July 2015 Commit Log

Number of Commits:
84
Number of Active Developers:
1
westram 2015-07-31 16:33 Rev.: 14122


* document primer design result window

33 lines of code changed in 3 files:

westram 2015-07-31 16:11 Rev.: 14121


* update documentation related to 'gene-species'
- added "Relink tree to organisms"
- describe how 'concat alignments' is intended to be used with gene-species
* fix broken link

42 lines of code changed in 6 files:

westram 2015-07-31 15:33 Rev.: 14120


* remove now unused fig (also from [1463])

0 lines of code changed in 1 file:

westram 2015-07-31 15:25 Rev.: 14119


* remove stub added with [1463]

0 lines of code changed in 3 files:

westram 2015-07-31 15:15 Rev.: 14118


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

136 lines of code changed in 10 files:

westram 2015-07-31 13:30 Rev.: 14117


* add missing check for filter validity

3 lines of code changed in 1 file:

westram 2015-07-31 10:43 Rev.: 14116


* adds a "no color" entry to colorset in test DB (as generated by pre-[14094] versions)
* auto-remove such entries in rename-session

17 lines of code changed in 3 files:

westram 2015-07-31 10:21 Rev.: 14115


* correct stored colorsets when committing rename-session (fixes #660)
* summarize failures when restoring a colorset

63 lines of code changed in 4 files:

westram 2015-07-31 09:22 Rev.: 14114


* add a colorset to test DB

35 lines of code changed in 3 files:

westram 2015-07-30 18:36 Rev.: 14112


* sync code with gtk branch

398 lines of code changed in 4 files:

westram 2015-07-30 13:17 Rev.: 14102


* delete existing 'ARB_color' entries when color is set to 0

6 lines of code changed in 1 file:

westram 2015-07-30 12:48 Rev.: 14101


* fix assertion when loading "UNIT_TESTER/run/TEST_opti_ascii_in.arb" into ARB_NTREE (DB has no alignment at all)

14 lines of code changed in 1 file:

westram 2015-07-30 11:30 Rev.: 14100


* document colorset functions
* slightly fix layout of colorset window

71 lines of code changed in 4 files:

westram 2015-07-30 11:29 Rev.: 14099


* ignore .bak while checking resources

2 lines of code changed in 1 file:

westram 2015-07-30 11:05 Rev.: 14098


* refactored colorset handling
- moved basics to ARBDB
- remove attributes stub from AWT (was done for #443; redo if needed)
- replace {{{AW_find_color_group}}} with {{{AW_find_active_color_group}}} (w/o bool-param) and {{{GBT_get_color_group}}}
- colorset functions (create,restore,save+load) all operate on string arrays (containing "name=color" entries)

287 lines of code changed in 23 files:

westram 2015-07-29 10:07 Rev.: 14097


* trigger item refresh after
- colorize queried
- color 'Reset'
- colorset 'Load'/'Overlay'
* fix error handling in {{{restore_colorset_representation}}}

23 lines of code changed in 1 file:

westram 2015-07-29 09:49 Rev.: 14096


* add item-specific refresh mechanism

32 lines of code changed in 6 files:

westram 2015-07-29 09:24 Rev.: 14095


* restrict use of {{{color_save_data}}} (singleton; only exists if GUI used)
- instead pass {{{BoundItemSel}}} where possible

43 lines of code changed in 1 file:

westram 2015-07-29 08:25 Rev.: 14094


* "no color" was stored in colorgroups
- 'Overlay' was working like 'Load'
- fix: don't store or load "no color"
* eliminate member {{{items_name}}} from {{{color_save_data}}}

17 lines of code changed in 1 file:

westram 2015-07-28 15:42 Rev.: 14093


* SAI/PROBE match
- 'Select display field' window
* document
* fix layout
* fix crash when selecting 'no field'
- link other 'Properties' menu entries to existing helpfiles

134 lines of code changed in 7 files:

westram 2015-07-28 15:31 Rev.: 14092


* no special help for 'Hide/Delete field' button

0 lines of code changed in 1 file:

westram 2015-07-28 13:52 Rev.: 14091


* RNA3D
- help-link buttons in main window
- remove unfinished help-window (replace by standard help) + remove now unused resources
- create stub for 'Change molecule' (23s only, undocumented and probably broken)

