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(1 files, 31 lines)
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(1 files, 31 lines)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| westram | 983 (100.0%) | 4775 (100.0%) | 4.8 |
* reintegrates 'species' into 'trunk'
- provides species selections in mergetool (#868)
* adds: log:branches/species@19693:19730
78 lines of code changed in 7 files:
* update doc+gui:
- avoid terms "ARB_NT" (=former name of main arb window), "ARB_NTREE" and similar
* instead talk about "ARB main window"
- correct refs to 'ARB/Probes/PT_SERVER Admin'.
- update 'What are marked species?'.
- update protection level documentation (parts already done with previous commit).
445 lines of code changed in 215 files:
* update doc
- improve doc of global protection level.
- eliminate references to 'Protection' menu (pre-svn)
28 lines of code changed in 6 files:
* update doc+gui:
- mention focus strategies.
- use term 'SAI admin'.
- arb introduction (updated + linked missing modules).
70 lines of code changed in 3 files:
* reintegrates 'macros' into 'trunk'
- fixes macro IDs for mergetool (completing #870).
* most common problem:
- several modules were reused (twice) for items of same type, but in different databases.
- auto-generated IDs were identical.
* adds: log:branches/macros@19667:19690
2 lines of code changed in 2 files:
* reintegrates 'macros' into 'trunk'
- implements #870
* provide macro playback from CLI for merge tool
* adds: log:branches/macros@19656:19661
2 lines of code changed in 2 files:
* reintegrates 'help' into 'trunk'
- preformatted text gets checked for width now (to enforce it fits into the arb help window).
- fixed help following these checks, using the following steps:
* ignore problems in foreign documentation.
* increase default help window width.
* introduce control comments to
- accept oversized preformatted sections.
- enforce preformatted style for whole sections.
- simply define single-line preformatted sections\\Used intensive for definition of internal script languages.
- fixed several non-related problems found in documentation.
- minor layout changes for HTML version of arb help (more compacted; highlight anchored/all sections).
- refactor system interface (GUI version) and use it from help module.
* adds: log:branches/help@19532:19574
675 lines of code changed in 21 files:
* reintegrates 'sync' into 'trunk'
- fixes #869
* introduces synchronisation of external commands via DB
* macros now wait for these external commands to finish => macro can continue with results
* adds: log:branches/sync@19535:19548
7 lines of code changed in 1 file:
* tweaks {{{Track alignment changes}}}:
- automatically adds changekeys for generated fields.
- enhances documentation (recommended workflow; why to use unique IDs).
- uses {{{GBS_strstruct}}} to build reports and history entries.
- changes terminology (initials -> session ID).
- annotates errors with species name.
- improves report:
* always reports unchanged species.
* reverts order.
* changes format and horizontal padding.
- refactors (renames; size_t for counters; DRY)
38 lines of code changed in 1 file:
* reintegrates 'help' into 'trunk'
- tweak arb documentation:
* automatically link
- ticket references to arb bug tracker (only affects html version).
- found URLs.
* page titles
- warn about long titles.
- introduce {{{SUBTITLE}}}s (automatically triggered by multi-line titles in source files).
- increase allowed length (limited by subwindow width).
* cleanup header sections in all helpfiles.
* fix and/or update several help files.
* document syntax of help sources.
* build issues:
- when xml validation fails, next build no longer uses invalid xml => keeps failing.
- remove output files on error (including files below {{{ARBHOME/lib}}}).
- pipe output through logs to ensure proper wrapping in {{{Entering/Leaving}}} lines.
- moves {{{Tree admin}}} + {{{NDS}}} menu entries to top of menu
* adds: log:branches/help@18783:19531
2796 lines of code changed in 664 files:
* fix typo.
1 lines of code changed in 1 file:
* document automation using macros.
20 lines of code changed in 2 files:
* allow to reduce the time-to-wait on error, by defining {{{ARB_SCRIPTED_SECS_WAIT_ON_ERROR}}}.
7 lines of code changed in 2 files:
* implements #863
* add new ACI command "dupidx" (active in group search).
* update group-enumeration presets: use '~' instead of '_'. use new ACI command 'dupidx'.
