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westram 2024-10-01 17:45 Rev.: 19499

* implements #863
* add new ACI command "dupidx" (active in group search).
* update group-enumeration presets: use '~' instead of '_'. use new ACI command 'dupidx'.

11 lines of code changed in 2 files:

• NTREE: NT_group_search.cxx (+6 -6), NT_tree_cmp.cxx (+5 -5)

westram 2023-07-11 11:38 Rev.: 19432

* {{{GBT_get_alignment_len}}}
- now also reports error if alignment length is zero
* this case often was unhandled and did easily lead to allocation problems.
- catch error in case of zero alignment length => fixes alloc-size-larger-than-warning (in {{{NT_count_different_chars}}}).
- check + fix callers.

5 lines of code changed in 4 files:

• NTREE: AP_consensus.cxx (+2 -2), ColumnStat_2_gnuplot.cxx (+1 -1), NT_split_ali.cxx (+1 -1), ad_spec.cxx (+1 -1)

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.

5 lines of code changed in 3 files:

• NTREE: NT_edconf.cxx (+3 -3), NT_extern.cxx (+1 -1), NT_split_ali.cxx (+1 -1)

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).

11 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+11 -15)

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

224 lines of code changed in 3 files:

• NTREE: Makefile (+1), NT_edconf.cxx (+223 -60), NT_extern.cxx (-50)

westram 2022-10-21 15:04 Rev.: 19277

* use {{{MessageSpamFilter}}} when generating groups:
- from callers which may spam arbs message box.
* part of #832

3 lines of code changed in 2 files:

• NTREE: Makefile (+1), NT_tree_cmp.cxx (+2)

westram 2022-10-21 14:56 Rev.: 19275

* make group renaming from group-search macro-capable (adds missing IDs).

2 lines of code changed in 1 file:

• NTREE: NT_group_search.cxx (+2 -2)

westram 2022-09-05 15:02 Rev.: 19262

* add 'View sysinfo' entry to arb 'Tools' menu.
- shows 'sys.info' generated by arb_launcher.
* document 'ARB session log archive'.

1 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+1)

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

28 lines of code changed in 3 files:

• NTREE: Makefile (+1), NT_extern.cxx (+22 -8), NT_main.cxx (+5 -3)

westram 2022-08-06 18:25 Rev.: 19222

* reintegrates 'split' into 'trunk'
- completes #846
* adds: log:branches/split@19169:19221

52 lines of code changed in 2 files:

• NTREE: Makefile (+1), NT_split_ali.cxx (+51 -10)

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

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

183 lines of code changed in 8 files:

• NTREE: AP_consensus.cxx (+23 -10), AP_pos_var_pars.cxx (+12 -9), NT_concatenate.cxx (+26 -15), NT_import.cxx (+1 -1), NT_ins_col.cxx (+1 -1), NT_split_ali.cxx (+1 -1), ad_ext.cxx (+12 -12), ad_spec.cxx (+107 -90)

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

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

277 lines of code changed in 6 files:

• NTREE: AP_consensus.cxx (+1 -1), Makefile (+4), NT_concatenate.cxx (+8 -4), NT_extern.cxx (+1 -2), NT_local_proto.h (-1), NT_split_ali.cxx (+263 -66)

westram 2022-06-29 13:54 Rev.: 19100

* reintegrates 'split' into 'trunk'
- implemented beta version of alignment splitter
* adds: log:branches/split@19077:19099

416 lines of code changed in 4 files:

• NTREE: Makefile (+39), NT_extern.cxx (+4 -2), NT_local_proto.h (+4), NT_split_ali.cxx (new 369)

westram 2022-06-29 10:28 Rev.: 19078

* pass properties (not DB) -> store initials in properties (not in DB).
* remove unneeded header.

