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westram 2018-10-19 15:18 Rev.: 17491

* partial merge from 'fix' into 'trunk'
- fix OSX build (was broken by [17387]):
* uses wrapper {{{ARB_strchrnul}}} instead of directly using {{{strchrnul}}}
* OSX version uses replacement code
* adds: log:branches/fix@17486:17490

2 lines of code changed in 1 file:

• ARBDB: admatch.cxx (+2 -2)

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

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

98 lines of code changed in 3 files:

• ARBDB: TreeNode.cxx (+52 -32), TreeNode.h (+30 -23), adtree.cxx (+16 -5)

westram 2018-10-08 14:29 Rev.: 17451

* fix NDEBUG compilation with {{{PROVIDE_TREE_STRUCTURE_TESTS}}} defined

2 lines of code changed in 2 files:

• ARBDB: TreeNode.cxx (+1 -1), TreeNode.h (+1 -1)

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

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

1 lines of code changed in 1 file:

• ARBDB: TreeNode.h (+1 -1)

westram 2018-10-02 15:08 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

116 lines of code changed in 4 files:

• ARBDB: Makefile (+1), TreeNode.cxx (+49 -11), TreeNode.h (+48 -18), adtree.cxx (+18 -17)

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

77 lines of code changed in 17 files:

• ARBDB: ad_cb.cxx (+2 -2), ad_cb_prot.h (-2), ad_config.cxx (+3 -64), ad_config.h (+1 -3), ad_core.cxx (+2 -2), ad_prot.h (+1 -3), ad_t_prot.h (-1), adali.cxx (+2 -3), adcache.cxx (+8 -12), adhash.cxx (+33 -17), admatch.cxx (+1 -1), adsocket.cxx (+9 -9), adstring.cxx (+7 -11), adtools.cxx (+2 -4), adtree.cxx (+5 -5), arbdb.cxx (+1 -1), gb_prot.h (-2)

westram 2018-09-19 18:54 Rev.: 17388

* full update from child 'fix' into 'trunk'
- fixes bug in wildcard matcher
* adds: log:branches/fix@17381:17387

64 lines of code changed in 3 files:

• ARBDB: ad_prot.h (+1 -1), adfile.cxx (+3 -3), admatch.cxx (+60 -38)

westram 2018-09-19 08:18 Rev.: 17379

* document bug in wildcard string matcher (GBS_string_matches)

55 lines of code changed in 3 files:

• ARBDB: Makefile (+2), adfile.cxx (+5), admatch.cxx (+48)

westram 2018-09-14 17:07 Rev.: 17373

* {{{GBS_read_dir}}}
- do not report errors caused by trying to be too smart
- optionally try finding files by appending mask to (wildcarded) name

19 lines of code changed in 1 file:

• ARBDB: adfile.cxx (+19 -5)

westram 2018-09-13 12:56 Rev.: 17369

* fix unittest broken by [17364]

5 lines of code changed in 1 file:

• ARBDB: adtools.cxx (+5 -5)

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

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

20 lines of code changed in 1 file:

• ARBDB: adsocket.cxx (+20 -6)

westram 2018-09-11 14:22 Rev.: 17359

* fix two interdependent bugs in GBT_scan_db:
- non-container childs below caller-container (e.g. {{{/description}}} and {{{/genom_db}}} in unittested database) caused empty entries to be inserted into hash
- inserting empty entries caused re-addition of (previously added) entry - probably with wrong type
* should fix problems with unittest failing under OSX

30 lines of code changed in 1 file:

• ARBDB: adtools.cxx (+30 -23)

westram 2018-09-11 11:23 Rev.: 17358

* OSX unittest "fixes":
- TEST_open_socket (disabled; this test is a PITA anyway)
- results provided by regex lib versions differs (should test sth different)

10 lines of code changed in 1 file:

• ARBDB: gb_aci.cxx (+10 -2)

westram 2018-08-30 16:24 Rev.: 17342

* reintegrates 'group' into 'trunk'
- implements #780
* adds: log:branches/group@17162:17190,17261:17341

34 lines of code changed in 4 files:

• ARBDB: TreeNode.cxx (+5), TreeNode.h (+2), adtree.cxx (+16 -10), arbdbt.h (+11 -2)

westram 2018-08-30 09:58 Rev.: 17336

* typos
- some had ''two'' good language skills ;-)
- fix some plural forms

1 lines of code changed in 1 file:

• ARBDB: ad_save_load.cxx (+1 -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

37 lines of code changed in 5 files:

• ARBDB: adGene.cxx (+1 -1), ad_prot.h (+1 -1), adname.cxx (+10 -11), adoptimize.cxx (+1 -1), adseqcompr.cxx (+24 -21)

westram 2018-07-06 15:02 Rev.: 17160

* reintegrates 'group' into 'trunk'
- misc. cleanup:
* group related functions now all accessible via menu of 1st ntree window
* DRY selection of 2 trees
* warn if annotated tree isnt visible
* fix mnemonics
* fix error handling (compare taxonomy)
* unittest comments added to tree remarks
* names
* adds: log:branches/group@17139:17159

