Directory SL/PRONUC/

Total Files:
8
Deleted Files:
0
Lines of Code:
2771

[root]/SL/PRONUC

Lines of Code

SL/PRONUC/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
westram 122 (100.0%) 2217 (100.0%) 18.1

Most Recent Commits

westram 2018-10-31 10:52 Rev.: 17593


* reintegrates 'fix' into 'trunk'
- performs #798
* adds genetic code tables (24-31)
* adds combined amino acid J (I or L)
* improved translate and/or realign
- handle optional start-/stop-codons
- improve recognition of nuc-triples containing IUPAC-codes
* error messages now always list EMBL table numbers
* adds:
- log:branches/fix@17480:17485,17491:17492,17494:17507,17509:17528,17534:17592
- log:branches/optional@17481:17568

684 lines of code changed in 6 files:

  • SL/PRONUC: AP_codon_table.cxx (+602 -162), AP_codon_table.hxx (+33 -17), AP_pro_a_nucs.cxx (+25 -18), AP_pro_a_nucs.hxx (+20 -7), Makefile (+1), iupac.cxx (+3 -3)
westram 2018-10-24 15:58 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

4 lines of code changed in 2 files:

  • SL/PRONUC: AP_codon_table.cxx (+3 -2), Makefile (+1)
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

1 lines of code changed in 1 file:

  • SL/PRONUC: AP_codon_table.cxx (+1 -1)
westram 2018-04-20 13:04 Rev.: 16904


* reintegrates 'pvp' into 'trunk'
- fixes #782
- implements #701
* adds: log:branches/pvp@16882:16903

16 lines of code changed in 2 files:

  • SL/PRONUC: AP_pro_a_nucs.cxx (+4 -4), AP_pro_a_nucs.hxx (+12 -8)
westram 2018-04-05 12:09 Rev.: 16873


* fix typos ("neither")

1 lines of code changed in 1 file:

  • SL/PRONUC: AP_codon_table.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

3 lines of code changed in 2 files:

  • SL/PRONUC: AP_codon_table.cxx (+1 -2), iupac.cxx (+2 -4)
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

39 lines of code changed in 6 files:

  • SL/PRONUC: AP_codon_table.cxx (+23 -23), AP_codon_table.hxx (+1 -1), AP_pro_a_nucs.cxx (+8 -8), AP_pro_a_nucs.hxx (+4 -4), iupac.cxx (+2 -2), iupac.h (+1 -1)
westram 2017-07-26 13:22 Rev.: 16181


* fix (unused-)warnings for {{{!ENABLE_CRASH_TESTS}}}

2 lines of code changed in 1 file:

  • SL/PRONUC: AP_pro_a_nucs.cxx (+2)
westram 2017-04-05 11:06 Rev.: 15738


* rename only

1 lines of code changed in 1 file:

  • SL/PRONUC: AP_pro_a_nucs.cxx (+1 -1)
westram 2016-08-11 11:05 Rev.: 15176


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

7 lines of code changed in 3 files:

  • SL/PRONUC: AP_codon_table.cxx (+1 -1), AP_pro_a_nucs.cxx (+4 -6), Makefile (+2)
westram 2015-10-28 11:58 Rev.: 14425


* reintegrates 'consensus' into 'trunk'
- fixes #663 (consistent consensus calculation)
- allow to load SAI into existing EDIT4 config
- tweaked "View differences"
- minor fixes for SAI MAX_FREQUENCY
* adds:
- log:branches/addtest@14319:14326
- log:branches/consensus@14276:14424

6 lines of code changed in 2 files:

  • SL/PRONUC: iupac.cxx (+5 -4), iupac.h (+1 -1)
westram 2015-04-21 13:18 Rev.: 13755


* reintegrates 'pars' into 'trunk'
- only refactored some code and added a few missing tests
* adds:
- log:branches/pars@13627,13639:13754

1 lines of code changed in 1 file:

  • SL/PRONUC: AP_pro_a_nucs.cxx (+1 -1)
westram 2015-03-30 10:28 Rev.: 13639


* full update from child 'pars' into 'trunk'
- cleanup patches
* adds:
- log:branches/pars@13628:13638

0 lines of code changed in 1 file:

  • SL/PRONUC: AP_pro_a_nucs.cxx (-3)
westram 2015-03-29 12:47 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

34 lines of code changed in 2 files:

  • SL/PRONUC: AP_pro_a_nucs.cxx (+21 -27), AP_pro_a_nucs.hxx (+13 -9)
westram 2015-01-23 15:19 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/PRONUC: Makefile (+2 -2)
westram 2014-10-09 18:48 Rev.: 13018


* merge a bunch of fixes from 'gcc' into 'trunk'
- detected using !AddressSanitizer
- fixing #613, #580 and other (undetected) bugs
* adds:
- log:branches/gcc@12996,13001:13003,13005:13006,13010:13014,13016

4 lines of code changed in 1 file:

  • SL/PRONUC: AP_codon_table.cxx (+4 -6)
westram 2014-08-07 11:41 Rev.: 12706


* reintegrates 'alilink' into 'trunk'
- minor fixes (messages, rare cases)
- refactored some code
* adds:
- log:branches/alilink@12669:12705

185 lines of code changed in 3 files:

  • SL/PRONUC: AP_codon_table.cxx (+135 -109), AP_codon_table.hxx (+49 -44), Makefile (+1)
westram 2014-08-04 17:25 Rev.: 12667


* reintegrates 'alilink' into 'trunk'
- fixes #419, #145, #563
* adds:
- log:branches/addtest@12468:12472
- log:branches/alilink@12419:12421,12423:12429,12431:12432,12437:12601,12603:12666
- log:branches/oldrealign@12499,12501,12537,12541,12548,12595,12607,12612,12616,12620,12625,12628,12634,12641

475 lines of code changed in 4 files:

  • SL/PRONUC: AP_codon_table.cxx (+415 -120), AP_codon_table.hxx (+21 -10), AP_pro_a_nucs.cxx (+36 -35), Makefile (+3)
westram 2014-03-25 12:06 Rev.: 11889


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

1 lines of code changed in 1 file:

  • SL/PRONUC: iupac.cxx (+1 -1)
westram 2014-02-02 14:51 Rev.: 11547


* tests for equality that are marked as broken ({{{TEST_EXPECT_EQUAL__BROKEN}}}) did not protect vs regression
- added mandatory argument specifying the broken value (and fail when it changes)
- drawback: argument is evaluated twice

1 lines of code changed in 1 file:

  • SL/PRONUC: iupac.cxx (+1 -1)
westram 2013-11-02 21:28 Rev.: 11048


* use typed DB callbacks (rest)

3 lines of code changed in 1 file:

  • SL/PRONUC: AP_pro_a_nucs.cxx (+3 -3)
westram 2013-11-02 17:41 Rev.: 11034


* depends for [11033]

1 lines of code changed in 1 file:

  • SL/PRONUC: Makefile (+1)
westram 2013-11-01 15:50 Rev.: 11023


* publish DB callback interface separately from rest of DB interface

6 lines of code changed in 2 files:

  • SL/PRONUC: AP_pro_a_nucs.cxx (+1), Makefile (+5)
westram 2013-10-31 18:14 Rev.: 11007


* prototype for GBK_terminate differed between arb_core.h and arb_msg.h

1 lines of code changed in 1 file:

  • SL/PRONUC: Makefile (+1)
westram 2013-10-31 15:10 Rev.: 10996


* use cflags before cxxflags

1 lines of code changed in 1 file:

  • SL/PRONUC: Makefile (+1 -1)
westram 2013-10-30 16:58 Rev.: 10974


* renamed include variables

2 lines of code changed in 1 file:

  • SL/PRONUC: Makefile (+2 -2)
westram 2013-10-29 13:55 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/PRONUC: Makefile (+1 -1)
westram 2013-10-29 13:23 Rev.: 10955


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

2 lines of code changed in 1 file:

  • SL/PRONUC: Makefile (+2 -2)
westram 2013-10-29 12:43 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/PRONUC: Makefile (+1 -1)
westram 2013-09-09 16:36 Rev.: 10563


- include downcast.h from arbdbt.h
(this break C++11 compilation, i.e. gcc4.8 or newer)[[BR]]
amendment:
* also broke compilation on ubuntu 13.04 and with gcc 4.7.3 (due to nameclash with boost)

2 lines of code changed in 1 file:

  • SL/PRONUC: Makefile (+2)
westram 2013-02-13 13:24 Rev.: 9575


- effect of [9574] (comments only)

1 lines of code changed in 1 file:

  • SL/PRONUC: Makefile (+1 -1)
westram 2013-02-09 13:52 Rev.: 9521


- updated depends for [9520]

4 lines of code changed in 1 file:

  • SL/PRONUC: Makefile (+4)
westram 2013-02-09 12:16 Rev.: 9516


- reintegrated branch 'cxx11'

2 lines of code changed in 1 file:

  • SL/PRONUC: Makefile (+2)
westram 2013-01-03 12:36 Rev.: 9342


* fixed compilation of NDEBUG-version with assertions

1 lines of code changed in 1 file:

  • SL/PRONUC: AP_codon_table.hxx (+1 -1)
westram 2012-11-24 11:24 Rev.: 9228


* replaced several inlined conditions by more verboose expectations

2 lines of code changed in 1 file:

  • SL/PRONUC: iupac.cxx (+2 -2)
westram 2012-11-23 19:26 Rev.: 9227


* do not expect negations (in expectation)

1 lines of code changed in 1 file:

  • SL/PRONUC: iupac.cxx (+1 -1)
westram 2012-11-23 18:58 Rev.: 9225


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

14 lines of code changed in 1 file:

  • SL/PRONUC: iupac.cxx (+14 -14)
westram 2012-06-15 15:35 Rev.: 8814


- fixed some warnings in NDEBUG mode (unused warnings)

4 lines of code changed in 1 file:

  • SL/PRONUC: AP_codon_table.cxx (+4)
westram 2012-05-11 12:32 Rev.: 8725


* comments cleanup

5 lines of code changed in 1 file:

  • SL/PRONUC: AP_pro_a_nucs.cxx (+5 -10)
westram 2012-04-26 18:25 Rev.: 8676


- cppchecked (1.54)

0 lines of code changed in 1 file:

  • SL/PRONUC: AP_codon_table.cxx (-2)

(31 more)

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