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

* remove trailing whitespace from c source.

4 lines of code changed in 2 files:

• SL/FILTER: RangeList.cxx (+3 -3), RangeList.h (+1 -1)

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

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

1 lines of code changed in 1 file:

• SL/FILTER: AP_filter.cxx (+1 -1)

westram 2018-04-11 15:48 Rev.: 16880

* reintegrates 'multicore' into 'trunk'
- derive sequence classes able to be combined from new class {{{AP_combinableSeq}}}
* elim dummy functions from rest of hierarchy
- implements non-writing combine for add-species (speedup: 25-35%)
- introduce type {{{Mutations}}} => uses long everywhere (before mostly, but not always used float)
- allows use of {{{future}}}s
* nucleotide combine is able to calculate async (disabled via define atm -> {{{NEVER_COMBINE_ASYNC}}}; needs more work on calling algorithm)
* adds: log:branches/multicore@16769:16879

1 lines of code changed in 1 file:

• SL/FILTER: AP_filter.hxx (+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

2 lines of code changed in 1 file:

• SL/FILTER: AP_filter.hxx (+2 -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

10 lines of code changed in 2 files:

• SL/FILTER: AP_filter.cxx (+8 -8), AP_filter.hxx (+2 -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

1 lines of code changed in 1 file:

• SL/FILTER: Makefile (+1)

westram 2017-07-10 11:29 Rev.: 16119

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

217 lines of code changed in 3 files:

• SL/FILTER: AP_filter.cxx (+201 -29), AP_filter.hxx (+15 -2), Makefile (+1)

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

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

5 lines of code changed in 2 files:

• SL/FILTER: AP_filter.cxx (+4 -6), Makefile (+1)

westram 2016-07-21 16:53 Rev.: 15082

* partial merge from 'fix' into 'trunk'
- default_copyability++
* adds: log:branches/fix@15072,15077:15081

0 lines of code changed in 1 file:

• SL/FILTER: AP_filter.cxx (-1)

westram 2015-03-29 11:47 Rev.: 13625

* reintegrates 'pars' into 'trunk'
- fixes #528, #609, #620, #631, #633, #640, #641
- implements #619, #627
* adds:
- log:branches/addtest@13123:13260,13523:13551,13570
- log:branches/check@13365:13375,13450:13457
- log:branches/check2@13458:13465
- log:branches/fix@13522:13588
- log:branches/fixres@13270:13277,13279:13293,13295:13326
- log:branches/pars@12938:13280,13282:13325,13327:13387,13389:13527,13530:13624

0 lines of code changed in 1 file:

• SL/FILTER: AP_filter.hxx (-2)

westram 2015-01-23 14:19 Rev.: 13443

* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

1 lines of code changed in 1 file:

• SL/FILTER: Makefile (+1 -1)

westram 2014-10-13 16:34 Rev.: 13044

* revert [13041:13043]
- instead forbid gcc 4.8.0

2 lines of code changed in 1 file:

• SL/FILTER: AP_filter.cxx (+2 -2)

westram 2014-10-12 16:18 Rev.: 13043

* ~~harden patches [13041:13042]~~
- ~~add safebool (=bool for non 4.8.0)~~
- ~~use in all bool-arrays~~

(reverted by [13044])

2 lines of code changed in 1 file:

• SL/FILTER: AP_filter.cxx (+2 -2)

westram 2014-09-30 13:24 Rev.: 12973

* [12967] got reverted by 'make proto'. fixed.

2 lines of code changed in 2 files:

• SL/FILTER: AP_filter.cxx (+1 -1), Makefile (+1)

epruesse 2014-09-30 10:45 Rev.: 12968

- cheat around using array if filter is unweighted (i.e. all = 1)
- use aligned memory for weights
- add function to access this directly (for vectorized access)

24 lines of code changed in 2 files:

• SL/FILTER: AP_filter.cxx (+15 -9), AP_filter.hxx (+9 -2)

westram 2014-08-27 11:21 Rev.: 12783

* publish TESTs for which nm 2.24 fails to export source location

1 lines of code changed in 1 file:

• SL/FILTER: RangeList.cxx (+1)

westram 2014-04-30 13:36 Rev.: 12138

* reintegrates 'fix' into 'trunk'
- fixes #522
* adds:
- log:branches/fix@12058:12137

37 lines of code changed in 2 files:

• SL/FILTER: AP_filter.cxx (+15), AP_filter.hxx (+22)

westram 2013-11-03 14:42 Rev.: 11060

* reintegrates 'ptsfix' into 'trunk':
* adds:
- log:branches/ptsdump@8966:9000
- log:branches/ptsfix@8965:9012,9014:9017,9019:9023,9025:9046,9048:9089,9091:9114,9116:9132,9134:9139,9141:9145,9147:9151,9153:9158,9160:9379,9381:11059
- log:branches/ptsstartup@9160:9235,9237:9278,9280:9336,9339:9361,9363:9446
- log:branches/ptsundef@9061:9358

2 lines of code changed in 1 file:

• SL/FILTER: RangeList.cxx (+2 -2)

westram 2013-10-31 15:23 Rev.: 11001

* undo todays clang-inspired bogus-patches concerning char-indices

1 lines of code changed in 1 file:

• SL/FILTER: AP_filter.cxx (+1 -1)

westram 2013-10-31 14:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• SL/FILTER: Makefile (+1 -1)

westram 2013-10-31 11:46 Rev.: 10992

* fix misc warnings (char index, extra parens, trap via NULL ptr indirection, ...)

1 lines of code changed in 1 file:

• SL/FILTER: AP_filter.cxx (+1 -1)

westram 2013-10-30 15:58 Rev.: 10974

* renamed include variables

1 lines of code changed in 1 file:

• SL/FILTER: Makefile (+1 -1)

westram 2013-10-29 12:55 Rev.: 10956

* made A_CC and A_CXX consistent
- A_CXX previously contained cxxflags
- cxxflags are now passed down and used separately

1 lines of code changed in 1 file:

• SL/FILTER: Makefile (+1 -1)

westram 2013-10-29 12:23 Rev.: 10955

- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

1 lines of code changed in 1 file:

• SL/FILTER: Makefile (+1 -1)

westram 2013-10-29 11:43 Rev.: 10954

- document mechanism used by ARB to export variables to submakefiles
- document most important variables

1 lines of code changed in 1 file:

• SL/FILTER: Makefile (+1 -1)

westram 2013-02-28 16:01 Rev.: 9633

* reintegrated branch 'sai'
- providing basic insert/delete by SAI

44 lines of code changed in 2 files:

• SL/FILTER: RangeList.cxx (+34 -13), RangeList.h (+10 -4)

westram 2013-02-13 15:00 Rev.: 9581

* updated depends fixed by [9580]

5 lines of code changed in 1 file:

• SL/FILTER: Makefile (+5 -1)

westram 2012-11-23 17:58 Rev.: 9225

* rename unit test macros
- TEST_ASSERT.. -> TEST_EXPECT..

30 lines of code changed in 1 file:

• SL/FILTER: RangeList.cxx (+30 -30)

westram 2012-09-24 14:27 Rev.: 8936

* fixed cppcheck warnings

8 lines of code changed in 1 file:

• SL/FILTER: AP_filter.cxx (+8 -7)

westram 2012-05-02 19:21 Rev.: 8696

* merge from saiali log:branches/saiali@8635-8695
- unalign center (blockop)
- modify SAI range (using ACI/SRT)
- align ranges defined by SAI
- refactorings
* block ops
* selection lists

230 lines of code changed in 3 files:

• SL/FILTER: Makefile (+12 -6), RangeList.cxx (new 150), RangeList.h (new 68)

westram 2012-04-19 08:13 Rev.: 8607

merge from e4fix [8135] [8136] [8137] [8138] [8139] [8140] [8141] [8142] [8143] [8144] [8222]
(this revives the reverted patches [8129] [8130] [8131] [8132]; see [8133])

* fixes
- some free/delete mismatches
- wrong definition of ORF objects (Level was no bit value)
- amino consensus (failed for columns only containing 'C')
* rename
- AA_sequence_term -> orf_term
- ED4_sequence_terminal_basic -> ED4_abstract_sequence_terminal
* cleaned up hierarchy dumps
* tweaked is_terminal()/to_terminal()

0 lines of code changed in 2 files:

• SL/FILTER: AP_filter.cxx (changed), AP_filter.hxx (changed)

westram 2012-04-11 12:19 Rev.: 8574

* [8567] failed on WCs where shared libs were up-to-date, but not yet present in $ARBHOME/lib
- link libs directly in $ARBHOME/lib
* no longer create 'SHARED.a' in shared-library-dirs
* unit tests caused build of 'SHARED.so' (instead of 'libSHARED.so'). Every library existed twice.
- changed test-target-names for shared libaries (e.g. ARBDB/ARBDB.test -> ARBDB/libARBDB.test)
- added failing stopper targets to main-Makefile and shared-lib-Makefiles
* changed all dependencies to shared libs
* fixed dependency scripts to perform correct translations from lib/libUNIT.so <-> UNIT/UNIT.(dummy|a). omg :/
* updated predefined RESTRICT_LIB entries in UNIT_TESTER/Makefile.setup.template
- check whether RESTRICT_LIB uses obsolete test-names (e.g. ARBDB instead of libARBDB) and fail if.