6 lines of code changed in 1 file:

• ARBDB: adtree.cxx (+6 -1)

westram 2018-07-03 16:19 Rev.: 17140

* full update from child 'fix' into 'trunk'
- fixes deadlock (for search/replace expressions containing {{{\/}}})
* adds: log:branches/fix@17124:17138

7 lines of code changed in 1 file:

• ARBDB: gb_aci.cxx (+7)

westram 2018-06-15 12:08 Rev.: 17110

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

442 lines of code changed in 7 files:

• ARBDB: TreeNode.cxx (+62 -43), TreeNode.h (+141 -25), ad_t_prot.h (+2 -1), adlang1.cxx (+24 -6), adname.cxx (+1 -1), adseqcompr.cxx (+6 -6), adtree.cxx (+206 -54)

westram 2018-05-19 13:44 Rev.: 17051

* checked behavior of ACI command "extract_words" (adds a few tests)

10 lines of code changed in 1 file:

• ARBDB: gb_aci.cxx (+10 -4)

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]

29 lines of code changed in 8 files:

• ARBDB: ad_cb.cxx (+10), ad_cb_prot.h (+1), ad_prot.h (-1), adlang1.cxx (+4 -4), adperl.cxx (+5 -5), adtools.cxx (+2 -2), arbdb.cxx (+6 -39), gb_main.h (+1 -1)

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

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

3 lines of code changed in 1 file:

• ARBDB: arbdb.cxx (+3 -8)

westram 2018-04-05 11:09 Rev.: 16873

* fix typos ("neither")

2 lines of code changed in 2 files:

• ARBDB: adfile.cxx (+1 -1), adseqcompr.cxx (+1 -1)

westram 2018-02-02 16:41 Rev.: 16831

* fix sanitizer warning ("left shift of negative value")

8 lines of code changed in 1 file:

• ARBDB: adseqcompr.cxx (+8 -8)

westram 2017-12-08 13:30 Rev.: 16799

* reintegrates 'fix' into 'trunk'
- implements #773
- tested with asan + fixed harmless undefined behavior
* adds: log:branches/fix@16793:16798

20 lines of code changed in 5 files:

• ARBDB: ad_load.cxx (+1 -1), ad_prot.h (+1), adcompr.cxx (+2 -2), arbdb.cxx (+7), arbdb.h (+9)

westram 2017-12-04 11:55 Rev.: 16785

* loop vectorize count varies

1 lines of code changed in 1 file:

• ARBDB: adoptimize.cxx (+1 -1)

westram 2017-12-02 11:56 Rev.: 16777

* {{{GB_random_seed(0)}}} is not valid

1 lines of code changed in 1 file:

• ARBDB: admath.cxx (+1)

westram 2017-11-30 15:47 Rev.: 16770

* show full path in error message (in case of invalid database file)

1 lines of code changed in 1 file:

• ARBDB: ad_load.cxx (+1 -1)

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

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

330 lines of code changed in 20 files:

• ARBDB: adRevCompl.cxx (+2 -4), ad_core.cxx (+7 -14), ad_load.cxx (+16 -28), ad_save_load.cxx (+3 -6), adali.cxx (+4 -5), adcompr.cxx (+3 -4), adindex.cxx (+4 -5), aditem.cxx (+1 -2), adlang1.cxx (+159 -161), admalloc.cxx (+18 -36), admap.cxx (+24 -43), admatch.cxx (+11 -12), adname.cxx (+1 -2), adoptimize.cxx (+39 -52), adseqcompr.cxx (+1 -1), adsocket.cxx (+2 -4), adstring.cxx (+5 -9), arbdb.cxx (+27 -41), gb_aci.h (+2 -1), gb_map.h (+1 -2)

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

1333 lines of code changed in 52 files:

• ARBDB: TreeNode.cxx (+8 -8), TreeNode.h (+25 -25), adChangeKey.cxx (+10 -10), adGene.cxx (+31 -31), adGene.h (+1 -1), adRevCompl.cxx (+1 -1), adTest.cxx (+12 -12), ad_cb.cxx (+27 -27), ad_colorset.cxx (+5 -5), ad_config.cxx (+9 -9), ad_config.h (+3 -3), ad_core.cxx (+43 -45), ad_load.cxx (+54 -53), ad_save_load.cxx (+58 -58), ad_t_prot.h (+1 -1), adali.cxx (+41 -41), adcache.cxx (+4 -4), adcomm.cxx (+70 -70), adcompr.cxx (+18 -18), adfile.cxx (+20 -20), adhash.cxx (+14 -14), adindex.cxx (+33 -32), aditem.cxx (+16 -17), adlang1.cxx (+114 -115), admalloc.cxx (+21 -21), admap.cxx (+20 -20), admatch.cxx (+17 -17), admath.cxx (+2 -2), adname.cxx (+9 -10), adoptimize.cxx (+62 -62), adperl.cxx (+7 -7), adquery.cxx (+40 -40), adseqcompr.cxx (+14 -14), adsocket.cxx (+69 -69), adstring.cxx (+74 -71), adsystem.cxx (+17 -17), adtcp.cxx (+23 -23), adtools.cxx (+47 -47), adtree.cxx (+55 -55), arbdb.cxx (+150 -164), arbdbpp.cxx (+4 -4), gb_aci.cxx (+54 -53), gb_aci.h (+4 -4), gb_aci_impl.h (+8 -8), gb_cb.h (+1 -1), gb_data.h (+8 -8), gb_header.h (+1 -1), gb_index.h (+1 -1), gb_localdata.h (+1 -1), gb_main.h (+4 -4), gb_memory.h (+1 -1), gb_ts.h (+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

