Directory SL/FAST_ALIGNER/

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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

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

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

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

28 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+28 -31)

westram 2022-06-20 11:40 Rev.: 19069

* fix vectorize-checks for gcc 5.4

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

westram 2022-06-20 11:19 Rev.: 19068

* fix vectorize-checks for gcc 6.5

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

westram 2022-06-20 11:18 Rev.: 19067

* fix vectorize-checks for gcc 5.5

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

westram 2022-06-20 11:15 Rev.: 19065

* fix vectorize-checks for gcc 8.x-series

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

westram 2022-06-20 11:12 Rev.: 19063

* fixed LOOP_VECTORIZED expressions that used '*'-count (for gcc 10.x-series).

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

westram 2022-06-20 11:03 Rev.: 19061

* fix loop vectorization checks failing with gcc 10.x

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

westram 2022-06-17 10:41 Rev.: 19055

* accept gcc 9.4.0
* loop vectorizations failing with gcc 9.1 - 9.3 also fail with 9.4.

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

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 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+5 -5)

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

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

4 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+4 -4)

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

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

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: Makefile (+2)

westram 2022-02-08 13:27 Rev.: 18929

* check whether data exists before checking its protection (fixes #842)

6 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+6 -1)

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

* remove trailing whitespace from c source.

58 lines of code changed in 4 files:

• SL/FAST_ALIGNER: ClustalV.cxx (+1 -1), fast_aligner.cxx (+35 -35), seq_search.cxx (+17 -17), seq_search.hxx (+5 -5)

westram 2021-09-15 12:37 Rev.: 18724

* directly use {{{OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/FAST_ALIGNER: Makefile (+1 -2)

westram 2021-09-15 12:31 Rev.: 18723

* remove .c rules.
* add .c suffix (in SOURCE_TOOLS).

1 lines of code changed in 1 file:

• SL/FAST_ALIGNER: Makefile (+1 -4)

westram 2021-09-15 11:53 Rev.: 18718

* eliminate unused {{{C_OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/FAST_ALIGNER: Makefile (+1 -2)

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

* change many WARN_TODO triggered warnings into todo markers.

12 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+12 -27)

westram 2020-03-16 13:13 Rev.: 18380

* tested vectorization with misc gcc versions:
- number of reported loops differs with 7.5.0
- one vectorization succeeds for gcc 6.5.0

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

westram 2020-03-13 11:43 Rev.: 18379

* accept gcc 9.3.0
- vectorizations failing with 9.1 and 9.2 still fail with 9.3.

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

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

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

1 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+1 -1)

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

25 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+25 -21)

westram 2019-08-16 11:53 Rev.: 18011

* document vectorizations failing with gcc 9.2.
* document vectorizations refused as "not worthwhile" by gcc 9.2.
* cannot check loop vectorization in header (seq.h).

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

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.

5 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+5 -7)

westram 2019-06-25 12:08 Rev.: 17941

* fix warnings:
- two maybe-uninitialized-warning (one def. bogus).
- conditionally compile code which is only used from unittests.

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+2 -2)

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

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

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2)

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

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

1 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.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

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: Makefile (+2)

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

15 lines of code changed in 4 files:

• SL/FAST_ALIGNER: Makefile (+3), fast_aligner.cxx (+1 -1), seq_search.cxx (+3 -9), seq_search.hxx (+8 -2)

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

2 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+2 -2)

westram 2018-07-10 15:48 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

1 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+1 -1)

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

* fix typos ("neither")

1 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.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

7 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+7 -7)

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

128 lines of code changed in 4 files:

• SL/FAST_ALIGNER: ClustalV.cxx (+4 -4), fast_aligner.cxx (+112 -114), seq_search.cxx (+1 -1), seq_search.hxx (+11 -11)

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

1 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+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

1 lines of code changed in 1 file:

• SL/FAST_ALIGNER: seq_search.cxx (+1 -1)

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

6 lines of code changed in 1 file:

• SL/FAST_ALIGNER: ClustalV.cxx (+6 -6)

westram 2017-08-23 12:42 Rev.: 16237

* fix spelling for 'occurrence'

6 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+6 -6)

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

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

14 lines of code changed in 4 files:

• SL/FAST_ALIGNER: ClustalV.cxx (+2 -2), Makefile (+4), fast_aligner.cxx (+3 -3), seq_search.hxx (+5 -2)

westram 2016-07-27 10:30 Rev.: 15094

* reintegrates 'fix' into 'trunk'
* adds: log:branches/fix@15066,15073:15076,15082,15086:15093

10 lines of code changed in 1 file:

• SL/FAST_ALIGNER: fast_aligner.cxx (+10 -8)

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