29 lines of code changed in 6 files:

westram 2015-07-28 13:07 Rev.: 14090


* document genemap 'new view' and 'mode buttons'

76 lines of code changed in 3 files:

westram 2015-07-28 11:31 Rev.: 14089


* merge 2 genemap property windows
* document genemap properties, jump, display types

243 lines of code changed in 9 files:

westram 2015-07-26 14:32 Rev.: 14088


* documentation
- fix broken help for search/info of organisms (linked to species)
- add missing help for search/info of experiments
- fix occurrences
- mention experiments

140 lines of code changed in 27 files:

westram 2015-07-26 13:18 Rev.: 14087


* deny to use source- as target-alignment in "concat alignments"

70 lines of code changed in 2 files:

westram 2015-07-26 12:54 Rev.: 14086


* fix assertion failure in concat alignments
- occurred while saving concat-SAI, after an existing alignment has been overwritten

4 lines of code changed in 1 file:

westram 2015-07-26 12:11 Rev.: 14085


* concat alignments
- default to alignment type of current alignment (at startup)
- remove interactive questions by GUI-toggles
- add button to "use" selected alignment as target

86 lines of code changed in 5 files:

westram 2015-07-26 10:03 Rev.: 14084


* concat alignments
- fix counters (how often each alignment occurred/was missing)
- uncaps
- stop with error if one species does contain none of the selected alignments

16 lines of code changed in 1 file:

westram 2015-07-26 09:22 Rev.: 14083


* fix NDEBUG compilation and some warnings

5 lines of code changed in 3 files:

westram 2015-07-25 13:58 Rev.: 14082


* merge species / concat alignments
- fix help-links in NT-menu-entries
- update documentation
* added example for 'merge species'
- use typed callbacks
- use different title/button to avoid getting confused about the two 'merge species' windows

132 lines of code changed in 6 files:

westram 2015-07-25 12:06 Rev.: 14081


* documentation
- 'questions' and 'advices' (de-/re-activation)
- adjust general references to properties menu

84 lines of code changed in 9 files:

westram 2015-07-24 15:17 Rev.: 14080


* move sativa help template

15 lines of code changed in 2 files:

westram 2015-07-24 15:04 Rev.: 14079


* resource-checker
- warn about duplicate resource (e.g. genhelp+oldhelp)

21 lines of code changed in 1 file:

westram 2015-07-24 14:25 Rev.: 14078


* documentation
- update help on
* edit4 search patterns
* edit4 column statistic
* ways to colorize items and where these colors are used
- document edit4 background priority
- delete unused helpfile {{{markcolor.hlp}}}

193 lines of code changed in 17 files:

westram 2015-07-24 14:03 Rev.: 14077


* use some typed callbacks (eliminating useless wrappers)

11 lines of code changed in 1 file:

westram 2015-07-24 13:22 Rev.: 14075


mark motif-only

2 lines of code changed in 1 file:

westram 2015-07-24 13:14 Rev.: 14074


(forgot help)

25 lines of code changed in 1 file:

westram 2015-07-24 13:13 Rev.: 14073


* fixed weird bugs concerned with storing window positions (motif only; feature not supported in gtk)
- trace max frame-size seen and use it
* to estimate real size of not-yet-shown window
* as fallback, if frame-detection fails
- more strictly move window into viewport (using same user account with different resolutions caused problems)
* warn about over-sized windows (default size > 1280x800)
* allow to reset window layout properties

178 lines of code changed in 6 files:

westram 2015-07-24 10:47 Rev.: 14067


* allow to call {{{SOURCE_TOOLS/needed_libs.pl -h}}} w/o error
* add code which generates custom dependency gifs

12 lines of code changed in 2 files:

westram 2015-07-24 10:25 Rev.: 14066


- remove unused dependency

0 lines of code changed in 1 file:

westram 2015-07-24 09:48 Rev.: 14065


* fix link error (NDEBUG)
- pull down {{{init_itemType_specific_window}}} into {{{SL/ITEMS.a}}}
- reason: DB_UI depends on DB_QUERY, so DB_QUERY should not (and since [14038] cannot) call functions from DB_UI. Unclear why linking works in DEBUG mode?!
[[Image(ticket:152:libdep.gif)]]

