Directory SL/MATRIX/

Total Files:
4
Deleted Files:
0
Lines of Code:
336

[root]/SL/MATRIX

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SL/MATRIX/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
westram 50 (100.0%) 326 (100.0%) 6.5

Most Recent Commits

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

2 lines of code changed in 1 file:

  • SL/MATRIX: AP_matrix.hxx (+2 -2)
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

5 lines of code changed in 2 files:

  • SL/MATRIX: AP_matrix.cxx (+3 -3), AP_matrix.hxx (+2 -2)
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/MATRIX: AP_matrix.cxx (+1 -1)
westram 2017-01-09 16:10 Rev.: 15529


* reintegrates 'warnings' into 'trunk'
- use gnu++14-standard for gcc>=6
- use gnu++0x-standard for gcc<4.7 (bugfix)
- defines many inlines as constexpr
* adds: log:branches/warnings@15515:15522,15525:15528

1 lines of code changed in 1 file:

  • SL/MATRIX: AP_matrix.hxx (+1 -1)
westram 2016-08-11 11:05 Rev.: 15176


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

8 lines of code changed in 3 files:

  • SL/MATRIX: AP_matrix.cxx (+4 -4), AP_matrix.hxx (+3 -3), Makefile (+1)
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

62 lines of code changed in 2 files:

  • SL/MATRIX: AP_matrix.cxx (+38 -32), AP_matrix.hxx (+24 -9)
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/MATRIX: Makefile (+2 -2)
westram 2014-04-16 16:13 Rev.: 12043


* reintegrates 'fix' into 'trunk' (fixes #519)
- this patch wasn't really straightforward, instead each change caused new unexpected side effects. It's quite likely that i didn't detect all of them.
* adds:
- log:branches/fix@12023,12027:12042

4 lines of code changed in 1 file:

  • SL/MATRIX: AP_matrix.hxx (+4)
westram 2013-12-26 13:48 Rev.: 11401


* reintegrates 'tree' into 'trunk':
- consensus trees:
* support for merging partial trees ("worked" before, but results were crap; implements #65)
* generated trees are automatically re-rooted and -ordered
* always list source trees in consensus-tree-comment; show info about partial trees
* fixed progress bar
- made GBT_TREE a base class of other tree classes (implements #31)
- save tree properties in properties (not in DB)
- new functions 'Remove zombies/marked from ALL trees'
- tree load/save: layout fixes
- unit tests
* added tests for basic tree modifications (PARSIMONY)
- performance:
* compute_tree updates tree information in one traversal
* tree generators are now capable to generate any type of tree (w/o needing to copy it once)
- bugfixes:
* NNI (of marked species) was also always performed for colored species
* centered beautify-order is stable now
* improved 'search optimal root'
* adds:
- log:branches/tree@10500:10534,10542:11182,11184:11186,11188:11400
- log:branches/treeTests@11198:11335

40 lines of code changed in 2 files:

  • SL/MATRIX: AP_matrix.cxx (+22 -8), AP_matrix.hxx (+18 -5)
westram 2013-11-02 17:41 Rev.: 11034


* depends for [11033]

1 lines of code changed in 1 file:

  • SL/MATRIX: Makefile (+1)
westram 2013-10-31 15:10 Rev.: 10996


* use cflags before cxxflags

1 lines of code changed in 1 file:

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


* renamed include variables

2 lines of code changed in 1 file:

  • SL/MATRIX: 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/MATRIX: 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/MATRIX: 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/MATRIX: Makefile (+1 -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)

1 lines of code changed in 1 file:

  • SL/MATRIX: Makefile (+1)
westram 2013-07-04 16:49 Rev.: 10212


* depends for recent patches

3 lines of code changed in 1 file:

  • SL/MATRIX: Makefile (+3)
westram 2013-02-13 13:24 Rev.: 9575


- effect of [9574] (comments only)

1 lines of code changed in 1 file:

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


- updated depends for [9520]

1 lines of code changed in 1 file:

  • SL/MATRIX: Makefile (+1)
westram 2013-02-09 12:16 Rev.: 9516


- reintegrated branch 'cxx11'

1 lines of code changed in 1 file:

  • SL/MATRIX: Makefile (+1)
westram 2012-09-24 15:47 Rev.: 8937


* AP_matrix (made members private)

22 lines of code changed in 2 files:

  • SL/MATRIX: AP_matrix.cxx (+6 -21), AP_matrix.hxx (+16 -8)
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 2 files:

  • SL/MATRIX: AP_matrix.cxx (changed), AP_matrix.hxx (changed)
westram 2012-04-11 13:19 Rev.: 8574


* [8567] failed on WCs where shared libs were up-to-date, but not yet present in $ARBHOME/lib
- link libs directly in $ARBHOME/lib
* no longer create 'SHARED.a' in shared-library-dirs
* unit tests caused build of 'SHARED.so' (instead of 'libSHARED.so'). Every library existed twice.
- changed test-target-names for shared libaries (e.g. ARBDB/ARBDB.test -> ARBDB/libARBDB.test)
- added failing stopper targets to main-Makefile and shared-lib-Makefiles
* changed all dependencies to shared libs
* fixed dependency scripts to perform correct translations from lib/libUNIT.so <-> UNIT/UNIT.(dummy|a). omg :/
* updated predefined RESTRICT_LIB entries in UNIT_TESTER/Makefile.setup.template
- check whether RESTRICT_LIB uses obsolete test-names (e.g. ARBDB instead of libARBDB) and fail if.

