Directory SL/SEQUENCE/

Total Files:
10
Deleted Files:
1
Lines of Code:
1757

[root]/SL/SEQUENCE

Lines of Code

SL/SEQUENCE/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 138 (100.0%) 1089 (100.0%) 7.8
westram 135 (97.8%) 990 (90.9%) 7.3
epruesse 3 (2.2%) 99 (9.1%) 33.0

Most Recent Commits

westram 2018-10-31 10:52 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

3 lines of code changed in 1 file:

  • SL/SEQUENCE: AP_seq_protein.hxx (+3 -2)
westram 2018-07-10 16:48 Rev.: 17178


* reintegrates 'gcc' into 'trunk'
- complete arb port to gcc 8.1
- fixes NDEBUG-related issues (not handled by [16986])
* adds: log:branches/gcc@17164:17177

1 lines of code changed in 1 file:

  • SL/SEQUENCE: AP_seq_dna.cxx (+1 -1)
westram 2018-04-11 16:48 Rev.: 16880


* reintegrates 'multicore' into 'trunk'
- derive sequence classes able to be combined from new class {{{AP_combinableSeq}}}
* elim dummy functions from rest of hierarchy
- implements non-writing combine for add-species (speedup: 25-35%)
- introduce type {{{Mutations}}} => uses long everywhere (before mostly, but not always used float)
- allows use of {{{future}}}s
* nucleotide combine is able to calculate async (disabled via define atm -> {{{NEVER_COMBINE_ASYNC}}}; needs more work on calling algorithm)
* adds: log:branches/multicore@16769:16879

255 lines of code changed in 8 files:

  • SL/SEQUENCE: AP_seq_dna.cxx (+163 -58), AP_seq_dna.hxx (+6 -8), AP_seq_protein.cxx (+20 -25), AP_seq_protein.hxx (+6 -8), AP_seq_simple_pro.cxx (-25), AP_seq_simple_pro.hxx (-10), AP_sequence.cxx (+3 -3), AP_sequence.hxx (+57 -25)
westram 2018-02-15 12:51 Rev.: 16861


* reintegrates 'unittest' into 'trunk'
- fixed non-deterministic behavior of add-species:
* 2 sequences in test-DB were identical (changed 1 bp)
* {{{AP_tree_edge}}} cannot be used to store insert-positions (uses pair of {{{AP_tree_nlen}}} instead)
* corrected some undefined behavior (results did depend on compiler version+flags):
- general order of inserts was undefined
- order of initial-insert was undefined (used by complete tree reconstruction)
- bugs fixed:
* not all possible insert-positions were tested
* sometimes species were added at wrong positions
* if multiple species were inserted at the same position, the following optimization
- did modify topology
- now optimizes all multi-inserts globally
- at leaf-positions: includes the leaf (Note: this does not modify the original topology)
* insert order now is "longest sequence first" (was "shortest sequence first")
- fixed unwanted behavior when testing for content of generated files
* adds: log:branches/unittest@16807:16860

42 lines of code changed in 7 files:

  • SL/SEQUENCE: AP_seq_dna.cxx (+16), AP_seq_dna.hxx (+1), AP_seq_protein.cxx (+17), AP_seq_protein.hxx (+1), AP_seq_simple_pro.cxx (+5), AP_seq_simple_pro.hxx (+1), AP_sequence.hxx (+1)
westram 2017-11-28 19:22 Rev.: 16766


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

6 lines of code changed in 4 files:

  • SL/SEQUENCE: AP_seq_dna.cxx (+2 -4), AP_seq_protein.cxx (+1 -2), AP_seq_simple_pro.cxx (+2 -2), AP_sequence.cxx (+1 -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

33 lines of code changed in 7 files:

  • SL/SEQUENCE: AP_seq_dna.cxx (+6 -6), AP_seq_protein.cxx (+9 -9), AP_seq_protein.hxx (+1 -1), AP_seq_simple_pro.cxx (+2 -2), AP_seq_simple_pro.hxx (+1 -1), AP_sequence.cxx (+8 -8), AP_sequence.hxx (+6 -6)
westram 2017-01-04 18:06 Rev.: 15513


* reintegrates 'warnings' into 'trunk'
- activate additional warnings (gcc 5.x++)
- Cxx11-forward final (classes+methods)
- fix tag problems caused by using preprocessor
* adds: log:branches/warnings@15486:15489,15491:15501,15506:15512

2 lines of code changed in 2 files:

  • SL/SEQUENCE: AP_seq_dna.hxx (+1 -1), AP_seq_protein.hxx (+1 -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!)

