* document primer design result window
33 lines of code changed in 3 files:
* 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:
* remove now unused fig (also from [1463])
0 lines of code changed in 1 file:
* remove stub added with [1463]
0 lines of code changed in 3 files:
* added {{{awt_create_filter_awars}}}
- made all awars 'tmp' (saving them did not work)
136 lines of code changed in 10 files:
* add missing check for filter validity
3 lines of code changed in 1 file:
* 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:
* correct stored colorsets when committing rename-session (fixes #660)
* summarize failures when restoring a colorset
63 lines of code changed in 4 files:
* add a colorset to test DB
35 lines of code changed in 3 files:
* sync code with gtk branch
398 lines of code changed in 4 files:
* delete existing 'ARB_color' entries when color is set to 0
6 lines of code changed in 1 file:
* 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:
* document colorset functions
* slightly fix layout of colorset window
71 lines of code changed in 4 files:
* ignore .bak while checking resources
2 lines of code changed in 1 file:
* 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:
* 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:
* add item-specific refresh mechanism
32 lines of code changed in 6 files:
* 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:
* "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:
* SAI/PROBE match
- 'Select display field' window
* document
* fix layout
* fix crash when selecting 'no field'
- link other 'Properties' menu entries to existing helpfiles
136 lines of code changed in 6 files:
* no special help for 'Hide/Delete field' button
0 lines of code changed in 1 file:
* 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:
* document genemap 'new view' and 'mode buttons'
76 lines of code changed in 3 files:
* merge 2 genemap property windows
* document genemap properties, jump, display types
245 lines of code changed in 8 files:
* 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:
* deny to use source- as target-alignment in "concat alignments"
70 lines of code changed in 2 files:
* 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:
* 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:
* 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:
* fix NDEBUG compilation and some warnings
5 lines of code changed in 3 files:
* 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:
* documentation
- 'questions' and 'advices' (de-/re-activation)
- adjust general references to properties menu
84 lines of code changed in 9 files:
* move sativa help template
15 lines of code changed in 1 file:
* resource-checker
- warn about duplicate resource (e.g. genhelp+oldhelp)
21 lines of code changed in 1 file:
* 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 16 files:
* use some typed callbacks (eliminating useless wrappers)
11 lines of code changed in 1 file:
mark motif-only
2 lines of code changed in 1 file:
(forgot help)
25 lines of code changed in 1 file:
* 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:
* 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:
- remove unused dependency
0 lines of code changed in 1 file:
* 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:
* fix NDEBUG warning
1 lines of code changed in 1 file:
* localized window-ids of "write to fields of listed" and "set protection of field of listed"
64 lines of code changed in 6 files:
* rename/publish itemtype specific window initialization
* fix one macro id shared between organism/species info
16 lines of code changed in 2 files:
* fix duplicate macro IDs in windows opening from item 'FIELDS' menu
28 lines of code changed in 1 file:
* 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:
* 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:
* localize more macro IDs (2nd arb genome view)
10 lines of code changed in 1 file:
* localize some macro IDs (arb genome)
5 lines of code changed in 2 files:
* 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:
* 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:
* 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:
* accept '{{{static __ATTR__XXX}}}' (caused several prototypes to be skipped)
15 lines of code changed in 1 file:
* 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:
- fix some broken (usused) test macros
6 lines of code changed in 1 file:
* revert part of [14048]:
- accept broken LINKs in non-RELEASE modes
4 lines of code changed in 1 file:
* 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
409 lines of code changed in 23 files:
* 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:
* 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:
* use one help for all "Colors and fonts"
21 lines of code changed in 7 files:
* rename only (fixes warning in resource-checker)
4 lines of code changed in 1 file:
* remove refs to missing helpfile for db-browser (DEBUG)
1 lines of code changed in 1 file:
* remove leftovers from [12758]
0 lines of code changed in 2 files:
* merge [14031] from 'markers' into 'trunk'
74 lines of code changed in 6 files:
* and NDEBUG version contains file {{{__.SYMDEF SORTED}}}. delete all {{{__.*}}}
1 lines of code changed in 1 file:
* ar on OSX contains file {{{__.SYMDEF}}}. delete
3 lines of code changed in 1 file:
* show what is inside serverlib
1 lines of code changed in 1 file:
* 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:
* added gcc 5.2.0
1 lines of code changed in 1 file:
* reintegrates 'markers' into 'trunk'
* adds:
- log:branches/markers@13954:14024
5077 lines of code changed in 48 files:
* add more greylevels to motif-version
31 lines of code changed in 1 file:
* merge [14000] from 'alilink' into 'trunk'
1 lines of code changed in 1 file:
* 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:
* 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:
* DRY {{{charpLess}}} vs {{{ltstr}}} and {{{lessCCP}}}
8 lines of code changed in 4 files:
* separate merge of AWT-changes in [13978] and [13981] (from branch 'markers' to 'trunk')
27 lines of code changed in 2 files:
* allow to install callback called on {{{AW_selection_list::update()}}}
18 lines of code changed in 2 files:
* reintegrates 'ptsfix' into 'trunk'
- fixes #659
* adds:
- log:branches/ptsfix@13960:13969
95 lines of code changed in 13 files:
* added libxerces-c dependency
5 lines of code changed in 2 files:
* 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:
* 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:
* code move
79 lines of code changed in 1 file:
* 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: