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westram 2019-07-24 17:34 Rev.: 17991

* rename CLI params:
- complement -> complementFirst
- reversed -> alsoRevCompl
- matchcomplement -> matchAlsoRevcomp
* improve CLI help: mention precedence and interaction between complementFirst + alsoRevCompl.

13 lines of code changed in 2 files:

• TOOLS: arb_probe.cxx (+6 -6), arb_probe_match.cxx (+7 -4)

westram 2019-07-24 17:32 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.

21 lines of code changed in 2 files:

• TOOLS: arb_probe.cxx (+8 -8), arb_probe_match.cxx (+13 -13)

westram 2019-07-24 17:24 Rev.: 17988

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

8 lines of code changed in 2 files:

• TOOLS: arb_probe.cxx (+3 -3), arb_probe_match.cxx (+5 -5)

westram 2019-07-17 16:22 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.

1 lines of code changed in 1 file:

• TOOLS: arb_gene_probe.cxx (+1 -2)

westram 2019-07-08 10:19 Rev.: 17951

* change priority of tests depending on database {{{"TEST_loadsave_ascii.arb"}}} to get executed after {{{TEST_SLOW_loadsave}}}
- needed if that database should get auto-updated.

1 lines of code changed in 1 file:

• TOOLS: arb_test.cxx (+1 -1)

westram 2019-05-10 13:57 Rev.: 17877

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

28 lines of code changed in 2 files:

• TOOLS: arb_dnarates.cxx (+25 -25), arb_primer.cxx (+3 -3)

westram 2019-04-29 14:44 Rev.: 17836

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

2 lines of code changed in 2 files:

• TOOLS: arb_export_sequences.cxx (+1 -1), arb_sub2ascii.cxx (+1 -1)

westram 2019-04-02 18:15 Rev.: 17729

* fix test condition "contains":
- checking for empty part
* always returned 'true'
* now fails assertion and returns 'false' (it is unwanted to test that)
- fix callers

6 lines of code changed in 1 file:

• TOOLS: arb_consensus_tree.cxx (+6 -6)

westram 2018-10-17 11:00 Rev.: 17478

* reintegrates 'svalues' into 'trunk'
- implements #614
* adds: log:branches/svalues@17357:17419,17428:17464,17469,17471:17477

2 lines of code changed in 2 files:

• TOOLS: arb_consensus_tree.cxx (+1 -1), arb_read_tree.cxx (+1)

westram 2018-10-02 16:08 Rev.: 17428

* partial merge from 'svalues' into 'trunk'
- root branches always need to have identical remarks (associated with the root-edge)
* condition previously implicit, now hardened by tests/assertions/...
* fixed several bugs that violated this condition
* adds: log:branches/svalues@17420:17427

10 lines of code changed in 1 file:

• TOOLS: arb_read_tree.cxx (+10 -7)

westram 2018-09-20 18:43 Rev.: 17396

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

13 lines of code changed in 2 files:

• TOOLS: arb_primer.cxx (+12 -13), arb_probe_match.cxx (+1 -1)

westram 2018-07-10 16:48 Rev.: 17178

* reintegrates 'gcc' into 'trunk'
- complete arb port to gcc 8.1
- fixes NDEBUG-related issues (not handled by [16986])
* adds: log:branches/gcc@17164:17177

10 lines of code changed in 1 file:

• TOOLS: arb_primer.cxx (+10 -3)

westram 2018-06-25 17:04 Rev.: 17121

* reintegrates 'saiexport' into 'trunk'
- no longer expand dangerous ranges (e.g. {{{--pass allbut .-=012345}}})
* adds: log:branches/saiexport@17112:17120

36 lines of code changed in 2 files:

• TOOLS: arb_export_seq_filtered.cxx (+3 -1), arb_test.cxx (+33 -18)

westram 2018-06-15 13:08 Rev.: 17110

* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109

4 lines of code changed in 2 files:

• TOOLS: arb_consensus_tree.cxx (+2 -2), arb_read_tree.cxx (+2 -2)

westram 2018-05-19 10:30 Rev.: 17050

* fix builds w/o unit tests (e.g. RELEASE)
- was broken by [16919]
- complained about dependency file for "unknown" binary {{{arb_sub2ascii}}} (only build for UNIT_TESTS)
* dependencies in TOOLS change with variable UNIT_TESTS (force to 1 for 'depends')

