Directory SL/SEQIO/

Directory Created:
2010-03-23 21:04
Total Files:
5
Deleted Files:
0
Lines of Code:
1125

[root]/SL/SEQIO

Lines of Code

SL/SEQIO/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
westram 69 (100.0%) 1495 (100.0%) 21.6

Most Recent Commits

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

3 lines of code changed in 2 files:

  • SL/SEQIO: Makefile (+1), seq_export.cxx (+2 -1)
westram 2018-07-23 16:52 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 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

47 lines of code changed in 2 files:

  • SL/SEQIO: seq_export.cxx (+43 -43), seqio.cxx (+4 -4)
westram 2017-11-06 14:54 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 13:40 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 14:03 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 15:23 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 12:29 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 11:05 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 09:33 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 12:34 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 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

4 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+4 -4)
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/SEQIO: Makefile (+2 -2)
westram 2015-01-21 16:10 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 16:42 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 14:10 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 14:36 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 15:10 Rev.: 10996


* use cflags before cxxflags

1 lines of code changed in 1 file:

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


* renamed include variables

2 lines of code changed in 1 file:

  • SL/SEQIO: 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/SEQIO: 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/SEQIO: 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/SEQIO: Makefile (+1 -1)
westram 2013-10-03 13:11 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 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/SEQIO: Makefile (+2)
westram 2013-05-13 15:41 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 16:33 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 13:24 Rev.: 9575


- effect of [9574] (comments only)

1 lines of code changed in 1 file:

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


- updated depends for [9520]

2 lines of code changed in 1 file:

  • SL/SEQIO: Makefile (+2)
westram 2013-02-09 12:16 Rev.: 9516


- reintegrated branch 'cxx11'

2 lines of code changed in 1 file:

  • SL/SEQIO: Makefile (+2)
westram 2012-11-23 19:15 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 18:58 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 18:47 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)
westram 2012-09-24 16:48 Rev.: 8939


* fix cppcheck warnings

1 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+1 -2)
westram 2012-06-15 12:50 Rev.: 8809


- use unistd.h (gcc 4.7 fix)

1 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+1)
westram 2012-04-19 09:13 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 1 file:

  • SL/SEQIO: seq_export.cxx (changed)
westram 2011-12-20 13:29 Rev.: 8309


* moved much code into static scope

(partly reverted by [8310])

2 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+2 -2)
westram 2011-11-29 18:42 Rev.: 8257


* removed unused(-but-set) variables/params

0 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (-3)
westram 2011-10-17 14:29 Rev.: 8103


merge from ptpan_back [8071] [8075] [8076] [8077] [8079]
* moved ARBDB/GB_system -> CORE/GBK_system
* moved basic file related functions from ARBDB to CORE
- GB_time_of_file (no longer automatically evaluates given path)

3 lines of code changed in 2 files:

  • SL/SEQIO: Makefile (+1), seq_export.cxx (+2 -1)
westram 2011-08-07 18:22 Rev.: 7800


merge from dev [7687] [7692] [7693] [7694] [7695] [7697] [7706] [7707] [7708]
* replaced 'char**' (heap-array of heap-char*) by new class !StrArray
- added several tests for !StrArray
- removed function flavours using element result parameter (e.g. GBT_get_tree_names_and_count)
* split !StrArray into !StrArray (heap), !ConstStrArray (just pointers) and base class (!CharPtrArray)
- use !ConstStrArray in several cases (e.g. config, tree and alignment names)
* GBT_split_string
- changed allocation: dups source and does destructive split (similar to strtok)
- returns !ConstStrArray instead of char**
- added destructive versions (GBT_splitNdestroy_string)
* refactored parsePositions / parseCSV using !ConstStrArray

6 lines of code changed in 1 file:

  • SL/SEQIO: seq_export.cxx (+6 -5)
westram 2011-07-28 11:18 Rev.: 7770


merge from dev [7679] [7683] [7684] [7685] [7686]
* ARBDB -> CORE
- functions handling string arrays
- adsort
* unit test for GBT_scan_db
* reorder item keys
- fixed crash/stupid warning message when moving beyond end of list
- added sorting (name, type, freq)
* removed obsolete default field (relict from old version showing groups in species information window)

2 lines of code changed in 2 files:

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

(12 more)

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