Directory PROBE_DESIGN/

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westram 2025-10-29 16:15 Rev.: 19551

* add missing dependency: PROBE_DESIGN->SL/MACROS.

1 lines of code changed in 1 file:

• PROBE_DESIGN: needs_libs (+1 -3)

westram 2025-10-29 10:27 Rev.: 19549

* 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

8 lines of code changed in 2 files:

• PROBE_DESIGN: Makefile (+1), probe_design.cxx (+7 -6)

westram 2023-05-31 08:21 Rev.: 19365

* string splitters:
- unittests for {{{GBT_split_string}}}:
* add tests for dropEmptyTokens.
* document special behavior for empty string.
- define enum {{{SplitMode}}}. use enum instead of bool param for GBT_splitNdestroy_string + GBT_split_string.

2 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+2 -2)

westram 2022-11-26 10:49 Rev.: 19349

* fix mnemonics:
- in 'Tree' menu:
* p: was used for 'Print tree' + 'Compare topology...'
* o: 'Sync tree scrolling..' -> 'Compare topology...'
* e: 'Beautify tree' -> 'Sync tree scrolling..'
* u: 'Mark duplicates' -> 'Beautify tree'
* k: now used for 'Mark duplicates'
* removed 'Select tree' (also bound to tree button).
* T: used for 'Tree admin' now (was 'Select tree')
* i: used for (genome-only) 'Relink tree to organisms' (was 'Tree admin')
- in 'Sequence' menu:
* S: was used for 'Split sequences' + 'Align Sequences'.
* l: now used for 'Align sequences'.
- in species transfer of merge tool.
- in properties menu of 'ARB gene map'.
- in properties menu of 'PROBE and SAI' (most changed).

5 lines of code changed in 1 file:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+5 -5)

westram 2022-11-13 15:47 Rev.: 19339

* reintegrates 'refactor' into 'trunk'
- eliminates old interface of {{{GBS_strstruct}}}
- add a few new unittests (editor-config string + some PT-SERVER-functions)
* adds: log:branches/refactor@19300:19338

99 lines of code changed in 2 files:

• PROBE_DESIGN: Makefile (+1), probe_design.cxx (+98 -30)

westram 2022-11-06 16:09 Rev.: 19297

* reintegrates 'refactor' into 'trunk'
- refactored MULTI_PROBE to support unittest.
* adds: log:branches/refactor@19286:19296

2 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+2 -21)

westram 2022-09-01 15:19 Rev.: 19245

* reintegrates 'sina' into 'trunk'
- build/deliver sina together with arb
* adds: log:branches/sina@18984:19043,19046:19069,19072:19244

50 lines of code changed in 2 files:

• PROBE_DESIGN: Makefile (+1), probe_design.cxx (+49 -31)

westram 2022-08-03 14:52 Rev.: 19206

* reintegrates 'ali' into 'trunk'
* adds: log:branches/ali@19183:19205

276 lines of code changed in 2 files:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+120 -103), probe_design.cxx (+156 -127)

westram 2022-03-04 15:20 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.

5 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+5 -5)

westram 2022-03-04 11:26 Rev.: 18959

* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958

4 lines of code changed in 1 file:

• PROBE_DESIGN: Makefile (+4)

westram 2021-10-08 15:07 Rev.: 18760

* change layout of 'Color Translation Table' properties window (make space for HELP button).
* add help button (fixes #326)
* change documentation of 'Define Color Translations'.

19 lines of code changed in 1 file:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+19 -12)

westram 2021-09-15 12:39 Rev.: 18725

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

5 lines of code changed in 1 file:

• PROBE_DESIGN: Makefile (+5 -5)

westram 2021-09-15 12:00 Rev.: 18720

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

1 lines of code changed in 1 file:

• PROBE_DESIGN: Makefile (+1 -1)

westram 2021-09-07 09:37 Rev.: 18704

* reintegrates 'tree' into 'trunk'
* adds: log:branches/tree@18666:18703

2 lines of code changed in 2 files:

