Lines of Code
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 144 (100.0%) | 1102 (100.0%) | 7.6 |
| westram | 141 (97.9%) | 1003 (91.0%) | 7.1 |
| epruesse | 3 (2.1%) | 99 (9.0%) | 33.0 |
* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958
4 lines of code changed in 1 file:
* remove trailing whitespace from c source.
1 lines of code changed in 1 file:
* directly use {{{OBJECTS}}}.
1 lines of code changed in 1 file:
* remove .c rules.
* add .c suffix (in SOURCE_TOOLS).
1 lines of code changed in 1 file:
* eliminate unused {{{C_OBJECTS}}}.
1 lines of code changed in 1 file:
* 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
5 lines of code changed in 1 file:
* 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:
* 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:
* 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:
* 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:
* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765
6 lines of code changed in 4 files:
* 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:
* 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:
* 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:
* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175
6 lines of code changed in 2 files:
* 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:
* full update from child 'pars' into 'trunk'
- cleanup patches
* adds:
- log:branches/pars@13628:13638
1 lines of code changed in 3 files:
* 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:
* 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:
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:
* [12967] got reverted by 'make proto'. fixed.
2 lines of code changed in 2 files:
(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:
use arb_alloc_aligned to allocate seq_pars char*
7 lines of code changed in 1 file:
* merge from 'alilink' into 'trunk'
* adds:
- log:branches/alilink@12801:12802
1 lines of code changed in 1 file:
- 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:
* 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:
* undo todays clang-inspired bogus-patches concerning char-indices
2 lines of code changed in 1 file:
* use cflags before cxxflags
1 lines of code changed in 1 file:
* fix misc warnings (char index, extra parens, trap via NULL ptr indirection, ...)
2 lines of code changed in 1 file:
* renamed include variables
2 lines of code changed in 1 file:
* 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:
- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)
2 lines of code changed in 1 file:
- document mechanism used by ARB to export variables to submakefiles
- document most important variables
1 lines of code changed in 1 file:
- 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:
- effect of [9574] (comments only)
1 lines of code changed in 1 file:
* use explicit override
- rest
18 lines of code changed in 3 files:
- include static_assert.h in downcast.h (fixed includes; updated depends)
3 lines of code changed in 1 file:
- 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:
- updated depends for [9520]
4 lines of code changed in 1 file:
- reintegrated branch 'cxx11'
4 lines of code changed in 1 file:
(26 more)