14 lines of code changed in 4 files:

• ARBDB: TreeNode.cxx (+6 -6), adindex.cxx (+3 -3), adquery.cxx (+3 -2), adsocket.cxx (+2 -2)

westram 2017-11-14 14:36 Rev.: 16653

* reintegrates 'gcc' into 'trunk' (fixes defect part of #752)
- allow compilation with gcc 7.x series (accepting 2 clang-test-results for gcc 7.x)
- vectorization:
* in {{{SL/CONSENSUS/chartable.cxx}}} works again with gcc 7.x (broken for 6.x series)
- checker: added syntax to exclude a range of versions
* check new 7.x vectorizations + fix vectorization-counts
* adds: log:branches/gcc@16578:16635,16649:16652

1 lines of code changed in 1 file:

• ARBDB: adseqcompr.cxx (+1 -1)

westram 2017-11-12 14:53 Rev.: 16649

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

7 lines of code changed in 4 files:

• ARBDB: ad_cb.cxx (+1 -1), adquery.cxx (+1 -1), adstring.cxx (+2 -2), gb_aci.cxx (+3 -3)

westram 2017-11-06 13:54 Rev.: 16628

* reintegrates 'vectorize' into 'trunk'
- fixes #700
* documented vectorization-checks
* fine-grained check based on gcc-version
- drops old gcc-versions (<4.4.3)
- new attribute {{{__ATTR__DONT_VECTORIZE}}}
* disabled vectorization of {{{POS_TREE2::init_static()}}} for newer gcc-versions (generated code fails tests)
- added a bunch of new vectorization-checks (probably irrelevant to overall performance)
* adds: log:branches/vectorize@15531:16585,16595:16627

21 lines of code changed in 7 files:

• ARBDB: adGene.cxx (+1 -1), adcompr.cxx (+7 -7), adlang1.cxx (+2 -2), adoptimize.cxx (+5 -5), adseqcompr.cxx (+4 -4), adstring.cxx (+1 -1), gb_aci.cxx (+1 -1)

westram 2017-10-18 13:54 Rev.: 16552

* partial merge from 'io' into 'trunk'
- {{{GB_rename_file}}} -> {{{GB_move_file}}}
- add {{{GB_copy_file}}}
- add safe versions of both
* adds: log:branches/io@16527:16532

4 lines of code changed in 1 file:

• ARBDB: ad_save_load.cxx (+4 -4)

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

11 lines of code changed in 3 files:

• ARBDB: Makefile (+1), adali.cxx (+8 -9), arbdbt.h (+2 -2)

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

7 lines of code changed in 5 files:

• ARBDB: ad_prot.h (-1), ad_t_prot.h (-3), adsocket.cxx (-10), adtcp.cxx (+7 -7), adtools.cxx (-206)

westram 2017-09-23 18:12 Rev.: 16434

* reintegrates 'aci' into 'trunk'
- fix/tweak parameter-handling of ACI commands
* adds: log:branches/aci@16427:16433

154 lines of code changed in 4 files:

• ARBDB: adlang1.cxx (+74 -103), gb_aci.cxx (+64 -39), gb_aci.h (+1), gb_aci_impl.h (+15 -9)

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

442 lines of code changed in 8 files:

• ARBDB: Makefile (+4 -1), ad_prot.h (-1), adlang1.cxx (+256 -51), admatch.cxx (-1), adstring.cxx (-54), gb_aci.cxx (+141 -82), gb_aci.h (+23 -3), gb_aci_impl.h (+18 -12)

westram 2017-09-21 17:34 Rev.: 16412

* reintegrates 'unittest' into 'trunk'
- limit memory for unittest code to 1Gb (not with sanitizer)
* instantly reveals accidental allocations caused by unsigned underflow
- fix underflows in ACI commands {{{format}}} + {{{format_sequence}}} (allocated 4Gb with certain parameters)
- reactivate sanitizer for builds
* adds: log:branches/unittest@16405:16411

71 lines of code changed in 2 files:

• ARBDB: adlang1.cxx (+9 -6), gb_aci.cxx (+62 -49)

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