Directory GENOM_IMPORT/

Lines of Code

Developers

Most Recent Commits

westram 2022-03-04 12:26 Rev.: 18959

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

2 lines of code changed in 1 file:

• GENOM_IMPORT: Makefile (+2)

westram 2021-10-10 09:33 Rev.: 18781

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

1 lines of code changed in 1 file:

• GENOM_IMPORT: Importer.cxx (+1 -1)

westram 2021-09-15 13:39 Rev.: 18725

* rename {{{CPP_OBJECTS}}} -> {{{OBJECTS}}}.

6 lines of code changed in 1 file:

• GENOM_IMPORT: Makefile (+6 -6)

westram 2021-09-15 13:31 Rev.: 18723

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

0 lines of code changed in 1 file:

• GENOM_IMPORT: Makefile (-3)

westram 2020-09-04 10:33 Rev.: 18475

* DRY base counter test (and empty data warning).

18 lines of code changed in 2 files:

• GENOM_IMPORT: Importer.cxx (+16 -15), Importer.h (+2)

westram 2020-09-04 10:32 Rev.: 18474

* extra warning if sequence data of genome flat file is empty (EMBL+genebank).

10 lines of code changed in 1 file:

• GENOM_IMPORT: Importer.cxx (+10 -2)

westram 2020-09-04 10:31 Rev.: 18473

* support genebank entry "DBLINK"
- store in arb field 'db_xref'.

5 lines of code changed in 1 file:

• GENOM_IMPORT: Importer.cxx (+5 -4)

westram 2020-09-04 10:28 Rev.: 18472

* do not append empty lines from wrapped tag content
- genebank only
- embl has strictly defined formatting of wrapped content

4 lines of code changed in 1 file:

• GENOM_IMPORT: Importer.cxx (+4 -2)

westram 2020-09-04 10:26 Rev.: 18471

* accept uncommon indentation occurring in genebank flat files
- remove assertion failures for wrapped lines starting behind column 12.

3 lines of code changed in 1 file:

• GENOM_IMPORT: Importer.cxx (+3 -3)

westram 2019-09-17 15:13 Rev.: 18088

* reintegrates 'fts' into 'trunk'
* adds:
- log:branches/fts@17653,17655:17717,17724:18087
- [17925/branches/gui]

2 lines of code changed in 2 files:

• GENOM_IMPORT: DBwriter.cxx (+1 -22), Makefile (+1)

westram 2019-05-10 13:57 Rev.: 17877

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

2 lines of code changed in 1 file:

• GENOM_IMPORT: SequenceBuffer.cxx (+2 -2)

westram 2017-11-28 19:22 Rev.: 16766

* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

15 lines of code changed in 3 files:

• GENOM_IMPORT: DBwriter.cxx (+4 -8), Feature.cxx (+3 -6), MetaInfo.cxx (+8 -16)

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

32 lines of code changed in 10 files:

• GENOM_IMPORT: DBwriter.cxx (+5 -5), DBwriter.h (+5 -7), Feature.cxx (+3 -3), GenomeImport.cxx (+1 -1), Importer.cxx (+5 -5), MetaInfo.cxx (+3 -3), MetaInfo.h (+4 -1), MetaTag.h (+1 -1), SequenceBuffer.h (+3 -2), tools.h (+2 -2)

westram 2017-01-16 18:16 Rev.: 15587

* reintegrates 'fix' into 'trunk'
- fix OSX unittest for jenkins project names (up to max. 16 chars long)
- optimize {{{GB_log_fak}}}
- forward {{{RegExpr}}}-compile-errors (or at least assert on failure)
* adds: log:branches/fix@15582:15586

2 lines of code changed in 2 files:

• GENOM_IMPORT: Makefile (+1), MetaInfo.cxx (+1)

westram 2016-08-17 20:39 Rev.: 15198

* remove {{{virtual}}} if {{{OVERRIDE}}} is present
- OVERRIDE implies 'implicit virtual' (if code compiles as C++11 <- tested on build server!)

8 lines of code changed in 1 file:

• GENOM_IMPORT: Importer.h (+8 -8)

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

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

3 lines of code changed in 1 file:

• GENOM_IMPORT: Makefile (+3)

westram 2016-07-21 17:53 Rev.: 15082

* partial merge from 'fix' into 'trunk'
- default_copyability++
* adds: log:branches/fix@15072,15077:15081

2 lines of code changed in 1 file:

• GENOM_IMPORT: DBwriter.cxx (+2 -7)

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:

• GENOM_IMPORT: Makefile (+2 -2)

westram 2014-03-22 10:34 Rev.: 11844

* merge [11840:11843] from 'customize' into 'trunk'
* adds:
- log:branches/customize@11841:11843
* skipped changes in ARB_GDE
- log:branches/customize/ARB_GDE@11841:11843 ~~(might fail to reintegrate)~~