• PROBE_DESIGN: Makefile (+1), SaiProbeVisualization.cxx (+1 -1)

westram 2020-12-18 14:05 Rev.: 18638

* fixes crash in "PROBE AND SAI"
- occurred when clicking into background area

1 lines of code changed in 1 file:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+1 -1)

westram 2019-10-30 11:41 Rev.: 18194

* full update from child 'fix' into 'trunk'
* adds: log:branches/fix@18190:18193

1 lines of code changed in 1 file:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+1 -1)

westram 2019-10-08 16:51 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

2 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+2 -2)

westram 2019-07-24 16:32 Rev.: 17990

* rename client variables:
- match_kompl -> match_also_revcompl
- COMPLEMENT -> ALSO_REVCOMPL
- reversed -> alsoRevCompl
- complement -> alsoRevcompl (probe_design)
- complement -> complementFirst (arb_probe_match)
* rename AWAR: AWAR_PD_MATCH_COMPLEMENT -> AWAR_PD_MATCH_ALSO_REVCOMP
* fix doc.

19 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+19 -19)

westram 2019-07-24 16:24 Rev.: 17988

* rename ptserver flags
- MATCH_COMPLEMENT -> COMPLEMENT_FIRST
- MATCH_REVERSED -> MATCH_ALSO_REVCOMP
* comments and TODOs.

2 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+2 -2)

westram 2019-04-01 16:41 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

3 lines of code changed in 2 files:

• PROBE_DESIGN: Makefile (+3), probe_design.cxx (-1)

westram 2018-11-01 16:34 Rev.: 17599

* full update from child 'fix' into 'trunk'
* adds: log:branches/fix@17597:17598

2 lines of code changed in 1 file:

• PROBE_DESIGN: SaiProbeVisualization.hxx (+2 -1)

westram 2018-10-24 14:58 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

4 lines of code changed in 1 file:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+4 -4)

westram 2018-07-23 15:52 Rev.: 17262

* partial merge from 'group' into 'trunk'
- fixes to arb_progress
* adds:
- log:branches/group@17191:17218,17220:17260
- log:branches/progress@17195:17216,17218:17259

8 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+8 -7)

westram 2018-05-04 17:06 Rev.: 16986

* reintegrates 'gcc' into 'trunk'
- ports arb to gcc 8.1 (fixing warnings)
* adds: log:branches/gcc@16965:16985

Update: continued by [17178]

1 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+1 -1)

westram 2018-05-02 10:32 Rev.: 16961

* partial merge from 'fix' into 'trunk'
- refactored {{{AW_device}}} text output
* reduces calls to strlen (using {{{SizedCstr}}})
* eliminated/modernized several parameters/functions (esp. in {{{TextOverlayCallback}}}s)
* adds: log:branches/fix@16939:16960

8 lines of code changed in 2 files:

• PROBE_DESIGN: Makefile (+2), SaiProbeVisualization.cxx (+6 -6)

westram 2017-11-28 18:22 Rev.: 16766

* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

32 lines of code changed in 4 files:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+3 -4), probe_collection.cxx (+27 -29), probe_collection.hxx (+1 -1), probe_design.cxx (+1 -1)

westram 2017-11-28 17:09 Rev.: 16763

* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

209 lines of code changed in 5 files:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+20 -19), probe_collection.cxx (+70 -82), probe_collection.hxx (+4 -4), probe_design.cxx (+100 -99), probe_match_parser.cxx (+15 -12)

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

3 lines of code changed in 2 files:

• PROBE_DESIGN: Makefile (+1), probe_design.cxx (+2 -2)

westram 2017-09-23 13:03 Rev.: 16425

* reintegrates 'aci' into 'trunk'
- extends ACI language (implementing #707)
* boolean operators: {{{And}}},{{{Or}}},{{{Not}}}
* numeric comparison: {{{isAbove}}},{{{isBelow}}},{{{isEqual}}}
* floating point arithmetic: {{{fplus}}},{{{fminus}}},{{{fmult}}},{{{fdiv}}}
* misc: {{{round}}},{{{inRange}}},{{{isEmpty}}}
- enforce parameter checks in ACI function code
- case of commands completely ignored
* adds: log:branches/aci@16385,16391:16424

