fix missing/duplicated/invalid mnemonics in ARB_NTREE (incl. genome)

8 lines of code changed in 5 files:

• GDEHELP/MENUS: align.menu (+2 -2), phyml.menu (+2 -2), phyml_20130708.menu (+2 -1), puzzle.menu (+1 -1), raxml.menu (+1 -1)

westram 2014-02-15 15:51 Rev.: 11626

* reintegrates 'fix' into 'trunk'
- implements: #158
- fixes: #386, #463, #459
* adds:
- log:branches/fix@11579:11625

197 lines of code changed in 16 files:

• GDEHELP/MENUS: align.menu (+50 -49), desoete.menu (+9 -8), dnamlrates.menu (+5 -6), export.menu (+2 -2), fastdnaml.menu (+4 -6), import.menu (+2 -2), inc_fastdnaml.menu (+6 -8), phylip_dist.menu (+7 -7), phylip_dist_org.menu (+4 -4), phylip_ml.menu (+5 -4), phylip_pars.menu (+8 -8), phyml.menu (+12 -7), phyml_20130708.menu (+13 -7), pretty_print.menu (+7 -4), puzzle.menu (+40 -32), raxml.menu (+23 -15)

westram 2013-08-28 16:23 Rev.: 10513

* DRYed PHYML interface (Amino vs DNA)

42 lines of code changed in 1 file:

• GDEHELP/MENUS: phyml_20130708.menu (+42 -134)

westram 2013-08-28 15:41 Rev.: 10511

* swap order (first DNA, then Amino) to match other tools in this menu

33 lines of code changed in 1 file:

• GDEHELP/MENUS: phyml_20130708.menu (+33 -33)

westram 2013-08-28 15:38 Rev.: 10510

* split menu-sources for both versions of phyml

234 lines of code changed in 2 files:

• GDEHELP/MENUS: phyml.menu (-236), phyml_20130708.menu (new 234)

westram 2013-08-28 15:29 Rev.: 10509

* remove trailing '3' in fastdnaml.menu (was ignored by arb_read_tree)
* split menu-sources for phylip_ml and phyml

344 lines of code changed in 3 files:

• GDEHELP/MENUS: fastdnaml.menu (+1 -1), phylip_ml.menu (-345), phyml.menu (new 343)

westram 2013-08-27 11:40 Rev.: 10497

* replaced 'consense tree' by 'consensus tree' (user-visible terminology)
* added documentation for ARBs consensus tree algorithm

1 lines of code changed in 1 file:

• GDEHELP/MENUS: raxml.menu (+1 -1)

aboeckma 2013-08-15 11:48 Rev.: 10456

Added rudimentary fasttree menu (need to know which options to use)

40 lines of code changed in 1 file:

• GDEHELP/MENUS: puzzle.menu (+40)

aboeckma 2013-08-15 10:37 Rev.: 10455

Added !MrBayes custom command file menu

31 lines of code changed in 1 file:

• GDEHELP/MENUS: puzzle.menu (+31)

aboeckma 2013-08-15 09:12 Rev.: 10454

Added !MrBayes help

2 lines of code changed in 1 file:

• GDEHELP/MENUS: puzzle.menu (+2)

aboeckma 2013-08-14 14:35 Rev.: 10448

mafft changed default value for offset

7 lines of code changed in 1 file:

• GDEHELP/MENUS: align.menu (+7 -6)

aboeckma 2013-08-14 14:28 Rev.: 10447

Added mrBayes gde menu

80 lines of code changed in 1 file:

• GDEHELP/MENUS: puzzle.menu (+80)

aboeckma 2013-08-14 14:27 Rev.: 10446

mafft preserve case

1 lines of code changed in 1 file:

• GDEHELP/MENUS: align.menu (+1 -1)

aboeckma 2013-08-13 10:01 Rev.: 10432

Added two missing switches to phyml

54 lines of code changed in 1 file:

• GDEHELP/MENUS: phylip_ml.menu (+54 -31)

(103 more)