13 lines of code changed in 4 files:

• GENOM_IMPORT: GenomeImport.cxx (+1 -1), Importer.cxx (+3 -3), Importer.h (+6 -6), Makefile (+3 -3)

westram 2013-11-03 15:42 Rev.: 11060

* reintegrates 'ptsfix' into 'trunk':
* adds:
- log:branches/ptsdump@8966:9000
- log:branches/ptsfix@8965:9012,9014:9017,9019:9023,9025:9046,9048:9089,9091:9114,9116:9132,9134:9139,9141:9145,9147:9151,9153:9158,9160:9379,9381:11059
- log:branches/ptsstartup@9160:9235,9237:9278,9280:9336,9339:9361,9363:9446
- log:branches/ptsundef@9061:9358

1 lines of code changed in 1 file:

• GENOM_IMPORT: GenomeImport.cxx (+1 -1)

westram 2013-11-02 17:41 Rev.: 11034

* depends for [11033]

1 lines of code changed in 1 file:

• GENOM_IMPORT: Makefile (+1)

westram 2013-10-31 18:14 Rev.: 11007

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

3 lines of code changed in 1 file:

• GENOM_IMPORT: Makefile (+3)

westram 2013-10-31 15:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• GENOM_IMPORT: Makefile (+1 -1)

westram 2013-10-31 12:44 Rev.: 10991

- fix struct/class mismatches

1 lines of code changed in 1 file:

• GENOM_IMPORT: DBwriter.h (+1 -1)

westram 2013-10-30 17:04 Rev.: 10975

* fixed wrong include variables (CC-CXX-mix). Harmless since includes do not differ atm

1 lines of code changed in 1 file:

• GENOM_IMPORT: Makefile (+1 -1)

westram 2013-10-30 16:58 Rev.: 10974

* renamed include variables

2 lines of code changed in 1 file:

• GENOM_IMPORT: 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:

• GENOM_IMPORT: 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:

• GENOM_IMPORT: 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:

• GENOM_IMPORT: Makefile (+1 -1)

westram 2013-10-29 11:44 Rev.: 10953

* do not depend on '_GLIBCXX_STRING' for definition of inline helper functions (should fix another clang error)

4 lines of code changed in 3 files:

• GENOM_IMPORT: GenomeImport.cxx (+1 -1), Importer.cxx (+1 -1), Makefile (+2 -2)

westram 2013-10-28 23:08 Rev.: 10952

- fix another clang "error"

1 lines of code changed in 1 file:

• GENOM_IMPORT: DBwriter.cxx (+1 -1)

westram 2013-10-03 13:11 Rev.: 10704

- reintegrated branch 'helptest'

2 lines of code changed in 2 files:

• GENOM_IMPORT: GenomeImport.cxx (+1), Makefile (+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)

3 lines of code changed in 1 file:

• GENOM_IMPORT: Makefile (+3)

westram 2013-07-11 18:07 Rev.: 10271

* fix #335
- activate test (written+working in [7813]; now succeeding again)

5 lines of code changed in 4 files:

• GENOM_IMPORT: DBwriter.cxx (+2 -2), DBwriter.h (+1 -1), GenomeImport.cxx (+1 -1), Importer.cxx (+1 -1)

westram 2013-07-11 17:39 Rev.: 10270

- fix compile error (u1304)

3 lines of code changed in 2 files:

• GENOM_IMPORT: GenomeImport.cxx (+2 -1), Makefile (+1)

westram 2013-07-11 17:13 Rev.: 10269

* added a unit test for genome file importer (currently disabled because it segfaults)
- test uses flatfile attached to #335
- expected test result has been generated with [7813] where importer still worked

44 lines of code changed in 2 files:

• GENOM_IMPORT: GenomeImport.cxx (+43), Makefile (+1)

westram 2013-07-04 16:49 Rev.: 10212

* depends for recent patches

4 lines of code changed in 1 file:

• GENOM_IMPORT: Makefile (+4)

westram 2013-06-04 15:20 Rev.: 10113

* changed dynamic value-initializations into default-initializations
- i believe/know they were used with ignorance of [http://stackoverflow.com/questions/620137/do-the-parentheses-after-the-type-name-make-a-difference-with-new?answertab=active#tab-top ctor-behavior].

1 lines of code changed in 1 file:

• GENOM_IMPORT: GenomeImport.cxx (+1 -1)

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

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• GENOM_IMPORT: Makefile (+1 -1)

westram 2013-02-11 12:35 Rev.: 9533

* use explicit override
- rest

4 lines of code changed in 1 file:

• GENOM_IMPORT: Importer.h (+4 -4)

(134 more)