1 lines of code changed in 1 file:

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


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

6 lines of code changed in 2 files:

  • SL/SEQUENCE: AP_seq_dna.cxx (+3 -3), Makefile (+3)
westram 2015-04-30 11:39 Rev.: 13788


* fix bug introduced with [12975]; {{{count_weighted}}} calculated wrong results:[[BR]]{{{(weights[idx] * (c==0)) ? 1 : 0}}} instead of[[BR]]{{{weights[idx] * ((c==0) ? 1 : 0)}}}[[BR]]'*' binds stronger than '?:'; guided to by clang warning
* replaced {{{(c==0)?1:0}}} by {{{!c}}} where possible and vectorized
* checked vectorization with gcc 4.8.1, 4.9.2 and 5.1.0

10 lines of code changed in 2 files:

  • SL/SEQUENCE: AP_seq_dna.cxx (+9 -7), Makefile (+1 -5)
westram 2015-03-30 10:28 Rev.: 13639


* full update from child 'pars' into 'trunk'
- cleanup patches
* adds:
- log:branches/pars@13628:13638

1 lines of code changed in 3 files:

  • SL/SEQUENCE: AP_seq_dna.cxx (-4), AP_seq_dna.hxx (-1), AP_seq_protein.hxx (+1 -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

445 lines of code changed in 10 files:

  • SL/SEQUENCE: AP_parsimony_defaults.hxx (del), AP_seq_dna.cxx (+52 -38), AP_seq_dna.hxx (+13 -1), AP_seq_protein.cxx (+309 -88), AP_seq_protein.hxx (+41 -24), AP_seq_simple_pro.cxx (+6 -1), AP_seq_simple_pro.hxx (+7), AP_sequence.cxx (+1 -1), AP_sequence.hxx (+13 -9), Makefile (+3 -5)
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

3 lines of code changed in 2 files:

  • SL/SEQUENCE: AP_seq_dna.cxx (+1 -1), Makefile (+2 -2)
epruesse 2014-09-30 15:28 Rev.: 12975

rewrote parsimony combine loop to be vectorizable by gcc
speedup through use of SSE instructions should be on the order of 2x-4x

85 lines of code changed in 1 file:

  • SL/SEQUENCE: AP_seq_dna.cxx (+85 -48)
westram 2014-09-30 14:24 Rev.: 12973


* [12967] got reverted by 'make proto'. fixed.

2 lines of code changed in 2 files:

  • SL/SEQUENCE: AP_seq_dna.cxx (+1 -1), Makefile (+1)
epruesse 2014-09-30 12:08 Rev.: 12970

(performance) use filteredpos to alignment pos table to pick bases from alignment for
un-bootstrapped parsimony instead of scanning the entire alignment. speeds up set up
time a lot.

7 lines of code changed in 1 file:

  • SL/SEQUENCE: AP_seq_dna.cxx (+7 -10)
epruesse 2014-09-30 12:02 Rev.: 12969

use arb_alloc_aligned to allocate seq_pars char*

7 lines of code changed in 1 file:

  • SL/SEQUENCE: AP_seq_dna.cxx (+7 -6)
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/SEQUENCE: AP_sequence.cxx (+1 -1)
westram 2014-07-08 12:23 Rev.: 12490


- treat dots as 'X' when combining ancestor sequences in ARB_PARSIMONY (protein sequences)
- previously dots where treated as gaps
- dna/rna combine always treated dots as 'N'
- thx to Yan Shi for tracking down that misbehavior
- fixes #144

5 lines of code changed in 1 file:

  • SL/SEQUENCE: AP_seq_protein.cxx (+5 -5)
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

3 lines of code changed in 1 file:

  • SL/SEQUENCE: Makefile (+3)
westram 2013-10-31 16:23 Rev.: 11001


* undo todays clang-inspired bogus-patches concerning char-indices

2 lines of code changed in 1 file:

  • SL/SEQUENCE: AP_seq_simple_pro.cxx (+2 -2)
westram 2013-10-31 15:10 Rev.: 10996


* use cflags before cxxflags

1 lines of code changed in 1 file:

  • SL/SEQUENCE: Makefile (+1 -1)
westram 2013-10-31 12:46 Rev.: 10992


* fix misc warnings (char index, extra parens, trap via NULL ptr indirection, ...)

