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

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

5 lines of code changed in 4 files:

• EDIT4: ED4_block.cxx (+1 -1), ED4_cursor.cxx (+1 -1), ED4_dots.cxx (+1 -1), ED4_protein_2nd_structure.cxx (+2 -2)

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 8 files:

• EDIT4: ED4_ProteinViewer.cxx (+2 -2), ED4_cursor.cxx (+2 -2), ED4_dots.cxx (+1 -1), ED4_naligner.cxx (+1 -1), ED4_no_class.cxx (+1 -1), ED4_protein_2nd_structure.cxx (+1 -1), ED4_terminal.cxx (+1 -1), ED4_visualizeSAI.cxx (+2 -2)

westram 2019-07-17 15:27 Rev.: 17982

* reduced use of GB_change_my_security:
- use GB_securityLevel instead of manually fiddling around with GB_change_my_security.
- inspected and accepted leftover uses (see comments).

1 lines of code changed in 1 file:

• EDIT4: ED4_no_class.cxx (+1 -1)

westram 2019-07-17 15:22 Rev.: 17980

* use security objects instead of manually calling GB_push/pop_my_security.
* eliminate GB_push/pop_my_security.
* fix scoping using a TA object.

3 lines of code changed in 1 file:

• EDIT4: ED4_root.cxx (+3 -5)

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.

56 lines of code changed in 2 files:

• EDIT4: ED4_text_terminals.cxx (-1), Makefile (+56)

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

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

50 lines of code changed in 4 files:

• EDIT4: ED4_flags.cxx (+1 -1), ED4_protein_2nd_structure.cxx (+8 -5), ED4_seq_colors.cxx (+1 -1), ed4_class.hxx (+40 -39)

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

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

2 lines of code changed in 1 file:

• EDIT4: ED4_no_class.cxx (+2 -2)

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:

• EDIT4: ED4_no_class.cxx (+1 -1)

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

12 lines of code changed in 1 file:

• EDIT4: Makefile (+12)

westram 2019-03-07 17:30 Rev.: 17651

* reintegrates 'cleanup' into 'trunk'
* adds: log:branches/cleanup@17627:17650

4 lines of code changed in 1 file:

• EDIT4: ed4_visualizeSAI.hxx (+4 -4)

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

11 lines of code changed in 2 files:

• EDIT4: ED4_ProteinViewer.cxx (+10 -18), Makefile (+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

11 lines of code changed in 5 files:

• EDIT4: ED4_main.cxx (+1 -1), ED4_search.cxx (+5 -4), ED4_seq_colors.cxx (+2 -1), Makefile (+2), ed4_edit_string.hxx (+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:

• EDIT4: ED4_ProteinViewer.cxx (+2 -2)

westram 2018-10-04 14:17 Rev.: 17445

* use {{{SmartPtr::content()}}}

1 lines of code changed in 1 file:

• EDIT4: ED4_root.cxx (+1 -1)

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

7 lines of code changed in 2 files:

• EDIT4: ED4_cursor.cxx (+7 -7), ed4_class.hxx (-2)

westram 2018-09-12 09:54 Rev.: 17361

* fix {{{GB_xcmd}}} for OSX with SIP

1 lines of code changed in 1 file:

• EDIT4: ED4_naligner.cxx (+1)

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

3 lines of code changed in 2 files:

• EDIT4: ED4_cursor.cxx (+2 -2), ED4_no_class.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

68 lines of code changed in 6 files:

• EDIT4: ED4_cursor.cxx (+1 -1), ED4_flags.cxx (+2 -2), ED4_terminal.cxx (+4 -4), ED4_text_terminals.cxx (+33 -48), EDB_root_bact.cxx (+1 -1), Makefile (+27)

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

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

5 lines of code changed in 3 files:

• EDIT4: ED4_root.cxx (+3 -16), ed4_class.hxx (+2 -7), ed4_defs.hxx (-4)

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

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

212 lines of code changed in 20 files:

• EDIT4: ED4_ProteinViewer.cxx (+40 -45), ED4_base.cxx (+25 -50), ED4_container.cxx (+11 -13), ED4_cursor.cxx (+10 -18), ED4_edit_string.cxx (+8 -16), ED4_main.cxx (+1 -2), ED4_manager.cxx (+17 -22), ED4_naligner.cxx (+3 -3), ED4_nds.cxx (+2 -3), ED4_no_class.cxx (+3 -4), ED4_protein_2nd_structure.cxx (+1 -1), ED4_root.cxx (+15 -23), ED4_search.cxx (+33 -63), ED4_terminal.cxx (+16 -29), ED4_text_terminals.cxx (+4 -5), ED4_visualizeSAI.cxx (+1 -1), ED4_window.cxx (+13 -16), EDB_root_bact.cxx (+2 -4), ed4_defs.hxx (+5 -10), ed4_search.hxx (+2 -4)

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

585 lines of code changed in 32 files:

• EDIT4: ED4_ProteinViewer.cxx (+12 -12), ED4_base.cxx (+33 -33), ED4_block.cxx (+35 -35), ED4_colStat.cxx (+4 -4), ED4_consensus.cxx (+3 -3), ED4_container.cxx (+6 -6), ED4_cursor.cxx (+28 -28), ED4_dots.cxx (+7 -7), ED4_dump.cxx (+2 -2), ED4_edit_string.cxx (+35 -36), ED4_flags.cxx (+12 -12), ED4_main.cxx (+13 -13), ED4_manager.cxx (+30 -30), ED4_nds.cxx (+4 -4), ED4_no_class.cxx (+55 -55), ED4_objspec.cxx (+1 -1), ED4_plugins.cxx (+8 -8), ED4_protein_2nd_structure.cxx (+17 -17), ED4_root.cxx (+89 -89), ED4_search.cxx (+51 -51), ED4_seq_colors.cxx (+11 -11), ED4_terminal.cxx (+30 -30), ED4_text_terminals.cxx (+8 -8), ED4_visualizeSAI.cxx (+14 -14), ED4_window.cxx (+3 -3), EDB_root_bact.cxx (+7 -7), ed4_block.hxx (+1 -1), ed4_class.hxx (+38 -38), ed4_flags.hxx (+1 -1), ed4_list.hxx (+6 -6), ed4_protein_2nd_structure.hxx (+1 -1), graph_aligner_gui.cxx (+20 -20)

westram 2017-11-19 15:19 Rev.: 16683

* full update from child 'gcc' into 'trunk'
- more warning fixes
- fix bug in prettyprint
* adds: log:branches/gcc@16668:16682

17 lines of code changed in 2 files:

• EDIT4: ED4_main.cxx (+16 -14), ED4_manager.cxx (+1 -1)

westram 2017-11-17 12:54 Rev.: 16668

* full update from child 'gcc' into 'trunk'
- fix/suppress (new) compiler warnings
- skip vectorizer notes
* adds: log:branches/gcc@16656:16667

13 lines of code changed in 1 file:

• EDIT4: ED4_edit_string.cxx (+13 -13)

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

49 lines of code changed in 2 files:

• EDIT4: ED4_visualizeSAI.cxx (+48 -90), Makefile (+1)

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

2 lines of code changed in 1 file:

• EDIT4: Makefile (+2)

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

20 lines of code changed in 3 files:

• EDIT4: ED4_block.cxx (+12 -10), ED4_nds.cxx (+6 -4), Makefile (+2)

westram 2017-07-08 10:55 Rev.: 16112

* reintegrates 'fix' into 'trunk'
- fixes #267
- adds new default color translation table 'PVP'
* adds: log:branches/fix@16107:16111

14 lines of code changed in 1 file:

• EDIT4: ED4_visualizeSAI.cxx (+14 -19)

westram 2017-05-29 10:15 Rev.: 15974

* solve remaining confusion in terminology (concerning "selected species"):
- sequence-range-blocks in EDIT4 are now called "highlighted species" or "highlighted block"
- Note: code still talks about selected species

16 lines of code changed in 1 file:

• EDIT4: ED4_root.cxx (+16 -16)

westram 2017-04-05 10:06 Rev.: 15738

* rename only

1 lines of code changed in 1 file:

• EDIT4: ED4_root.cxx (+1 -1)

westram 2017-03-31 13:13 Rev.: 15715

* fix click on species flags
- did not work when display was scrolled vertically

1 lines of code changed in 1 file:

• EDIT4: ED4_terminal.cxx (+1 -1)

westram 2017-01-09 15:10 Rev.: 15529

* reintegrates 'warnings' into 'trunk'
- use gnu++14-standard for gcc>=6
- use gnu++0x-standard for gcc<4.7 (bugfix)
- defines many inlines as constexpr
* adds: log:branches/warnings@15515:15522,15525:15528

1 lines of code changed in 1 file:

• EDIT4: ed4_class.hxx (+1 -1)

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

36 lines of code changed in 4 files:

• EDIT4: ED4_base.cxx (-6), ED4_manager.cxx (+3 -3), ED4_terminal.cxx (-14), ed4_class.hxx (+33 -27)

westram 2017-01-04 10:51 Rev.: 15506

* partial merge from 'warnings' into 'trunk'
- remove some useless virtuality (mostly functions only usable with ED4_manager)
- other design fixes (get_parent returns ED4_manager, ...)
* adds: log:branches/warnings@15502:15505

44 lines of code changed in 7 files:

• EDIT4: ED4_base.cxx (+6 -26), ED4_colStat.cxx (+1 -1), ED4_cursor.cxx (+1 -1), ED4_manager.cxx (+12 -23), ED4_no_class.cxx (+2 -2), ED4_terminal.cxx (+1 -33), ed4_class.hxx (+21 -25)

westram 2016-12-17 12:12 Rev.: 15425

* reintegrates 'mladd' into 'trunk'
- improves raxml8 interface
* new functions
- score tree (=calculate likelihood and append to comment)
- calculate branchlengths
- optimize tree
- add to tree (implements #681)
* calculate bootstraps (as separate function or combined with other functions)
- allow to skip bootstrap calculation
* writes comment to generated trees (similar to raxml7-interface)
* fix key-wait on terminate
* time all functions
* fix thread usage
- use 'distinct alignment patterns' (as reported by RAxML) to select maximum threads
- slightly reduce threads in favor of asynchronous bootstrapping
- allow to override (used) cores and used threads separate
- adds {{{arb_write_tree_comment}}}
* adds: log:branches/mladd@15394,15396,15398:15424

1 lines of code changed in 1 file:

• EDIT4: EDB_root_bact.cxx (+1 -1)

westram 2016-10-19 12:04 Rev.: 15346

* remove outdated link

1 lines of code changed in 1 file:

• EDIT4: graph_aligner_gui.cxx (+1 -2)

westram 2016-10-02 14:02 Rev.: 15290

* add some predefined settings for editor flags

9 lines of code changed in 1 file:

• EDIT4: ED4_flags.cxx (+9 -1)

westram 2016-09-30 15:16 Rev.: 15288

* reintegrates 'flags' into 'trunk'
- implements #261
* adds: log:branches/flags@15225:15230,15232:15238,15240:15241,15243:15246,15248,15250:15287

825 lines of code changed in 17 files:

• EDIT4: ED4_base.cxx (+9), ED4_dump.cxx (+2), ED4_flags.cxx (new 266), ED4_main.cxx (+2 -1), ED4_manager.cxx (+13 -16), ED4_no_class.cxx (+27 -3), ED4_root.cxx (+32 -19), ED4_seq_colors.cxx (+6 -1), ED4_terminal.cxx (+172 -82), ED4_text_terminals.cxx (+28 -40), ED4_window.cxx (+1 -1), EDB_root_bact.cxx (+7), Makefile (+54), ed4_class.hxx (+62 -25), ed4_defs.hxx (+3), ed4_extern.hxx (+11 -9), ed4_flags.hxx (new 130)

westram 2016-09-27 15:23 Rev.: 15279

* reintegrates 'errhandle' into 'trunk'
* adds: log:branches/errhandle@15275:15278

3 lines of code changed in 1 file:

• EDIT4: ED4_no_class.cxx (+3 -4)

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:

• EDIT4: graph_aligner_gui.cxx (+1 -1)

westram 2016-09-23 07:53 Rev.: 15265

* document used references from display-elements to database-entries

12 lines of code changed in 1 file:

• EDIT4: ed4_class.hxx (+12)

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