Directory CONSENSUS_TREE/

Directory Created:
2000-11-23 10:41
Total Files:
13
Deleted Files:
5
Lines of Code:
2235

[root]/CONSENSUS_TREE

Lines of Code

CONSENSUS_TREE/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 328 (100.0%) 5724 (100.0%) 17.4
westram 311 (94.8%) 4411 (77.1%) 14.1
oldcode 16 (4.9%) 1194 (20.9%) 74.6
meierh 1 (0.3%) 119 (2.1%) 119.0

Most Recent Commits

westram 2018-10-17 10:00 Rev.: 17478


* 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:

  • CONSENSUS_TREE: CT_ctree.cxx (+1 -1), CT_ctree.hxx (+1 -1)
westram 2018-07-23 15:52 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:

  • CONSENSUS_TREE: CT_ctree.cxx (+1 -1)
westram 2018-06-15 12:08 Rev.: 17110


* 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:

  • CONSENSUS_TREE: CT_ctree.hxx (+1 -1), CT_dtree.cxx (+5 -5), CT_rbtree.cxx (+5 -5)
westram 2017-11-28 18:22 Rev.: 16766


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

3 lines of code changed in 2 files:

  • CONSENSUS_TREE: CT_ctree.hxx (+1 -2), CT_ntree.cxx (+2 -3)
westram 2017-11-28 17:09 Rev.: 16763


* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

35 lines of code changed in 7 files:

  • CONSENSUS_TREE: CT_ctree.cxx (+9 -9), CT_ctree.hxx (+2 -2), CT_dtree.cxx (+2 -2), CT_hash.cxx (+3 -3), CT_ntree.cxx (+12 -12), CT_part.cxx (+3 -3), CT_rbtree.cxx (+4 -4)
westram 2017-11-06 13:54 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

5 lines of code changed in 2 files:

  • CONSENSUS_TREE: CT_part.cxx (+4 -4), CT_part.hxx (+1 -1)
westram 2017-01-09 15:10 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

5 lines of code changed in 1 file:

  • CONSENSUS_TREE: CT_part.hxx (+5 -4)
westram 2017-01-04 17:06 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

1 lines of code changed in 1 file:

  • CONSENSUS_TREE: CT_ctree.hxx (+1 -1)
westram 2016-12-17 12:12 Rev.: 15425


* 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:

  • CONSENSUS_TREE: CT_ctree.cxx (+1 -1)
westram 2016-08-11 10:05 Rev.: 15176


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

23 lines of code changed in 6 files:

  • CONSENSUS_TREE: CT_mem.cxx (del), CT_mem.hxx (del), CT_ntree.cxx (+3 -3), CT_part.hxx (+4 -4), CT_rbtree.cxx (+4 -4), Makefile (+12 -11)
westram 2015-03-29 11:47 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

61 lines of code changed in 6 files:

  • CONSENSUS_TREE: CT_ctree.cxx (+1 -1), CT_ctree.hxx (+24 -15), CT_dtree.cxx (+20 -20), CT_rbtree.cxx (+11 -11), Makefile (+4 -4), needs_libs (+1 -1)
westram 2015-01-23 14:19 Rev.: 13443


* 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:

  • CONSENSUS_TREE: Makefile (+1 -1)
westram 2014-04-13 13:39 Rev.: 12014


* reintegrates 'fix' into 'trunk'
- slightly changes consensus tree generation
* adds:
- log:branches/fix@12008,12012:12013

8 lines of code changed in 2 files:

  • CONSENSUS_TREE: CT_part.cxx (+4 -2), CT_rbtree.cxx (+4 -2)
westram 2014-04-13 13:31 Rev.: 12013


* 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:

  • CONSENSUS_TREE: CT_def.hxx (-5), CT_part.cxx (+2 -2), CT_rbtree.cxx (+2 -2)
westram 2014-01-20 16:08 Rev.: 11488


* 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:

  • CONSENSUS_TREE: CT_ctree.cxx (+1 -1), CT_hash.cxx (+2 -2), CT_part.hxx (-6), CT_rbtree.cxx (+2 -19)
westram 2014-01-14 14:42 Rev.: 11471


- fix compiler warnings

1 lines of code changed in 1 file:

  • CONSENSUS_TREE: CT_part.cxx (+1 -1)
westram 2013-12-26 12:48 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

725 lines of code changed in 11 files:

  • CONSENSUS_TREE: CT_ctree.cxx (+107 -15), CT_ctree.hxx (+116 -23), CT_dtree.cxx (+103 -23), CT_hash.cxx (+121 -13), CT_hash.hxx (+21 -3), CT_ntree.cxx (+74 -33), CT_part.cxx (+81 -53), CT_part.hxx (+62 -15), CT_rbtree.cxx (+29 -24), Makefile (+10), needs_libs (+1 -1)
westram 2013-10-31 14:10 Rev.: 10996


* use cflags before cxxflags

1 lines of code changed in 1 file:

  • CONSENSUS_TREE: Makefile (+1 -1)
westram 2013-10-31 11:44 Rev.: 10991


- fix struct/class mismatches

6 lines of code changed in 1 file:

  • CONSENSUS_TREE: CT_ctree.hxx (+6 -6)
westram 2013-10-30 15:58 Rev.: 10974


* renamed include variables

1 lines of code changed in 1 file:

  • CONSENSUS_TREE: Makefile (+1 -1)
westram 2013-10-29 12:55 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:

  • CONSENSUS_TREE: Makefile (+1 -1)
westram 2013-10-29 12:23 Rev.: 10955


- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

1 lines of code changed in 1 file:

  • CONSENSUS_TREE: Makefile (+1 -1)
westram 2013-09-09 15:36 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)

12 lines of code changed in 1 file:

  • CONSENSUS_TREE: Makefile (+12)
westram 2013-06-04 14:20 Rev.: 10113


* 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:

  • CONSENSUS_TREE: CT_ctree.cxx (+1 -1)
westram 2013-02-13 12:24 Rev.: 9575


- effect of [9574] (comments only)

1 lines of code changed in 1 file:

  • CONSENSUS_TREE: Makefile (+1 -1)
westram 2013-02-09 12:52 Rev.: 9521


- updated depends for [9520]

6 lines of code changed in 1 file:

  • CONSENSUS_TREE: Makefile (+6)
westram 2013-02-09 11:16 Rev.: 9516


- reintegrated branch 'cxx11'

6 lines of code changed in 1 file:

  • CONSENSUS_TREE: Makefile (+6)
westram 2012-11-27 11:17 Rev.: 9233


* doxygen
- fixed warnings about undocumented parameters

1 lines of code changed in 1 file:

  • CONSENSUS_TREE: CT_ctree.cxx (+1 -1)
westram 2012-11-23 17:58 Rev.: 9225


* rename unit test macros
- TEST_ASSERT.. -> TEST_EXPECT..

17 lines of code changed in 1 file:

  • CONSENSUS_TREE: CT_part.cxx (+17 -17)
westram 2012-06-15 14:35 Rev.: 8814


- fixed some warnings in NDEBUG mode (unused warnings)

4 lines of code changed in 1 file:

  • CONSENSUS_TREE: CT_part.cxx (+4)
westram 2012-04-14 14:14 Rev.: 8585


* moved code from arb_consensus_tree -> class !ConsensusTreeBuilder

77 lines of code changed in 1 file:

  • CONSENSUS_TREE: CT_ctree.hxx (+77)
westram 2012-04-11 12:19 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:

  • CONSENSUS_TREE: needs_libs (+1 -1)
westram 2012-03-20 12:03 Rev.: 8507


* 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:

  • CONSENSUS_TREE: CT_ctree.cxx (+1 -1), CT_ctree.hxx (+4 -4), CT_def.hxx (+4), CT_dtree.cxx (+5 -9), CT_hash.cxx (+2 -2), CT_hash.hxx (+2 -2), CT_part.cxx (+4 -7), CT_part.hxx (+31 -16), CT_rbtree.cxx (+3 -7)
westram 2012-03-20 10:08 Rev.: 8506