2 lines of code changed in 1 file:

  • SL/SEQUENCE: AP_seq_simple_pro.cxx (+2 -2)
westram 2013-10-30 16:58 Rev.: 10974


* renamed include variables

2 lines of code changed in 1 file:

  • SL/SEQUENCE: 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/SEQUENCE: 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/SEQUENCE: 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/SEQUENCE: 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)

2 lines of code changed in 1 file:

  • SL/SEQUENCE: Makefile (+2)
westram 2013-02-13 13:24 Rev.: 9575


- effect of [9574] (comments only)

1 lines of code changed in 1 file:

  • SL/SEQUENCE: Makefile (+1 -1)
westram 2013-02-11 12:35 Rev.: 9533


* use explicit override
- rest

18 lines of code changed in 3 files:

  • SL/SEQUENCE: AP_seq_dna.hxx (+6 -6), AP_seq_protein.hxx (+6 -6), AP_seq_simple_pro.hxx (+6 -6)
westram 2013-02-10 17:02 Rev.: 9527


- include static_assert.h in downcast.h (fixed includes; updated depends)

3 lines of code changed in 1 file:

  • SL/SEQUENCE: Makefile (+3)
westram 2013-02-09 14:36 Rev.: 9522


- explicit override destructors of classes derived from virtual base classes
- skipped directories WINDOW and PROBE (should be done in branches gtk and ptsfix)

3 lines of code changed in 3 files:

  • SL/SEQUENCE: AP_seq_dna.hxx (+1 -1), AP_seq_protein.hxx (+1 -1), AP_seq_simple_pro.hxx (+1 -1)
westram 2013-02-09 13:52 Rev.: 9521


- updated depends for [9520]

4 lines of code changed in 1 file:

  • SL/SEQUENCE: Makefile (+4)
westram 2013-02-09 12:16 Rev.: 9516


- reintegrated branch 'cxx11'

4 lines of code changed in 1 file:

  • SL/SEQUENCE: Makefile (+4)
westram 2012-09-15 14:00 Rev.: 8887


* upcased names of several constants

2 lines of code changed in 1 file:

  • SL/SEQUENCE: AP_seq_simple_pro.hxx (+2 -2)
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 9 files:

  • SL/SEQUENCE: AP_parsimony_defaults.hxx (changed), AP_seq_dna.cxx (changed), AP_seq_dna.hxx (changed), AP_seq_protein.cxx (changed), AP_seq_protein.hxx (changed), AP_seq_simple_pro.cxx (changed), AP_seq_simple_pro.hxx (changed), AP_sequence.hxx (changed)
westram 2012-03-13 19:36 Rev.: 8479


* calculating bootstrap-trees with active filter
- now bootstraps filtered positions
- before it did bootstrap X random positions from the unfiltered alignment (with X=size of filter). That was more jackknifing than bootstrapping.

13 lines of code changed in 3 files:

  • SL/SEQUENCE: AP_seq_dna.cxx (+7 -8), AP_seq_protein.cxx (+1 -1), AP_seq_simple_pro.cxx (+5 -8)
westram 2011-08-08 01:06 Rev.: 7812


merge from dev [7751] [7752]
* updated many old-style typedefs (typedef struct/enum)

2 lines of code changed in 1 file:

  • SL/SEQUENCE: AP_seq_simple_pro.hxx (+2 -2)
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

4 lines of code changed in 4 files:

  • SL/SEQUENCE: AP_seq_dna.hxx (+1 -1), AP_seq_protein.hxx (+1 -1), AP_seq_simple_pro.hxx (+1 -1), AP_sequence.hxx (+1 -1)
westram 2011-04-16 11:33 Rev.: 7423


merged from dev [7320] [7418] [7419] [7420]
* !BasePosition
- uses int instead of size_t
- allow empty sequences (gap-only)
- allow to index just a part of a sequence
- use new class !CharPredicate to initialize custom gaps
* moved safeCharIndex() to dupstr.h
* unit tests
- collectIntFunResults (allowed range)
- slow test

0 lines of code changed in 2 files:

  • SL/SEQUENCE: AP_seq_dna.cxx (-1), Makefile (-1)

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