Lines of Code
[root]/CONSENSUS_TREE
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 345 (100.0%) | 7280 (100.0%) | 21.1 |
| westram | 328 (95.1%) | 5967 (82.0%) | 18.1 |
| oldcode | 16 (4.6%) | 1194 (16.4%) | 74.6 |
| meierh | 1 (0.3%) | 119 (1.6%) | 119.0 |
* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958
49 lines of code changed in 3 files:
* remove trailing whitespace from c source.
10 lines of code changed in 1 file:
* inline {{{SOURCES}}} where only used to generate list of objects.
1 lines of code changed in 1 file:
* reintegrates 'root' into 'trunk'
- implements #449
* adds: log:branches/root@18451:18633
1496 lines of code changed in 12 files:
* reintegrates 'svalues' into 'trunk'
- implements #614
* adds: log:branches/svalues@17357:17419,17428:17464,17469,17471:17477
2 lines of code changed in 2 files:
* 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:
* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109
11 lines of code changed in 3 files:
* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765
3 lines of code changed in 2 files:
* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751
35 lines of code changed in 7 files:
* 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
5 lines of code changed in 2 files:
* 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
5 lines of code changed in 1 file:
* 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
1 lines of code changed in 1 file:
* reintegrates 'mladd' into 'trunk'
- improves raxml8 interface
* new functions
- score tree (=calculate likelihood and append to comment)
- calculate branchlengths
- optimize tree
- add to tree (implements #681)
* calculate bootstraps (as separate function or combined with other functions)
- allow to skip bootstrap calculation
* writes comment to generated trees (similar to raxml7-interface)
* fix key-wait on terminate
* time all functions
* fix thread usage
- use 'distinct alignment patterns' (as reported by RAxML) to select maximum threads
- slightly reduce threads in favor of asynchronous bootstrapping
- allow to override (used) cores and used threads separate
- adds {{{arb_write_tree_comment}}}
* adds: log:branches/mladd@15394,15396,15398:15424
1 lines of code changed in 1 file:
* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175
23 lines of code changed in 6 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
61 lines of code changed in 6 files:
* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442
1 lines of code changed in 1 file:
* reintegrates 'fix' into 'trunk'
- slightly changes consensus tree generation
* adds:
- log:branches/fix@12008,12012:12013
8 lines of code changed in 2 files:
* merge [12008:12011] from 'fix' into 'trunk'
- fix broken double_cmp
* adds:
- log:branches/fix@12009:12011
4 lines of code changed in 3 files:
* reintegrates 'tree' into 'trunk'
- implements #417 (multifurcate tree)
- tree display
* adds MULTIFURC MODE
* reordered modes (synchronizes NTREE and PARSIMONY)
- branch analysis
* display number of multifurcations in 'mark long branches'
* display "in-tree-distance" and "per-species-distance"
- added function to toggle '100%' bootstraps
- document bug in GBT_remove_leafs (#452)
* adds:
- log:branches/tree@11425:11487
5 lines of code changed in 4 files:
- fix compiler warnings
1 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
725 lines of code changed in 11 files:
* use cflags before cxxflags
1 lines of code changed in 1 file:
- fix struct/class mismatches
6 lines of code changed in 1 file:
* renamed include variables
1 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)
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)
12 lines of code changed in 1 file:
* changed dynamic value-initializations into default-initializations
- i believe/know they were used with ignorance of [http://stackoverflow.com/questions/620137/do-the-parentheses-after-the-type-name-make-a-difference-with-new?answertab=active#tab-top ctor-behavior].
1 lines of code changed in 1 file:
- effect of [9574] (comments only)
1 lines of code changed in 1 file:
- updated depends for [9520]
6 lines of code changed in 1 file:
- reintegrated branch 'cxx11'
6 lines of code changed in 1 file:
* doxygen
- fixed warnings about undocumented parameters
1 lines of code changed in 1 file:
* rename unit test macros
- TEST_ASSERT.. -> TEST_EXPECT..
17 lines of code changed in 1 file:
- fixed some warnings in NDEBUG mode (unused warnings)
4 lines of code changed in 1 file:
* moved code from arb_consensus_tree -> class !ConsensusTreeBuilder
77 lines of code changed in 1 file:
* [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:
* use double for weights ([0..1] instead of [0..10000])
* added tests using weights != 1
- fixed weight/length calculation to make generated consense tree independent from used weight (as long as the same weight is used for all added trees)
* no longer generates zero-bootstrap at root
- strictly speaking it is wrong now (since the edge from virtual root to tree cant exist, ergo it's probability should be zero)
- practically
* that zero probability would be a special case (and is an error at all other edges)
* a probability of 100% is used (which gets skipped when saving the tree)
56 lines of code changed in 9 files:
* correctly round branch probabilities
4 lines of code changed in 1 file:
* replaced hash+list by set+vector
* weight parts via ctor
153 lines of code changed in 10 files:
* elim last global from CT_rbtree.cxx
- now multiple !ConsensusTree can be used at the same time
35 lines of code changed in 5 files:
(68 more)