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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:

• GENOM: GEN_interface.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).

1 lines of code changed in 1 file:

• GENOM: GEN_map.cxx (+1 -1)

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

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

16 lines of code changed in 1 file:

• GENOM: GEN_map.cxx (+16 -11)

westram 2022-07-21 13:01 Rev.: 19167

* reintegrates 'split' into 'trunk'
* adds: log:branches/split@19102:19166

4 lines of code changed in 1 file:

• GENOM: GEN_map.cxx (+4 -1)

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

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

8 lines of code changed in 1 file:

• GENOM: Makefile (+8)

westram 2021-09-15 12:52 Rev.: 18730

* remove trailing whitespace from c source.

8 lines of code changed in 3 files:

• GENOM: GEN_gene.hxx (+1 -1), GEN_interface.cxx (+3 -3), GEN_map.cxx (+4 -4)

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

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

5 lines of code changed in 1 file:

• GENOM: Makefile (+5 -5)

westram 2021-09-15 12:31 Rev.: 18723

* remove .c rules.
* add .c suffix (in SOURCE_TOOLS).

1 lines of code changed in 1 file:

• GENOM: Makefile (+1 -4)

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

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

1 lines of code changed in 1 file:

• GENOM: Makefile (+1 -9)

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:

• GENOM: GEN_nds.cxx (+1 -1), Makefile (+1)

westram 2021-08-17 14:15 Rev.: 18665

* change many WARN_TODO triggered warnings into todo markers.

10 lines of code changed in 3 files:

• GENOM: EXP_interface.cxx (+3 -15), GEN_interface.cxx (+4 -19), GEN_translations.cxx (+3 -8)

westram 2020-03-03 12:23 Rev.: 18352

* full update from child 'fix' into 'trunk'
* adds: log:branches/fix@18339:18351

0 lines of code changed in 1 file:

• GENOM: GEN_map.cxx (-2)

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:

• GENOM: GEN_map.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

11 lines of code changed in 4 files:

• GENOM: EXP_interface.cxx (+1 -1), GEN_gene.cxx (+1 -1), GEN_interface.cxx (+2 -2), GEN_map.cxx (+7 -4)

westram 2019-07-02 13:45 Rev.: 17944

* FIXES crash in RELEASE version (when invalid color group occurs in database).
* add assertions against
- invalid color_groups and
- invalid unshaded GCs.
* ARBDB color-group interface:
- define number of allowed color groups in ARBDB
- fix interface types (long->int)
- report error when color_group passed to {{{GBT_set_color_group}}} is out-of-range.
- {{{GBT_get_color_group}}} does range check. returns 0 if out-of-range.

2 lines of code changed in 2 files:

• GENOM: GEN_graphic.cxx (-1), Makefile (+2)

westram 2019-05-14 12:59 Rev.: 17890

* reintegrates 'dbui' into 'trunk'
* adds: log:branches/dbui@17881:17889

2 lines of code changed in 2 files:

• GENOM: EXP_interface.cxx (+1 -1), GEN_interface.cxx (+1 -1)

westram 2019-05-10 12:57 Rev.: 17877

* reintegrates 'gcc' into 'trunk'
* adds: log:branches/gcc@17850:17876

2 lines of code changed in 2 files:

• GENOM: GEN_interface.cxx (+1 -1), GEN_nds.cxx (+1 -1)

westram 2019-04-29 13:44 Rev.: 17836

* reintegrates 'clone' into 'trunk'
* adds: log:branches/clone@17813:17835

2 lines of code changed in 2 files:

• GENOM: EXP_interface.cxx (+1 -1), GEN_interface.cxx (+1 -1)

westram 2019-04-05 18:32 Rev.: 17748

* remove hardcoded 'markCreated==true' from
- GBT_find_or_create_species_rel_species_data and
- GBT_find_or_create_species.
* hardcode 'markCreated==false' in GBT_find_or_create_SAI.
- changes result DB.
- increase diff buf size (result DB has loooong lines).

1 lines of code changed in 1 file:

• GENOM: GEN_map.cxx (+1 -1)

westram 2018-10-31 09:52 Rev.: 17593

* reintegrates 'fix' into 'trunk'
- performs #798
* adds genetic code tables (24-31)
* adds combined amino acid J (I or L)
* improved translate and/or realign
- handle optional start-/stop-codons
- improve recognition of nuc-triples containing IUPAC-codes
* error messages now always list EMBL table numbers
* adds:
- log:branches/fix@17480:17485,17491:17492,17494:17507,17509:17528,17534:17592
- log:branches/optional@17481:17568

1 lines of code changed in 1 file:

• GENOM: GEN_translations.cxx (+1 -1)

westram 2018-10-23 09:36 Rev.: 17510

* partial merge from 'fix' into 'trunk'
* adds: [17508/branches/fix]

2 lines of code changed in 1 file:

• GENOM: GEN_translations.cxx (+2 -2)

westram 2018-09-20 17:43 Rev.: 17396

* reintegrates 'fix' into 'trunk'
- elim dead code
- use const hash loop
* adds: log:branches/fix@17380,17388:17395