63 lines of code changed in 6 files:

westram 2015-07-24 09:48 Rev.: 14064


* fix NDEBUG warning

1 lines of code changed in 1 file:

westram 2015-07-22 13:38 Rev.: 14063


* localized window-ids of "write to fields of listed" and "set protection of field of listed"

64 lines of code changed in 6 files:

westram 2015-07-22 11:59 Rev.: 14062


* rename/publish itemtype specific window initialization
* fix one macro id shared between organism/species info

16 lines of code changed in 2 files:

westram 2015-07-22 11:30 Rev.: 14061


* fix duplicate macro IDs in windows opening from item 'FIELDS' menu

28 lines of code changed in 1 file:

westram 2015-07-22 10:39 Rev.: 14060


* item 'FIELDS' menus
- localized macro-IDs for GENES/EXP
- unlocalized two macro-IDs for SPECIES
- move "Edit gene location" to 'GENE' menu (same bug as [14059])

14 lines of code changed in 3 files:

westram 2015-07-22 10:10 Rev.: 14059


* do not insert item-menu into detached item-info-windows
- opening detached window failed due to duplicate macro-id
- behavior of menu-entries was misleading anyway (always used the globally selected item, not the detached item)

24 lines of code changed in 3 files:

westram 2015-07-21 17:14 Rev.: 14058


* localize more macro IDs (2nd arb genome view)

10 lines of code changed in 1 file:

westram 2015-07-21 17:00 Rev.: 14057


* localize some macro IDs (arb genome)

5 lines of code changed in 2 files:

westram 2015-07-21 13:50 Rev.: 14056


* allow to use {{{GB_add_hierarchy_callback}}} with unknown keys (i.e. keys never used yet)
- already was used since [14012], but did crash in DEBUG mode (e.g. after import into new DB)
- location-based {{{GB_add_hierarchy_callback}}}/{{{GB_remove_hierarchy_callback}}} have to be used inside transaction now
- added unittest
* needed to change some tests (using previously invalid, now valid paths)

50 lines of code changed in 1 file:

westram 2015-07-21 13:22 Rev.: 14055


* missing target-dependency:
- 'links' has to depend on 'genheaders' (otherwise it may happen, that some target tries to include/check svn_revision.h before it has been generated)

3 lines of code changed in 1 file:

westram 2015-07-21 10:59 Rev.: 14054


* improve error handling in {{{adcomm.cxx}}}
- dont export errors (if avoidable)
- check error-results in callers
- define common error generators to
* get uniform messages
* be able to identify exact source location (using svn-rev + source line)
- added some missing checks for read/write failures
* remove useless parameter 'mode' from {{{gbcm_write_bin}}}

372 lines of code changed in 9 files:

westram 2015-07-20 13:13 Rev.: 14053


* accept '{{{static __ATTR__XXX}}}' (caused several prototypes to be skipped)

15 lines of code changed in 1 file:

westram 2015-07-20 12:07 Rev.: 14052


* somehow an empty key ("") found it's way into demo.arb
- delete such keys while loading key data
- protect against empty-key generation

27 lines of code changed in 5 files:

westram 2015-07-20 11:48 Rev.: 14051


- fix some broken (usused) test macros

6 lines of code changed in 1 file:

westram 2015-07-19 10:30 Rev.: 14050


* revert part of [14048]:
- accept broken LINKs in non-RELEASE modes

4 lines of code changed in 1 file:

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

403 lines of code changed in 29 files:

westram 2015-07-18 11:56 Rev.: 14048


* help-generation
- no longer accept broken LINKs
- when generating dependencies:
* delete .xml files with broken dependencies and delete dependency file
* fixes bad behavior after renaming a helpfile

77 lines of code changed in 4 files:

westram 2015-07-17 16:09 Rev.: 14047


* documentation
- separate help on ARB_EDIT4:GET/JUMP and related
- add help for ARB_EDIT4:mode-buttons
- update help on selected species

151 lines of code changed in 7 files:

westram 2015-07-17 15:18 Rev.: 14046


* use one help for all "Colors and fonts"

21 lines of code changed in 8 files:

westram 2015-07-17 15:16 Rev.: 14045


* rename only (fixes warning in resource-checker)

4 lines of code changed in 1 file:

westram 2015-07-17 15:15 Rev.: 14044


* remove refs to missing helpfile for db-browser (DEBUG)