1 lines of code changed in 1 file:

  • SL/MATRIX: needs_libs (+1 -1)
westram 2011-06-10 15:50 Rev.: 7623


- merge from dev [7450] [7452] [7456] [7457] [7458] [7459] [7460] [7461] [7464] [7465] [7466] [7467] [7468] [7469] [7482]
* tweaked compiler options
- activated -Weffc++
* postfilter warnings where Scott Meyers' advices are too general.
- base classes should not always have virtual destructors, since that renders tiny classes useless and
- members should not always be initialized via initialization list, since that often violates the DRY principle
* fix gcc's inability to detect that Noncopyable implements a private copy-ctor and op=
* this slows down complete ARB recompilation by ~5%
- added -Wold-style-cast (inactive)
- removed -Wno-non-template-friend added in [7447]
* postcompile.pl
- added option --original to show unmodified compiler output
* declared op= for classes which had a copy-ctor
* moved op= macros to arbtools.h
* derived classes containing pointers from Noncopyable (use Noncopyable virtually) or
* made them copyable if needed (awt_mask_item, KnownDB, Code, AWT_registered_itemtype, GEN_gene, !PosGene, !PartialSequence, !PlugIn, Range, Convaln_exception)
* other related changes
- user mask destruction working now

11 lines of code changed in 1 file:

  • SL/MATRIX: AP_matrix.hxx (+11 -4)
westram 2011-02-23 14:37 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/MATRIX: Makefile (+2 -1)
westram 2010-09-18 17:39 Rev.: 6868


- updated prototypes and dependencies

3 lines of code changed in 1 file:

  • SL/MATRIX: Makefile (+3 -2)
westram 2010-09-18 17:32 Rev.: 6867


* ARB GUI (merges [6844] [6845] [6847] [6858] [6861] from refactor)
* new central header cb.h (planned to define ALL callbacks used in ARB here later)
* refactored callback handling for some AW_root callbacks
- AW_root_callback hides function ptr + arguments
- AW_root_cblist hides lists of AW_root_callback
* DRYed AW_RCB
* reduced tight coupling between some of WINDOW/*.hxx (omg)
* removed AWUSE

2 lines of code changed in 1 file:

  • SL/MATRIX: AP_matrix.cxx (+2)
westram 2010-09-18 17:20 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/MATRIX: Makefile (+2 -2)
westram 2010-09-09 22:49 Rev.: 6817


- depends for [6816]

1 lines of code changed in 1 file:

  • SL/MATRIX: Makefile (+1)
westram 2010-09-09 20:25 Rev.: 6814


* depends updated for [6812] + [6813]

1 lines of code changed in 1 file:

  • SL/MATRIX: Makefile (+1)
westram 2010-05-14 13:58 Rev.: 6659


* free()
- removed unneeded casts of argument
- removed unneeded if-clauses

7 lines of code changed in 1 file:

  • SL/MATRIX: AP_matrix.cxx (+7 -11)
westram 2010-02-17 10:30 Rev.: 6448


- added library dependency declarations

4 lines of code changed in 1 file:

  • SL/MATRIX: needs_libs (new 4)
westram 2010-01-27 10:08 Rev.: 6383


- removed void

4 lines of code changed in 2 files:

  • SL/MATRIX: AP_matrix.cxx (+2 -2), AP_matrix.hxx (+2 -2)
westram 2010-01-27 09:05 Rev.: 6381


- fixed includes
- added MBI headers
- removed unused files

9 lines of code changed in 1 file:

  • SL/MATRIX: AP_matrix.cxx (+9 -1)
westram 2010-01-21 17:49 Rev.: 6366


* fixed whitespace (scripted)

60 lines of code changed in 3 files:

  • SL/MATRIX: AP_matrix.cxx (+54 -54), AP_matrix.hxx (new)
westram 2010-01-12 20:00 Rev.: 6345


- fixed hard readable '} else {'

2 lines of code changed in 2 files:

  • SL/MATRIX: AP_matrix.cxx (+2 -1)
westram 2010-01-07 15:07 Rev.: 6331


* removed GB_strdup
* moved freeset, nulldup, etc to own header (dupstr.h)
* added freenull
- replacement for freeset(var,NULL)
- freeset is a template now and does no longer work with NULL/0
- replaced all occurrances

1 lines of code changed in 1 file:

  • SL/MATRIX: Makefile (+1)
westram 2009-11-25 17:02 Rev.: 6280


* merge clusters branch back to trunk
- merged log:branches/clusters@6218:6261 at [6268]
- merged [6276] + [6278] at [6279]

54 lines of code changed in 2 files:

  • SL/MATRIX: Makefile (+54)
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