Directory SL/ARB_TREE/

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westram 2022-03-04 12:26 Rev.: 18959

* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958

1 lines of code changed in 1 file:

• SL/ARB_TREE: Makefile (+1)

westram 2021-09-15 13:37 Rev.: 18724

* directly use {{{OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/ARB_TREE: Makefile (+1 -2)

westram 2021-09-15 13:31 Rev.: 18723

* remove .c rules.
* add .c suffix (in SOURCE_TOOLS).

1 lines of code changed in 1 file:

• SL/ARB_TREE: Makefile (+1 -4)

westram 2021-09-15 13:00 Rev.: 18720

* select units using {{{wildcard}}}.

1 lines of code changed in 1 file:

• SL/ARB_TREE: Makefile (+1 -1)

westram 2021-09-15 12:53 Rev.: 18718

* eliminate unused {{{C_OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/ARB_TREE: Makefile (+1 -2)

westram 2019-05-10 13:57 Rev.: 17877

* reintegrates 'gcc' into 'trunk'
* adds: log:branches/gcc@17850:17876

13 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.hxx (+13 -3)

westram 2018-06-15 13:08 Rev.: 17110

* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109

7 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.cxx (+7 -7)

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

10 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.hxx (+10 -6)

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

20 lines of code changed in 2 files:

• SL/ARB_TREE: ARB_Tree.cxx (+13 -13), ARB_Tree.hxx (+7 -7)

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

3 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.hxx (+3 -1)

westram 2016-08-11 11:05 Rev.: 15176

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

2 lines of code changed in 2 files:

• SL/ARB_TREE: ARB_Tree.hxx (+1 -1), Makefile (+1)

westram 2016-07-14 15:15 Rev.: 15054

* reintegrates 'color' into 'trunk'
- implements #443 (+parts of #444)
* adds: log:branches/color@14920:14921,14923:14928,14930:14939,14941:14951,14954:14956,14958:14959,14961:14964,14968,14970:14981,14985,14988,14990:14992,14994:14999,15001:15004,15007,15009,15012:15026,15028:15035,15037:15039,15041:15053

1 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.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

21 lines of code changed in 4 files:

• SL/ARB_TREE: ARB_Tree.cxx (+3 -4), ARB_Tree.hxx (+17 -8), Makefile (+1 -1), needs_libs (-1)

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/ARB_TREE: Makefile (+2 -2)

westram 2014-11-06 15:51 Rev.: 13134

- fix warnings reported by NDEBUG compilation

1 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.cxx (+1 -1)

westram 2014-04-30 14:36 Rev.: 12138

* reintegrates 'fix' into 'trunk'
- fixes #522
* adds:
- log:branches/fix@12058:12137

14 lines of code changed in 2 files:

• SL/ARB_TREE: ARB_Tree.cxx (+13 -9), ARB_Tree.hxx (+1 -1)

westram 2014-04-29 13:46 Rev.: 12121

* reintegrates 'tree' into 'trunk'
- fixes #527
* adds:
- log:branches/tree@12116:12120

6 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.hxx (+6)

westram 2014-03-25 11:53 Rev.: 11888

- highlight differences in production code triggered by build-flag 'UNIT_TESTS'

1 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.hxx (+1 -1)

westram 2014-01-20 17:08 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

2 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.cxx (+2 -3)

westram 2014-01-04 14:48 Rev.: 11423

* reintegrates 'tree' into 'trunk':
- topology ordering (beautify trees):
* new orders for radial trees
* order tree according to other tree (implements #445)
- tweaked 'Move node info' / 'Compare topology' (implements #450)
* write log entry to tree comment
* verbose output into logfile
* updated help and GUI
* adds:
- log:branches/tree@11403:11422

1 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.cxx (+1 -1)

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

106 lines of code changed in 4 files:

• SL/ARB_TREE: ARB_Tree.cxx (+62 -180), ARB_Tree.hxx (+42 -225), Makefile (+1), needs_libs (+1)

westram 2013-11-02 21:14 Rev.: 11042

* use typed DB callbacks (tree related)

8 lines of code changed in 2 files:

• SL/ARB_TREE: ARB_Tree.cxx (+7 -9), ARB_Tree.hxx (+1 -1)

westram 2013-11-02 17:41 Rev.: 11034

* depends for [11033]

1 lines of code changed in 1 file:

• SL/ARB_TREE: Makefile (+1)

westram 2013-11-01 15:50 Rev.: 11023

* publish DB callback interface separately from rest of DB interface

7 lines of code changed in 2 files:

• SL/ARB_TREE: ARB_Tree.cxx (+2), Makefile (+5)

westram 2013-10-31 16:40 Rev.: 11002

* 'class { public' -> struct

1 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.hxx (+1 -2)

westram 2013-10-31 15:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• SL/ARB_TREE: Makefile (+1 -1)

westram 2013-10-30 16:58 Rev.: 10974

* renamed include variables

2 lines of code changed in 1 file:

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

westram 2013-02-13 13:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• SL/ARB_TREE: Makefile (+1 -1)

westram 2013-02-11 12:35 Rev.: 9533

* use explicit override
- rest

3 lines of code changed in 2 files:

• SL/ARB_TREE: ARB_Tree.cxx (+1 -1), ARB_Tree.hxx (+2 -2)

westram 2013-02-10 18:14 Rev.: 9529

* slightly refactored tree accessors

11 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.hxx (+11 -9)

westram 2013-02-10 17:02 Rev.: 9527

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

1 lines of code changed in 1 file:

• SL/ARB_TREE: Makefile (+1)

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)

1 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.hxx (+1 -1)

westram 2013-02-09 13:52 Rev.: 9521

- updated depends for [9520]

1 lines of code changed in 1 file:

• SL/ARB_TREE: Makefile (+1)

westram 2013-02-09 12:16 Rev.: 9516

- reintegrated branch 'cxx11'

1 lines of code changed in 1 file:

• SL/ARB_TREE: Makefile (+1)

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/ARB_TREE: ARB_Tree.cxx (changed), ARB_Tree.hxx (changed)

westram 2012-03-16 18:28 Rev.: 8493

* rename

1 lines of code changed in 1 file:

• SL/ARB_TREE: ARB_Tree.cxx (+1 -1)

westram 2011-08-30 18:07 Rev.: 7913

* fix cluster naming
- 'append to name'
* had no effect
* renamed into 'append original'
* appends '{was:ORIGINALNAME}'
- when removing/re-crating clusternames, always consider such "originalname"
* added class ARB_tree_predicate
* fixed ARB_countedTree::relative_position_in
- assertion failed when testing group vs self; now returns 0

14 lines of code changed in 2 files:

• SL/ARB_TREE: ARB_Tree.cxx (+6 -4), ARB_Tree.hxx (+8)

(23 more)