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

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

1 lines of code changed in 1 file:

• SL/TRANSLATE: Makefile (+1)

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

* directly use {{{OBJECTS}}}.

1 lines of code changed in 1 file:

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

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

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

1 lines of code changed in 1 file:

• SL/TRANSLATE: Makefile (+1 -3)

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

* eliminate unused {{{C_OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/TRANSLATE: Makefile (+1 -2)

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

1 lines of code changed in 1 file:

• SL/TRANSLATE: Translate.cxx (+1 -1)

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

86 lines of code changed in 2 files:

• SL/TRANSLATE: Makefile (+1), Translate.cxx (+85 -26)

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/TRANSLATE: Makefile (+1), Translate.cxx (+3 -1)

westram 2018-10-23 09:36 Rev.: 17510

* partial merge from 'fix' into 'trunk'
* adds: [17508/branches/fix]

19 lines of code changed in 2 files:

• SL/TRANSLATE: Translate.cxx (+12 -12), Translate.hxx (+7 -6)

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

2 lines of code changed in 1 file:

• SL/TRANSLATE: Translate.cxx (+2 -2)

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

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

1 lines of code changed in 1 file:

• SL/TRANSLATE: Makefile (+1)

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/TRANSLATE: Makefile (+2 -2)

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

* use cflags before cxxflags

1 lines of code changed in 1 file:

• SL/TRANSLATE: Makefile (+1 -1)

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

* renamed include variables

2 lines of code changed in 1 file:

• SL/TRANSLATE: 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/TRANSLATE: 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/TRANSLATE: 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/TRANSLATE: 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/TRANSLATE: Makefile (+2)

westram 2013-02-13 12:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• SL/TRANSLATE: Makefile (+1 -1)

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

- updated depends for [9520]

1 lines of code changed in 1 file:

• SL/TRANSLATE: Makefile (+1)

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

- reintegrated branch 'cxx11'

1 lines of code changed in 1 file:

• SL/TRANSLATE: Makefile (+1)

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/TRANSLATE: Translate.cxx (changed), Translate.hxx (changed)

westram 2011-12-13 14:01 Rev.: 8302

* merges [8301] from stable and fixes conflicts with partly duplicate [6600]

15 lines of code changed in 2 files:

• SL/TRANSLATE: Translate.cxx (+14), Translate.hxx (+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/TRANSLATE: Makefile (+2 -1)

westram 2010-10-21 14:38 Rev.: 7013

- when field 'codon_start' was missing, but field 'transl_table' was present, ARB wrote a default 'codon_start' as GB_INT, which caused a crash. Introduced in [5768]

1 lines of code changed in 1 file:

• SL/TRANSLATE: Translate.cxx (+1 -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/TRANSLATE: Makefile (+2 -2)

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

- depends for [6816]

1 lines of code changed in 1 file:

• SL/TRANSLATE: Makefile (+1)

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

* depends updated for [6812] + [6813]

1 lines of code changed in 1 file:

• SL/TRANSLATE: Makefile (+1)

westram 2010-04-07 13:28 Rev.: 6577

- depends/prototypes updated

3 lines of code changed in 2 files:

• SL/TRANSLATE: Makefile (new)

westram 2010-03-03 14:00 Rev.: 6490

* moved a few types to arbdb_base.h
* only use arbdb_base.h or arbdb.h where possible
* global included cleanup
* added MBI headers to many files
* moved SQ_ambiguities.SQ_count_ambiguities() to separate object

5 lines of code changed in 1 file:

• SL/TRANSLATE: Translate.cxx (+5 -2)

westram 2010-02-17 09:30 Rev.: 6448

- added library dependency declarations

4 lines of code changed in 1 file:

• SL/TRANSLATE: needs_libs (new 4)

westram 2010-01-27 09:48 Rev.: 6385

- removed trailing whitespace

6 lines of code changed in 1 file:

• SL/TRANSLATE: Translate.cxx (+6 -6)

westram 2010-01-27 08:05 Rev.: 6381

- fixed includes
- added MBI headers
- removed unused files

6 lines of code changed in 3 files:

• SL/TRANSLATE: Translate.cxx (+1 -6), Translate.hxx (new)

westram 2010-01-21 16:49 Rev.: 6366

* fixed whitespace (scripted)

3 lines of code changed in 1 file:

• SL/TRANSLATE: Translate.cxx (+3 -3)

westram 2010-01-06 14:03 Rev.: 6325

* ARBDB
- hide internal structures (GBDATA etc.) inside ARBDB. Fixed all layer violations
- splitted up big header files into many. Did not reduce much internal dependencies, but at least there's some kind of semantic separation now.
- moved many decls right into the .cxx file (if only used in one)
- removed several duplicated type-names like
{{{
typedef struct gb_main_type {
...
} GB_MAIN_TYPE;
}}}
- GB_HASHI -> GB_NUMHASH + functions renamed
- gb_assert no longer globally visible. replaced
- fixed includes
- local (ARBDB internal) headers all start with prefix 'gb_'

1 lines of code changed in 2 files:

• SL/TRANSLATE: Translate.cxx (new)