9 lines of code changed in 2 files:
* reintegrates 'macros' into 'trunk'
* implements #856
* adds: log:branches/macros@19482:19488
72 lines of code changed in 3 files:
* reintegrates 'ali' into 'trunk'
- refactorings + fixes related to SEQ_QUALITY + HELIX
* adds: log:branches/ali@19407:19424
15 lines of code changed in 3 files:
* update documentation of SEQ_QUALITY:
- non-evaluated fields
- usage of default helix base pairings.
0 lines of code changed in 2 files:
* reintegrates 'ali' into 'trunk'
- use bond settings from EDIT4 in SECEDIT
- fix refresh logic
- refactor underlying code
* adds: log:branches/ali@19393:19406
19 lines of code changed in 3 files:
* reintegrates 'ali' into 'trunk'
- refactored misused enum
- support for helix pairs:
* drop non-standard defs
* add more user defs
- change defaults
- add several predefined configs (esp. for IUPAC ambiguity codes)
* adds: log:branches/ali@19376:19392
2 lines of code changed in 2 files:
* reintegrates 'ali' into 'trunk'
- completes #854
* adds: log:branches/ali@19363:19375
17 lines of code changed in 1 file:
* reintegrates 'ali' into 'trunk'
* basically implements #854
* adds: log:branches/ali@19357:19362
35 lines of code changed in 1 file:
* added script to delete unlisted trees.
0 lines of code changed in 2 files:
* added script to delete unlisted species selections.
0 lines of code changed in 2 files:
* added script to delete unlisted SAIs.
0 lines of code changed in 2 files:
* emphasize reference- and ptserver-database have to be the same database!
18 lines of code changed in 1 file:
* allow to define a separator used to generate clusternames
- old hardcoded default was '_' (which interferes with groupname conventions)
- new customisable default is '-'
- use custom separator
* in get_upgroup_info().
* for matchrate.
- correctly handle empty separator.
* change other hardcoded characters
- avoid '_' in {{{WHOLE_TREE}}} (now uses {{{<WHOLE TREE>}}}).
- neighter use '/' nor '-' when inserting relative notation (old: {{{3-4/7}}} new {{{3.4[7]}}}).
* part of #832
2 lines of code changed in 1 file:
* document collaboration between 'create groups' with 'append original' and 'delete groups'.
0 lines of code changed in 2 files:
* document default of sina binary (was changed with [19240]).
* add warning.
2 lines of code changed in 1 file:
* add 'View sysinfo' entry to arb 'Tools' menu.
- shows 'sys.info' generated by arb_launcher.
* document 'ARB session log archive'.
10 lines of code changed in 2 files:
* reintegrates 'sina' into 'trunk'
- build/deliver sina together with arb
* adds: log:branches/sina@18984:19043,19046:19069,19072:19244
286 lines of code changed in 4 files:
* reintegrates 'split' into 'trunk'
- completes #846
* adds: log:branches/split@19169:19221
4 lines of code changed in 1 file:
* reintegrates 'split' into 'trunk'
* adds: log:branches/split@19102:19166
24 lines of code changed in 1 file:
* reintegrates 'split' into 'trunk'
- implemented beta version of alignment splitter
* adds: log:branches/split@19077:19099
51 lines of code changed in 5 files:
* add example macro for database maintainers
- allows to delete all fields except those listed in the script
- script needs to be edited (to allow execution and to maintain field list)
* mention script in "Delete Fields" help.
0 lines of code changed in 2 files:
* {{{next_expand_mode}}} now also expands all groups containing unmarked species:
- can be applied to subtrees by key 'x'.
- update documentation.
- impl: also count **unmarked** species in {{{AWT_graphic_tree_group_state}}}.
4 lines of code changed in 2 files:
* implement 'expand unmarked'
- call from 'collapse' menu.
- document.
1 lines of code changed in 2 files:
* mention various 'count species' menu entries.
* remove unused .hlp (count now refers to same helpfile as mark).
0 lines of code changed in 3 files:
* reintegrates 'nds' into 'trunk'
- fixes #841
* adds: log:branches/nds@18843:18882
33 lines of code changed in 4 files:
* 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.
2 lines of code changed in 2 files: