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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/PRONUC: Makefile (+2)

westram 2021-10-10 08:33 Rev.: 18781

* reintegrates 'help' into 'trunk'
- relocate help sources
* adds: log:branches/help@18763:18780

1 lines of code changed in 1 file:

• SL/PRONUC: AP_codon_table.cxx (+1 -1)

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

* remove trailing whitespace from c source.

2 lines of code changed in 1 file:

• SL/PRONUC: iupac.cxx (+2 -2)

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

* directly use {{{OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/PRONUC: 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/PRONUC: Makefile (+1 -4)

westram 2021-09-15 12:00 Rev.: 18720

* select units using {{{wildcard}}}.

1 lines of code changed in 1 file:

• SL/PRONUC: Makefile (+1 -5)

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

* eliminate unused {{{C_OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/PRONUC: Makefile (+1 -2)

westram 2018-10-31 09:52 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 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

4 lines of code changed in 2 files:

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

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

1 lines of code changed in 1 file:

• SL/PRONUC: AP_codon_table.cxx (+1 -1)

westram 2018-04-20 12:04 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 11:09 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 18:22 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 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

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 12:22 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 10:06 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 10:05 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 10:58 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 12:18 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 09:28 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 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

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 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/PRONUC: Makefile (+2 -2)

westram 2014-10-09 17:48 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 10:41 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 16:25 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 11:06 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 13:51 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 20:28 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 16:41 Rev.: 11034

* depends for [11033]

1 lines of code changed in 1 file:

• SL/PRONUC: Makefile (+1)

westram 2013-11-01 14:50 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 17:14 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 14:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• SL/PRONUC: Makefile (+1 -1)

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

* renamed include variables

2 lines of code changed in 1 file:

• SL/PRONUC: Makefile (+2 -2)

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/PRONUC: 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)

2 lines of code changed in 1 file:

• SL/PRONUC: Makefile (+2 -2)

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/PRONUC: Makefile (+1 -1)

westram 2013-09-09 15:36 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 12:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• SL/PRONUC: Makefile (+1 -1)

westram 2013-02-09 12:52 Rev.: 9521

- updated depends for [9520]

4 lines of code changed in 1 file:

• SL/PRONUC: Makefile (+4)

westram 2013-02-09 11:16 Rev.: 9516

- reintegrated branch 'cxx11'

2 lines of code changed in 1 file:

• SL/PRONUC: Makefile (+2)

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