Directory SL/SEQIO/

Directory Created:
2010-03-23 20:04
Total Files:
5
Deleted Files:
0
Lines of Code:
1219

[root]/SL/SEQIO

Lines of Code

SL/SEQIO/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
westram 80 (100.0%) 1638 (100.0%) 20.4

Most Recent Commits

westram 2022-08-03 14:52 Rev.: 19206


* reintegrates 'ali' into 'trunk'
* adds: log:branches/ali@19183:19205

13 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+13 -5)
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/SEQIO: Makefile (+1)
westram 2021-09-15 12:37 Rev.: 18724


* directly use {{{OBJECTS}}}.

1 lines of code changed in 1 file:

  • SL/SEQIO: 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/SEQIO: Makefile (+1 -4)
westram 2021-09-15 12:00 Rev.: 18720


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

1 lines of code changed in 1 file:

  • SL/SEQIO: Makefile (+1 -4)
westram 2021-09-15 11:53 Rev.: 18718


* eliminate unused {{{C_OBJECTS}}}.

1 lines of code changed in 1 file:

  • SL/SEQIO: 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/SEQIO: seq_export.cxx (+1 -1)
westram 2019-09-17 14:46 Rev.: 18092


* full update from child 'fts' into 'trunk'
- implements #562
* adds:
- [18091/branches/fts]
- log:branches/gui@17754:17924,17926:18090

124 lines of code changed in 4 files:

  • SL/SEQIO: Makefile (+2), needs_libs (+1), seq_export.cxx (+119 -29), seqio.hxx (+2 -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

3 lines of code changed in 2 files:

  • SL/SEQIO: Makefile (+1), seq_export.cxx (+2 -1)
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

1 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+1 -1)
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

47 lines of code changed in 2 files:

  • SL/SEQIO: seq_export.cxx (+43 -43), seqio.cxx (+4 -4)
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

1 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+1 -1)
westram 2017-10-21 12:40 Rev.: 16564


* reintegrates 'io' into 'trunk'
- implements #691
* adds: log:branches/io@16436:16510,16513:16514,16517,16533:16535,16537:16563

229 lines of code changed in 3 files:

  • SL/SEQIO: seq_export.cxx (+131 -84), seqio.cxx (+60 -58), seqio.hxx (+38 -7)
westram 2017-09-23 13:03 Rev.: 16425


* reintegrates 'aci' into 'trunk'
- extends ACI language (implementing #707)
* boolean operators: {{{And}}},{{{Or}}},{{{Not}}}
* numeric comparison: {{{isAbove}}},{{{isBelow}}},{{{isEqual}}}
* floating point arithmetic: {{{fplus}}},{{{fminus}}},{{{fmult}}},{{{fdiv}}}
* misc: {{{round}}},{{{inRange}}},{{{isEmpty}}}
- enforce parameter checks in ACI function code
- case of commands completely ignored
* adds: log:branches/aci@16385,16391:16424

1 lines of code changed in 1 file:

  • SL/SEQIO: Makefile (+1)
westram 2017-09-18 14:23 Rev.: 16374


* reintegrates 'aci' into 'trunk'
- refactored wide parts of ACI code (incl. SRT+REG)
* added more test
* ACI tracing
- more complete and readable
- automatically turned off when done with expression
* improved error messages (esp. diagnostics)
* documentation (updated, added missing)
* fixed a bunch of bugs (incl. SEGV and deadlock)
* ACI now runs inside execution environment
- ACI language may be extended with custom commands (implements #756)
* added ACI extension for group-batch-rename
* adds:
- log:branches/aci@16170:16373
- log:branches/addtest@16193:16316

17 lines of code changed in 2 files:

  • SL/SEQIO: Makefile (+1), seq_export.cxx (+16 -8)
westram 2017-07-10 11:29 Rev.: 16119


* reintegrates 'saiexport' into 'trunk'
- implements #743
* adds: log:branches/saiexport@16023:16118

3 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+3 -1)
westram 2016-08-11 10:05 Rev.: 15176


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

3 lines of code changed in 2 files:

  • SL/SEQIO: Makefile (+2), seq_export.cxx (+1 -1)
westram 2016-01-28 08:33 Rev.: 14682


* merge [14675:14681] from 'gde' into 'trunk'
- change DB interface function concerned with GB_FLOAT from double -> float
- introduce more stable ascii <-> float conversion
* adds: log:branches/gde@14676:14681

17 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+17 -20)
westram 2015-04-28 11:34 Rev.: 13772


* replace init-by-memset for {{{export_format}}}

14 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+14 -14)
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

4 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+4 -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/SEQIO: Makefile (+2 -2)
westram 2015-01-21 15:10 Rev.: 13423


* fix embl export filter (#638):
- print base count on right side of sequence (uses 'numright' added with [13420])

1 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+1 -1)
westram 2014-11-17 15:42 Rev.: 13191


* reintegrates 'slv' into 'trunk'
* performs #624
* adds:
- log:branches/slv@13152:13190

9 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+9 -2)
westram 2014-09-01 13:10 Rev.: 12803


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

1 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+1 -1)
westram 2014-04-30 13:36 Rev.: 12138


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

19 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+19 -10)
westram 2013-10-31 14:10 Rev.: 10996


* use cflags before cxxflags

1 lines of code changed in 1 file:

  • SL/SEQIO: Makefile (+1 -1)
westram 2013-10-30 15:58 Rev.: 10974


* renamed include variables

2 lines of code changed in 1 file:

  • SL/SEQIO: 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/SEQIO: 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/SEQIO: 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/SEQIO: Makefile (+1 -1)
westram 2013-10-03 12:11 Rev.: 10704


- reintegrated branch 'helptest'

2 lines of code changed in 2 files:

  • SL/SEQIO: Makefile (+1), seq_export.cxx (+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/SEQIO: Makefile (+2)
westram 2013-05-13 14:41 Rev.: 10027


- do not export errors

2 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+2 -2)
westram 2013-04-08 15:33 Rev.: 9838


* reintegrated branch 'db'
- GBDATA now is a base class of GBENTRY (new) and GBCONTAINER
* moved code into classes GBENTRY, GBCONTAINER and GB_MAIN_TYPE
* several functions now exist 2 (or 3) times (for GBENTRY and GBCONTAINER, and some for GBDATA as well)
* several functions changed their interface (caller has to explicitely pass GBENTRY or GBCONTAINER)
- dropped support for ARB DB-version 0
* adds:
- log:branches/db@9626:9837

4 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+4 -2)
westram 2013-02-13 12:24 Rev.: 9575


- effect of [9574] (comments only)

1 lines of code changed in 1 file:

  • SL/SEQIO: Makefile (+1 -1)
westram 2013-02-09 12:52 Rev.: 9521


- updated depends for [9520]

2 lines of code changed in 1 file:

  • SL/SEQIO: Makefile (+2)
westram 2013-02-09 11:16 Rev.: 9516


- reintegrated branch 'cxx11'

2 lines of code changed in 1 file:

  • SL/SEQIO: Makefile (+2)
westram 2012-11-23 18:15 Rev.: 9226


* do not expect negations (in macro names)

2 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+2 -2)
westram 2012-11-23 17:58 Rev.: 9225


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

7 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+7 -7)
westram 2012-11-23 17:47 Rev.: 9224


* eliminated old TEST_ASSERT (pre-[8219]-style)
- replaced by new TEST_ASSERT (expecting expression equals true), TEST_ASSERT_NOTNULL or TEST_ASSERT_NONZERO

2 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+2 -2)

(20 more)

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