1 lines of code changed in 4 files:

• NTREE: Makefile (-1), NT_extern.cxx (+1 -1), NT_trackAliChanges.cxx (-1), NT_trackAliChanges.h (del)

westram 2022-03-30 16:36 Rev.: 18979

* fix use of empty labels:
- {{{AW_window::label}}} no longer
* accepts empty labels.
* allows to overwrite existing labels (assume this happens by mistake).
- {{{create_toggle_field}}}:
* assert label is used (in flavor with label-parameter)
* remove empty and NULp labels passed (from callers).

4 lines of code changed in 3 files:

• NTREE: AP_consensus.cxx (+2 -2), NT_taxonomy.cxx (+1 -1), ad_transpro.cxx (+1 -1)

westram 2022-03-30 16:31 Rev.: 18978

* remove unused mnemonic parameter to 'create_toggle_field'
- makes no sense anyway: having mnemonic for each toggle is sufficient (hence not implemented).

5 lines of code changed in 4 files:

• NTREE: AP_consensus.cxx (+2 -2), NT_group_search.cxx (+1 -1), NT_taxonomy.cxx (+1 -1), ad_transpro.cxx (+1 -1)

westram 2022-03-30 16:29 Rev.: 18977

* use {{{AW_orientation}}} to specify orientation of radio button.

1 lines of code changed in 1 file:

• NTREE: ColumnStat_2_gnuplot.cxx (+1 -1)

westram 2022-03-17 13:11 Rev.: 18965

* quit prompt:
- print leading zero for seconds.
- do not plenk!
- increase noask-period after save.

3 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+3 -3)

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.

21 lines of code changed in 12 files:

• NTREE: AP_consensus.cxx (+2 -2), AP_pos_var_pars.cxx (+2 -2), ColumnStat_2_gnuplot.cxx (+1 -1), NT_cb.cxx (+1 -1), NT_edconf.cxx (+3 -3), NT_extern.cxx (+1 -1), NT_group_search.cxx (+2 -2), NT_sync_scroll.cxx (+1 -1), NT_syncroot.cxx (+1 -1), NT_validManual.cxx (+1 -1), ad_ext.cxx (+1 -1), ad_trees.cxx (+5 -5)

westram 2022-03-04 15:13 Rev.: 18962

* eliminate unused parameter {{{fallback2default}}} from {{{create_option_menu}}}.

24 lines of code changed in 6 files:

• NTREE: NT_concatenate.cxx (+1 -1), NT_extern.cxx (+2 -2), NT_group_search.cxx (+9 -9), NT_ins_col.cxx (+3 -3), ad_transpro.cxx (+2 -2), ad_trees.cxx (+7 -7)

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

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

36 lines of code changed in 3 files:

• NTREE: Makefile (+30), NT_extern.cxx (+4 -1), ad_trees.cxx (+2 -1)

westram 2021-12-20 17:44 Rev.: 18883

* reintegrates 'nds' into 'trunk'
- fixes #841
* adds: log:branches/nds@18843:18882

139 lines of code changed in 2 files:

• NTREE: NT_extern.cxx (+81 -14), ad_trees.cxx (+58 -49)

westram 2021-12-17 15:34 Rev.: 18864

* remove 'Start a slave ARB on a foreign host' (obsolete).

0 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (-5)

westram 2021-10-10 08:33 Rev.: 18781

* reintegrates 'help' into 'trunk'
- relocate help sources
* adds: log:branches/help@18763:18780

2 lines of code changed in 1 file:

• NTREE: AP_consensus.cxx (+2 -2)

westram 2021-10-07 18:18 Rev.: 18754

* define {{{ItemSelector}}} for SAIs (lacks changekey functionality, i.e. does not fit into a search&query).
* mark places where species-selector is misused for SAIs.

1 lines of code changed in 1 file:

• NTREE: ad_ext.cxx (+1 -1)

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

* remove trailing whitespace from c source.