16 lines of code changed in 2 files:

• GENOM: GEN_local.hxx (-1), GEN_map.cxx (+16 -19)

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

2 lines of code changed in 1 file:

• GENOM: GEN_map.cxx (+2 -2)

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

5 lines of code changed in 2 files:

• GENOM: GEN_graphic.cxx (+3 -3), Makefile (+2)

westram 2018-04-30 17:27 Rev.: 16936

* reintegrates 'cleanup' into 'trunk'
- performs #762 (shrink 3.7 k)
* adds: log:branches/cleanup@16924:16935

0 lines of code changed in 1 file:

• GENOM: GEN_map.cxx (-2)

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

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

4 lines of code changed in 3 files:

• GENOM: EXP_interface.cxx (+1 -1), GEN_interface.cxx (+2 -2), GEN_map.cxx (+1 -3)

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

162 lines of code changed in 8 files:

• GENOM: EXP_interface.cxx (+20 -20), EXP_main.cxx (+1 -1), GEN_gene.cxx (+13 -13), GEN_graphic.cxx (+4 -4), GEN_interface.cxx (+43 -43), GEN_map.cxx (+60 -61), GEN_nds.cxx (+13 -13), GEN_translations.cxx (+8 -8)

westram 2017-10-08 14:54 Rev.: 16508

* reintegrates 'macros' into 'trunk'
- introduce generic input prompt (related #179)
- use it instead of locally generated windows:
* species (rename + create)
* alignment (rename, copy + create)
* experiments (rename, copy + create)
* genes (rename, copy + extract)
* mergetool (rename SAI + configs)
* SAIviz color translation (copy + create)
- fixed bugs in mergetool ([16503],[16504])
* adds: log:branches/macros@16484:16507

129 lines of code changed in 8 files:

• GENOM: EXP_interface.cxx (+49 -108), EXP_local.hxx (-3), EXP_main.cxx (-1), GEN.hxx (+1 -2), GEN_interface.cxx (+48 -84), GEN_local.hxx (-3), GEN_map.cxx (+28 -53), Makefile (+3)

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:

• GENOM: Makefile (+1)

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

12 lines of code changed in 4 files:

• GENOM: GEN_gene.cxx (+2 -2), GEN_nds.cxx (+5 -2), GEN_nds.hxx (+1 -1), Makefile (+4)

westram 2017-06-08 16:59 Rev.: 16021

* reintegrates 'fix' into 'trunk'
- refactors {{{DbScanner}}} -> OO + shrink 1.4k
- fixes #251 and #506
* adds: log:branches/fix@15975,15982:16020

10 lines of code changed in 2 files:

• GENOM: EXP_interface.cxx (+5 -3), GEN_interface.cxx (+5 -3)

westram 2017-06-02 10:17 Rev.: 15982

* full update from child 'fix' into 'trunk'
- fixes #478
* adds: log:branches/fix@15976:15981

10 lines of code changed in 2 files:

• GENOM: EXP_interface.cxx (+5 -3), GEN_interface.cxx (+5 -3)

westram 2017-05-21 16:59 Rev.: 15966

* reintegrates 'group' into 'trunk'
- implements #652 (group search)
* adds: log:branches/group@15733:15740,15743:15748,15750:15752,15754,15756,15758:15777,15781:15793,15796,15798:15806,15808:15817,15819:15965

2 lines of code changed in 2 files:

• GENOM: EXP_interface.cxx (+1 -1), GEN_interface.cxx (+1 -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

43 lines of code changed in 3 files:

• GENOM: GEN_graphic.cxx (+8 -10), GEN_graphic.hxx (+2 -3), GEN_map.cxx (+33 -22)

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}}}

1 lines of code changed in 1 file:

• GENOM: GEN_map.cxx (+1 -1)

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:

• GENOM: GEN_map.cxx (+1 -1)

westram 2016-08-30 11:30 Rev.: 15254

* depends for [15253]

2 lines of code changed in 1 file:

• GENOM: Makefile (+2)

westram 2016-08-17 19:39 Rev.: 15198

* remove {{{virtual}}} if {{{OVERRIDE}}} is present
- OVERRIDE implies 'implicit virtual' (if code compiles as C++11 <- tested on build server!)

13 lines of code changed in 3 files:

• GENOM: EXP_main.cxx (+5 -5), GEN_graphic.hxx (+3 -3), GEN_map.cxx (+5 -5)

westram 2016-08-11 10:05 Rev.: 15176

* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

41 lines of code changed in 6 files:

• GENOM: EXP_interface.cxx (+2 -2), GEN_gene.cxx (+1 -1), GEN_interface.cxx (+6 -8), GEN_map.cxx (+4 -4), GEN_nds.cxx (+20 -23), Makefile (+8)

westram 2016-07-27 12:26 Rev.: 15096

* add scalers to genemap-options

50 lines of code changed in 1 file:

• GENOM: GEN_map.cxx (+50 -38)

(405 more)