1 lines of code changed in 1 file:

• TOOLS: Makefile (+1 -1)

westram 2018-05-04 18:06 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:

• TOOLS: arb_probe.cxx (+1 -1)

westram 2018-04-25 11:08 Rev.: 16919

* reintegrates 'pvp' into 'trunk'
- adds {{{arb_calc_pvp}}} (CLI tool to calculate posvar)
* adds: log:branches/pvp@16906:16918

369 lines of code changed in 4 files:

• TOOLS: Makefile (+55), arb_calc_pvp.cxx (new 188), arb_sub2ascii.cxx (new 79), arb_test.cxx (+47 -1)

westram 2017-12-04 12:18 Rev.: 16782

* typo

1 lines of code changed in 1 file:

• TOOLS: arb_2_ascii.cxx (+1 -1)

westram 2017-11-28 19:22 Rev.: 16766

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

32 lines of code changed in 9 files:

• TOOLS: arb_a2ps.c (+6 -8), arb_dnarates.cxx (+14 -14), arb_export_sequences.cxx (+1 -2), arb_gene_probe.cxx (+3 -6), arb_perf_test.cxx (+1 -2), arb_primer.cxx (+4 -8), arb_probe.cxx (+1 -2), arb_read_tree.cxx (+1 -2), arb_write_tree_comment.cxx (+1 -2)

westram 2017-11-28 18:09 Rev.: 16763

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

254 lines of code changed in 18 files:

• TOOLS: arb_2_ascii.cxx (+3 -3), arb_2_bin.cxx (+4 -4), arb_a2ps.c (+25 -25), arb_consensus_tree.cxx (+19 -19), arb_dnarates.cxx (+28 -28), arb_export_rates.cxx (+6 -6), arb_export_seq_filtered.cxx (+7 -7), arb_export_sequences.cxx (+16 -15), arb_export_tree.cxx (+3 -3), arb_gene_probe.cxx (+11 -11), arb_message.cxx (+2 -2), arb_perf_test.cxx (+7 -7), arb_primer.cxx (+12 -12), arb_probe.cxx (+61 -61), arb_probe_match.cxx (+21 -17), arb_read_tree.cxx (+12 -12), arb_test.cxx (+11 -11), arb_write_tree_comment.cxx (+6 -6)

westram 2017-11-17 13:54 Rev.: 16668

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

7 lines of code changed in 1 file:

• TOOLS: Makefile (+7 -1)

westram 2017-11-12 15:53 Rev.: 16649

* partial merge from 'gcc' into 'trunk'
- handles #770 by reducing optimizations of several bleeding test functions
* adds: log:branches/gcc@16636:16648

1 lines of code changed in 1 file:

• TOOLS: arb_probe.cxx (+1 -1)

westram 2017-10-21 13:40 Rev.: 16564

* reintegrates 'io' into 'trunk'
- implements #691
* adds: log:branches/io@16436:16510,16513:16514,16517,16533:16535,16537:16563

7 lines of code changed in 1 file:

• TOOLS: arb_export_sequences.cxx (+7 -8)

westram 2017-10-03 18:26 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

2 lines of code changed in 3 files:

• TOOLS: Makefile (-22), arb_notify.cxx (del), arb_test.cxx (+2 -53)

westram 2017-09-18 15:23 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

3 lines of code changed in 1 file:

• TOOLS: arb_replace.cxx (+3 -3)

westram 2017-08-23 13:42 Rev.: 16237

* fix spelling for 'occurrence'

1 lines of code changed in 1 file:

• TOOLS: arb_probe_match.cxx (+1 -1)

westram 2017-08-21 14:47 Rev.: 16234

* reintegrates 'saiexport' into 'trunk'
* adds: log:branches/saiexport@16229:16233

13 lines of code changed in 2 files:

• TOOLS: arb_export_seq_filtered.cxx (+12 -5), arb_test.cxx (+1)

westram 2017-08-09 14:59 Rev.: 16223

* reintegrates 'cover' into 'trunk'
- fixes compilation with COVERAGE
* ARB perl module failed to load (since [13739])
* linking executables broken (apparently since [14038])
* adds: log:branches/cover@16213:16222