15 lines of code changed in 9 files:

• NTREE: ColumnStat_2_gnuplot.cxx (+2 -2), NT_branchAnalysis.cxx (+1 -1), NT_concatenate.cxx (+2 -2), NT_dbrepair.cxx (+1 -1), NT_main.cxx (+4 -4), NT_tree_cmp.cxx (+2 -2), NT_validNameParser.h (+1 -1), ScrollSynchronizer.cxx (+1 -1), ad_spec.cxx (+1 -1)

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

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

16 lines of code changed in 3 files:

• NTREE: Makefile (+2), NT_extern.cxx (+6 -6), ad_trees.cxx (+8 -6)

westram 2021-09-02 08:46 Rev.: 18697

* full update from child 'stable' into 'trunk'
- merge changes done to arb-7.0 release candidate
* adds: log:branches/stable@18690:18695

1 lines of code changed in 1 file:

• NTREE: NT_main.cxx (+1 -1)

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

* change many WARN_TODO triggered warnings into todo markers.

4 lines of code changed in 4 files:

• NTREE: ColumnStat_2_gnuplot.cxx (+1 -3), NT_dbrepair.cxx (+1 -3), NT_extern.cxx (+2 -3), ad_trees.cxx (-3)

westram 2021-05-26 16:01 Rev.: 18652

* fix nameserver admin layout:
- status field now colored and resizeable
- change title
* change term 'name server' -> 'nameserver'.

1 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+1 -1)

westram 2021-05-26 15:50 Rev.: 18651

* add 'configure' button to 'synchronize ids'
- refactored AW_create_namesadmin_window -> AW_popup_namesadmin_window.
- document

1 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+1 -1)

westram 2021-02-18 16:33 Rev.: 18643

* allow to 'edit bootstraps'
- document example.
- when a replacement results in an empty string => remove remark.

2 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+2 -1)

westram 2021-02-01 17:10 Rev.: 18641

* fixes #824
- define stacksize required for tree-display in {{{TreeDisplay.hxx}}} (currently 20Mb)
- use that stacksize NTREE and PARSIMONY.

18 lines of code changed in 2 files:

• NTREE: Makefile (+14), NT_main.cxx (+4 -2)

westram 2020-11-10 16:24 Rev.: 18634

* reintegrates 'root' into 'trunk'
- implements #449
* adds: log:branches/root@18451:18633

975 lines of code changed in 4 files:

• NTREE: Makefile (+45), NT_extern.cxx (+3 -2), NT_local_proto.h (+3), NT_syncroot.cxx (new 924)

westram 2020-09-23 12:48 Rev.: 18481

* set "TAB separated" as default NDS column delimiter.
- rename AWAR to reset properties in userland.

4 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+4 -4)

westram 2020-05-14 18:21 Rev.: 18463

* reintegrates 'top' into 'trunk'
* adds: log:branches/top@18453:18462

37 lines of code changed in 4 files:

• NTREE: NT_edconf.cxx (+31 -17), NT_extern.cxx (+2), NT_local.h (+1), ad_ext.cxx (+3)

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

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

1 lines of code changed in 1 file:

• NTREE: NT_main.cxx (+1 -1)

westram 2020-02-26 18:46 Rev.: 18339

* full update from child 'fix' into 'trunk'
- fixes #754
* adds: log:branches/fix@18333:18338

2 lines of code changed in 1 file:

• NTREE: NT_main.cxx (+2)

westram 2020-02-25 16:32 Rev.: 18325

* result of sorting database by a criteria with non-strict species order is implementation dependent.
- test explicit order only for one OS (that test has only minor/no importance)

7 lines of code changed in 1 file:

• NTREE: NT_sort.cxx (+7)

westram 2020-02-21 13:07 Rev.: 18311

* reintegrates 'saicalc' into 'trunk'
- implements #730
* adds: log:branches/saicalc@18141:18310

7 lines of code changed in 5 files:

• NTREE: AP_consensus.cxx (+1 -1), Makefile (+1), NT_extern.cxx (+3 -1), NT_ins_col.cxx (+1 -1), needs_libs (+1)

(1077 more)