* correctly round branch probabilities

4 lines of code changed in 1 file:

  • CONSENSUS_TREE: CT_rbtree.cxx (+4 -4)
westram 2012-03-20 08:04 Rev.: 8505


* replaced hash+list by set+vector
* weight parts via ctor

153 lines of code changed in 10 files:

  • CONSENSUS_TREE: CT_ctree.cxx (+9 -10), CT_ctree.hxx (+1 -1), CT_dtree.cxx (+6 -7), CT_dtree.hxx (del), CT_hash.cxx (+29 -185), CT_hash.hxx (+21 -16), CT_ntree.cxx (+2 -7), CT_part.cxx (+68 -7), CT_part.hxx (+17 -6), Makefile (-2)
westram 2012-03-15 11:32 Rev.: 8490


* 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:

  • CONSENSUS_TREE: CT_ctree.cxx (+5 -11), CT_ctree.hxx (+16 -2), CT_rbtree.cxx (+11 -26), CT_rbtree.hxx (del), Makefile (+3 -2)
westram 2012-03-15 11:11 Rev.: 8489


* moved globals from CT_hash.cxx into class !PartRegistry
* increased hash size

52 lines of code changed in 5 files:

  • CONSENSUS_TREE: CT_ctree.cxx (+11 -9), CT_ctree.hxx (+4 -1), CT_dtree.cxx (+3 -3), CT_hash.cxx (+19 -28), CT_hash.hxx (+15 -6)
westram 2012-03-15 08:36 Rev.: 8488


* move globals from CT_part.cxx into class !PartitionSize
* class PART
- private member variables
- moved many global methods into
- stores und updates member-count

339 lines of code changed in 10 files:

  • CONSENSUS_TREE: CT_ctree.cxx (+7 -5), CT_ctree.hxx (+1), CT_dtree.cxx (+10 -9), CT_hash.cxx (+27 -28), CT_ntree.cxx (+45 -52), CT_ntree.hxx (+1 -2), CT_part.cxx (+123 -171), CT_part.hxx (+120 -24), CT_rbtree.cxx (+3 -4), Makefile (+2)
westram 2012-03-14 13:08 Rev.: 8482


* new class !ConsensusTree
- moved globals from CT_ctree.cxx there
- clients use class !ConsensusTree

53 lines of code changed in 5 files:

  • CONSENSUS_TREE: CT_ctree.cxx (+19 -44), CT_ctree.hxx (+28 -7), CT_dtree.cxx (+2 -3), CT_hash.cxx (+3 -4), CT_hash.hxx (+1 -2)
westram 2012-03-14 09:54 Rev.: 8481


* define a strict order on partitions. criteria are
- partition-freq / "leaf-edgeness"
- min. edge->tip distance
- branchlen to subtree
- unique partition id
* insert partitions in that order + strictly sort sons at furcations
- generated trees no longer depend on hashkey, hence it no longer depends on names-order
- removed code to sort names before tree-generation
- removed code to sort trees afterwards
* insert leaf-edges as final step (they always fit)
* do not insert root-edge as final-step (often a leaf edge was used)
- instead insert it as first step (using the most-probable non-leaf-edge as root-edge)
* updated test-results
* removed ARB-legend from help
- there never was any smart method which removed "wandering" species from consensus trees, it just was an ancient bug

208 lines of code changed in 11 files:

  • CONSENSUS_TREE: CT_ctree.cxx (+2 -24), CT_def.hxx (+2 -3), CT_dtree.cxx (+1), CT_hash.cxx (+80 -18), CT_ntree.cxx (+38 -9), CT_ntree.hxx (+3 -3), CT_part.cxx (+21 -11), CT_part.hxx (+5 -1), CT_rbtree.cxx (+53 -2), CT_rbtree.hxx (+1 -1), Makefile (+2)

(64 more)

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