1 lines of code changed in 1 file:

westram 2015-07-17 15:12 Rev.: 14043


* remove leftovers from [12758]

0 lines of code changed in 2 files:

westram 2015-07-17 15:07 Rev.: 14042


* merge [14031] from 'markers' into 'trunk'

74 lines of code changed in 6 files:

westram 2015-07-17 13:16 Rev.: 14041


* and NDEBUG version contains file {{{__.SYMDEF SORTED}}}. delete all {{{__.*}}}

1 lines of code changed in 1 file:

westram 2015-07-17 13:00 Rev.: 14040


* ar on OSX contains file {{{__.SYMDEF}}}. delete

3 lines of code changed in 1 file:

westram 2015-07-17 12:16 Rev.: 14039


* show what is inside serverlib

1 lines of code changed in 1 file:

westram 2015-07-17 12:11 Rev.: 14038


* fix #618 (use ar for linking)
- library order does matter now
* {{{PROBE_COM/server.a}}} and {{{PROBE/PROBE.a}}} depend on each other -> hack: unpack lib and directly link objects
- do not export {{{pt_init_bond_matrix}}} "extern C"
- {{{sym2testcode.pl}}}: ignore several additional lines from nm-output

49 lines of code changed in 8 files:

westram 2015-07-16 16:25 Rev.: 14037


* added gcc 5.2.0

1 lines of code changed in 1 file:

westram 2015-07-15 13:42 Rev.: 14025


* reintegrates 'markers' into 'trunk'
* adds:
- log:branches/markers@13954:14024

5077 lines of code changed in 48 files:

westram 2015-07-14 17:01 Rev.: 14016


* add more greylevels to motif-version

31 lines of code changed in 1 file:

westram 2015-07-10 18:22 Rev.: 14007


* merge [14000] from 'alilink' into 'trunk'

1 lines of code changed in 1 file:

westram 2015-07-10 17:41 Rev.: 14006


* partial merge from 'alilink' into 'trunk'
- adds GB_remove_hierarchy_callback
- adds new flavor of GB_add_hierarchy_callback (allows to install path before it exists)
- several refactoring in callback code
* adds:
- log:branches/alilink@12854,12856:12865,12867

1556 lines of code changed in 19 files:

westram 2015-07-08 09:15 Rev.: 13986


* automatically delete entry from {{{AW_subset_selection}}} if deleted in parent selection
- e.g. in consensus tree window

40 lines of code changed in 1 file:

westram 2015-07-08 09:12 Rev.: 13985


* DRY {{{charpLess}}} vs {{{ltstr}}} and {{{lessCCP}}}

8 lines of code changed in 4 files:

westram 2015-07-08 09:02 Rev.: 13984


* separate merge of AWT-changes in [13978] and [13981] (from branch 'markers' to 'trunk')

27 lines of code changed in 2 files:

westram 2015-07-08 08:52 Rev.: 13983


* allow to install callback called on {{{AW_selection_list::update()}}}

18 lines of code changed in 2 files:

westram 2015-07-04 13:00 Rev.: 13970


* reintegrates 'ptsfix' into 'trunk'
- fixes #659
* adds:
- log:branches/ptsfix@13960:13969

95 lines of code changed in 13 files:

westram 2015-07-04 08:13 Rev.: 13966


* added libxerces-c dependency

5 lines of code changed in 2 files:

westram 2015-07-03 09:29 Rev.: 13959


* fix some crashes in {{{probe_match_event}}} / {{{probe_match_event_using_awars}}}
- occurred when probe-auto-match active, probe-match-window never was opened and target-string changes
- probably introduced by [13934] + [13936]

9 lines of code changed in 1 file:

westram 2015-07-02 10:43 Rev.: 13953


* do not save matches of probe-collection in DB (too slow for big DBs)
- pass callback to !TreeDisplay, which directly retrieves matches from results-manager

58 lines of code changed in 3 files:

westram 2015-07-01 09:33 Rev.: 13952


* code move

79 lines of code changed in 1 file:

westram 2015-07-01 08:55 Rev.: 13951


* display of probe-matches for big folded groups was too slow
- added a cache for results of {{{enumerateClade}}}
- invalidate cache from {{{update_species_matched_string}}}

127 lines of code changed in 3 files:

June 2015 »

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