1 lines of code changed in 1 file:

• SL/FILTER: needs_libs (+1 -1)

westram 2012-03-13 18:36 Rev.: 8479

* calculating bootstrap-trees with active filter
- now bootstraps filtered positions
- before it did bootstrap X random positions from the unfiltered alignment (with X=size of filter). That was more jackknifing than bootstrapping.

20 lines of code changed in 2 files:

• SL/FILTER: AP_filter.cxx (+3 -3), AP_filter.hxx (+17 -4)

westram 2012-02-15 20:40 Rev.: 8393

- cppchecked (1.53)

1 lines of code changed in 1 file:

• SL/FILTER: AP_filter.cxx (+1 -1)

westram 2011-06-10 14:50 Rev.: 7623

- merge from dev [7450] [7452] [7456] [7457] [7458] [7459] [7460] [7461] [7464] [7465] [7466] [7467] [7468] [7469] [7482]
* tweaked compiler options
- activated -Weffc++
* postfilter warnings where Scott Meyers' advices are too general.
- base classes should not always have virtual destructors, since that renders tiny classes useless and
- members should not always be initialized via initialization list, since that often violates the DRY principle
* fix gcc's inability to detect that Noncopyable implements a private copy-ctor and op=
* this slows down complete ARB recompilation by ~5%
- added -Wold-style-cast (inactive)
- removed -Wno-non-template-friend added in [7447]
* postcompile.pl
- added option --original to show unmodified compiler output
* declared op= for classes which had a copy-ctor
* moved op= macros to arbtools.h
* derived classes containing pointers from Noncopyable (use Noncopyable virtually) or
* made them copyable if needed (awt_mask_item, KnownDB, Code, AWT_registered_itemtype, GEN_gene, !PosGene, !PartialSequence, !PlugIn, Range, Convaln_exception)
* other related changes
- user mask destruction working now

5 lines of code changed in 1 file:

• SL/FILTER: AP_filter.hxx (+5)

westram 2011-04-16 10:33 Rev.: 7423

merged from dev [7320] [7418] [7419] [7420]
* !BasePosition
- uses int instead of size_t
- allow empty sequences (gap-only)
- allow to index just a part of a sequence
- use new class !CharPredicate to initialize custom gaps
* moved safeCharIndex() to dupstr.h
* unit tests
- collectIntFunResults (allowed range)
- slow test

0 lines of code changed in 2 files:

• SL/FILTER: AP_filter.cxx (-1), Makefile (-1)

westram 2011-02-23 13:37 Rev.: 7183

merges [7084] [7086] [7087] [7088] from refactor
* added CORE lib
- added arb_progress (unused yet)
- moved some code from ARBDB to CORE
* added tests to CORE lib
* generate_all_links.sh
- now tests link targets
- able to replace links (if link stays the same, but target changes)
* fixed perl interface
- link with libCORE
- DRYed LINUX.PL and DARWIN.PL
- added wrapper functionality (ARBDB->CORE). Functions starting with GBC_ are wrappers for code that moved into libCORE (which is NOT xsub'd)

2 lines of code changed in 1 file:

• SL/FILTER: Makefile (+2 -1)

westram 2010-09-18 16:20 Rev.: 6866

* compiler-messages (merges [6848] [6849] [6850] [6851] [6853] [6855] [6856] [6860] from refactor)
- errors get listed before warnings
- pipe all compilations through postcompile filter
- optionally filter warnings and/or stop at 1st error (controllable by POST_COMPILE in ARB Makefile)
- no warnings for ptpan (too many; version in trunk is outdated)

2 lines of code changed in 1 file:

• SL/FILTER: Makefile (+2 -2)

westram 2010-09-09 21:49 Rev.: 6817

- depends for [6816]

1 lines of code changed in 1 file:

• SL/FILTER: Makefile (+1)

westram 2010-09-09 19:25 Rev.: 6814

* depends updated for [6812] + [6813]

2 lines of code changed in 1 file:

• SL/FILTER: Makefile (+2 -1)

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