1 lines of code changed in 1 file:

• PROBE_DESIGN: Makefile (+1)

westram 2017-09-19 13:40 Rev.: 16391

* full update from child 'aci' into 'trunk'
- allow to view console from inside ARB
- slightly tweaked ACI trace
* adds: log:branches/aci@16386:16390

10 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+10 -3)

westram 2017-09-18 14:23 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

9 lines of code changed in 3 files:

• PROBE_DESIGN: Makefile (+1), SaiProbeVisualization.cxx (+7 -2), probe_design.cxx (+1 -1)

westram 2017-04-14 16:47 Rev.: 15781

* partial merge from 'group' into 'trunk'
- improve {{{AW_selection_list}}}-functionality of non-{{{AW_STRING}}} lists
* adds: log:branches/group@15778:15780

2 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+2 -2)

westram 2017-03-28 14:32 Rev.: 15703

* reintegrates 'group' into 'trunk'
- implements #709
* adds: log:branches/group@15693:15702

1 lines of code changed in 1 file:

• PROBE_DESIGN: Makefile (+1)

westram 2017-03-24 12:04 Rev.: 15673

* reintegrates 'fix' into 'trunk'
- fixes "jump to species" broken by [15665] (didn't work when tree folding changed)
- still broken for IRS tree (see #748)
* adds: log:branches/fix@15668:15672

2 lines of code changed in 1 file:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+2 -1)

westram 2017-03-23 13:58 Rev.: 15665

* reintegrates 'refactor' into 'trunk'
- refactored AWT_graphic
* now have explicit states with different permissions
1. update model + request view/DB updates (AWT_auto_refresh)
- always preceeded by DB->model up-to-date-check
- automatically updates the view on destruction
2. update (DB and view) from model
3. neither
- benefits
* saves several view-updates
* unproblematic nesting of functions requesting view-updates
* will allow
- delayed view-updates and
- easier modification of update logic
- fixes a bunch of update-issues (found on the way)
* adds: log:branches/refactor@15613:15615,15627:15637,15639:15664

3 lines of code changed in 1 file:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+3 -2)

westram 2017-01-04 17:06 Rev.: 15513

* reintegrates 'warnings' into 'trunk'
- activate additional warnings (gcc 5.x++)
- Cxx11-forward final (classes+methods)
- fix tag problems caused by using preprocessor
* adds: log:branches/warnings@15486:15489,15491:15501,15506:15512

1 lines of code changed in 1 file:

• PROBE_DESIGN: probe_collection.hxx (+1 -1)

westram 2016-10-06 11:52 Rev.: 15306

* derive {{{TREE_canvas}}} from {{{AWT_canvas}}}
- move {{{awar_tree}}} -> {{{TREE_canvas}}}
- use {{{TREE_canvas}}} where required
- remove dummy-param from {{{AWT_canvas}}}-ctor
* rename {{{NT_canvas_registry}}} -> {{{TREE_canvas_registry}}}
* remove unused param from {{{AP_user_push_cb}}}

8 lines of code changed in 3 files:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+1 -1), probe_design.cxx (+5 -5), probe_gui.hxx (+2 -2)

westram 2016-10-05 11:39 Rev.: 15301

* full update from child 'sync' into 'trunk'
- register all NTREE canvases
- provide canvas selection list
- pass awar to canvas (not its name; expect awar already exists); no awar for non-tree-canvases
* adds: log:branches/sync@15292:15300

1 lines of code changed in 1 file:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+1 -1)

westram 2016-09-24 07:08 Rev.: 15268

* {{{GB_xcmd}}}
- remove from perl interface
- replace bool-flag-couple by enum
- guard unused case {{{XCMD_SYNC_WAITKEY}}}

1 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+1 -1)

westram 2016-08-30 13:26 Rev.: 15256

* replace redundant data {{{AW_font_limits::height}}} with {{{get_height()}}}

1 lines of code changed in 1 file:

• PROBE_DESIGN: SaiProbeVisualization.cxx (+1 -1)

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