Directory SL/FAST_ALIGNER/

Directory Created:
2009-04-30 21:34
Total Files:
8
Deleted Files:
6
Lines of Code:
5877

[root]/SL/FAST_ALIGNER

Lines of Code

SL/FAST_ALIGNER/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 297 (100.0%) 12382 (100.0%) 41.6
westram 295 (99.3%) 12379 (100.0%) 41.9
baderk 1 (0.3%) 2 (0.0%) 2.0
epruesse 1 (0.3%) 1 (0.0%) 1.0

Most Recent Commits

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)
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/FAST_ALIGNER: fast_aligner.cxx (-6)
westram 2015-12-16 15:13 Rev.: 14622


* reintegrates 'ui' into 'trunk'
- implements #656
- adds instant update for
* next neighbour search
* branch analysis (mark functions)
* arb-phylo (filter setup)
* adds: log:branches/ui@14588:14621

4 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+4 -3)
westram 2015-11-05 16:55 Rev.: 14476


* {{{AlignDataAccess}}}:
- use factory function (ensures proper initialization; was missing for SINA interface); removed global
- use callback to get helix-string (only used in island_hopping; optional)
- store alignment-name
- add proper ctor, copy-ctor and op=
* island_hopping
- store helix-string as copy

53 lines of code changed in 2 files:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+8 -2), fast_aligner.hxx (+45 -3)
westram 2015-11-05 15:57 Rev.: 14475


* fix range definition for islandhopper (i guess it was broken by [8614])

5 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+5 -1)
westram 2015-11-04 09:57 Rev.: 14453


* do not cast AW_POPDOWN

3 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+3 -3)
westram 2015-10-28 15:29 Rev.: 14430


* use typed callbacks in FAST_ALIGNER

15 lines of code changed in 2 files:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+14 -16), fast_aligner.hxx (+1 -1)
westram 2015-10-28 13:39 Rev.: 14426


* use typed window callbacks in EDIT4

6 lines of code changed in 3 files:

  • SL/FAST_ALIGNER: Makefile (+1), fast_aligner.cxx (+4 -5), fast_aligner.hxx (+1 -1)
westram 2015-04-15 16:37 Rev.: 13725


* add config manager to integrated aligners

46 lines of code changed in 2 files:

  • SL/FAST_ALIGNER: Makefile (+1), fast_aligner.cxx (+45 -1)
westram 2015-04-15 14:25 Rev.: 13722


* minor layout fixes for fast-aligner window (avoids some overlapping elements in gtk)

6 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+6 -4)
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

2 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: Makefile (+2 -2)
westram 2014-09-04 15:59 Rev.: 12831


* merge [12806:12810] from 'fix' into 'trunk'
- eliminates GBT_write_sequence
* adds:
- log:branches/fix@12807:12810

1 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+1 -1)
epruesse 2014-09-02 16:51 Rev.: 12815

fix common typos reported by lintian
- splitted -> split (irregular verb)
- ressources -> resources
- explicitely -> explicitly

1 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+1 -1)
westram 2014-09-01 13:10 Rev.: 12803


* merge from 'alilink' into 'trunk'
* adds:
- log:branches/alilink@12801:12802

14 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+14 -14)
westram 2014-08-14 11:18 Rev.: 12757


* unify selectionlist creator names
* awt_create_selection_list_on_pt_servers
- remove param 'popup', instead split into two function (button and list) as done for SAIs

1 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+1 -1)
westram 2014-05-12 14:22 Rev.: 12205


* inlined default param for create_option_menu

4 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+4 -4)
westram 2014-05-12 11:38 Rev.: 12192


* do not use more than 1 parameter in calls to create_option_menu
- 2nd parameter 'label' is dominated by a previous call to label (use direct label calls instead)
- 3rd parameter 'mnemonic' is w/o function in motif and is superfluous in gtk anyway
* reset 'gone_tree_name'

8 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+8 -4)
westram 2014-04-30 13:36 Rev.: 12138


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

9 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+9 -9)
westram 2014-04-16 15:13 Rev.: 12043


* reintegrates 'fix' into 'trunk' (fixes #519)
- this patch wasn't really straightforward, instead each change caused new unexpected side effects. It's quite likely that i didn't detect all of them.
* adds:
- log:branches/fix@12023,12027:12042

1 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+1 -1)
westram 2014-03-25 11:06 Rev.: 11889


- add missing comment to closing #endif of test-sections

1 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+1 -1)
westram 2014-02-10 14:43 Rev.: 11578


* reintegrates 'alilink' into 'trunk'
- implements #420
* adds:
- log:branches/alilink@11490:11577

9 lines of code changed in 1 file:

  • SL/FAST_ALIGNER: fast_aligner.cxx (+9 -9)

(133 more)

Generated by StatSVN 0.7.0