11 lines of code changed in 1 file:

• TOOLS: Makefile (+11 -11)

westram 2017-07-10 12:29 Rev.: 16119

* reintegrates 'saiexport' into 'trunk'
- implements #743
* adds: log:branches/saiexport@16023:16118

440 lines of code changed in 3 files:

• TOOLS: Makefile (+33 -3), arb_export_seq_filtered.cxx (new 293), arb_test.cxx (+114)

westram 2017-06-29 15:18 Rev.: 16043

* reintegrates 'fix' into 'trunk'
- valgrind fixes
* generally repaired valgrinding (external tools)
* {{{group_scaling}}} was not initialized correct (RUI)
- DRYed code to run external tools from unittests
* adds: log:branches/fix@16037:16042

11 lines of code changed in 2 files:

• TOOLS: Makefile (+3), arb_test.cxx (+8 -54)

westram 2017-05-03 15:31 Rev.: 15876

* reintegrates 'fix' into 'trunk'
- automatically deletes field 'group_name' at root of tree
- done while loading tree
- provides workaround for #753
* adds: log:branches/fix@15870:15875

1 lines of code changed in 1 file:

• TOOLS: arb_test.cxx (+1 -1)

westram 2017-01-16 18:16 Rev.: 15587

* reintegrates 'fix' into 'trunk'
- fix OSX unittest for jenkins project names (up to max. 16 chars long)
- optimize {{{GB_log_fak}}}
- forward {{{RegExpr}}}-compile-errors (or at least assert on failure)
* adds: log:branches/fix@15582:15586

4 lines of code changed in 2 files:

• TOOLS: arb_probe.cxx (+3 -2), arb_test.cxx (+1 -1)

westram 2017-01-04 18:06 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

2 lines of code changed in 1 file:

• TOOLS: arb_export_sequences.cxx (+2 -2)

westram 2016-12-30 13:31 Rev.: 15484

* reintegrates 'warnings' into 'trunk'
- fixes compiler warnings (gcc 5.x)
* adds: log:branches/warnings@15468,15471,15473,15477,15481:15483

27 lines of code changed in 2 files:

• TOOLS: arb_read_tree.cxx (+17 -16), arb_write_tree_comment.cxx (+10 -10)

westram 2016-12-17 13:12 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

167 lines of code changed in 2 files:

• TOOLS: Makefile (+25), arb_write_tree_comment.cxx (new 142)

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

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

41 lines of code changed in 10 files:

• TOOLS: Makefile (+18), arb_consensus_tree.cxx (+2 -2), arb_dnarates.cxx (+2 -2), arb_export_rates.cxx (+1 -1), arb_message.cxx (+1 -1), arb_notify.cxx (+1 -1), arb_primer.cxx (+7 -7), arb_probe.cxx (+3 -3), arb_read_tree.cxx (+5 -9), arb_test.cxx (+1 -1)

westram 2016-05-07 10:07 Rev.: 14833

* reintegrates 'fixwarn' into 'trunk'
* adds: log:branches/fixwarn@14815:14832

6 lines of code changed in 1 file:

• TOOLS: arb_dnarates.cxx (+6 -2)

westram 2016-01-28 09:33 Rev.: 14682

* merge [14675:14681] from 'gde' into 'trunk'
- change DB interface function concerned with GB_FLOAT from double -> float
- introduce more stable ascii <-> float conversion
* adds: log:branches/gde@14676:14681

1 lines of code changed in 1 file:

• TOOLS: arb_test.cxx (+1 -1)

westram 2015-12-03 18:50 Rev.: 14587

* fix error-forwarding (from external tools -> ARB GUI)
- {{{GBK_singlequote}}} error message (replaces various wrong ways to do that)
- always call {{{arb_message}}} asynchronously

4 lines of code changed in 1 file:

• TOOLS: arb_export_rates.cxx (+4 -7)

westram 2015-11-27 20:31 Rev.: 14556

* reintegrates 'dbsave' into 'trunk'
- implements #665
* adds: log:branches/dbsave@14521:14555

148 lines of code changed in 3 files:

• TOOLS: arb_2_ascii.cxx (+59 -30), arb_2_bin.cxx (+50 -31), arb_test.cxx (+39 -3)

(350 more)