Directory SL/TREE_WRITE/

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westram 2022-11-13 15:47 Rev.: 19339

* reintegrates 'refactor' into 'trunk'
- eliminates old interface of {{{GBS_strstruct}}}
- add a few new unittests (editor-config string + some PT-SERVER-functions)
* adds: log:branches/refactor@19300:19338

8 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+8 -8)

westram 2022-03-04 11:26 Rev.: 18959

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

1 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+1)

westram 2021-12-20 17:44 Rev.: 18883

* reintegrates 'nds' into 'trunk'
- fixes #841
* adds: log:branches/nds@18843:18882

129 lines of code changed in 3 files:

• SL/TREE_WRITE: TreeLabeler.h (+5 -2), TreeWrite.cxx (+115 -84), TreeWrite.h (+9 -7)

westram 2021-09-15 12:37 Rev.: 18724

* directly use {{{OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+1 -2)

westram 2021-09-15 12:31 Rev.: 18723

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

1 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+1 -4)

westram 2021-09-15 12:00 Rev.: 18720

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

1 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+1 -1)

westram 2021-09-15 11:53 Rev.: 18718

* eliminate unused {{{C_OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+1 -2)

westram 2021-09-07 09:37 Rev.: 18704

* reintegrates 'tree' into 'trunk'
* adds: log:branches/tree@18666:18703

61 lines of code changed in 4 files:

• SL/TREE_WRITE: Makefile (+1), TreeLabeler.h (new 33), TreeWrite.cxx (+25 -32), TreeWrite.h (+2 -18)

westram 2021-08-17 14:15 Rev.: 18665

* change many WARN_TODO triggered warnings into todo markers.

1 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+1 -4)

westram 2018-08-30 09:58 Rev.: 17336

* typos
- some had ''two'' good language skills ;-)
- fix some plural forms

2 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+2 -2)

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

27 lines of code changed in 2 files:

• SL/TREE_WRITE: Makefile (+1), TreeWrite.cxx (+26 -10)

westram 2017-11-28 18:22 Rev.: 16766

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

1 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+1 -2)

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

18 lines of code changed in 2 files:

• SL/TREE_WRITE: TreeWrite.cxx (+15 -15), TreeWrite.h (+3 -3)

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:

• SL/TREE_WRITE: TreeWrite.cxx (+1 -1)

westram 2016-08-11 10:05 Rev.: 15176

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

3 lines of code changed in 2 files:

• SL/TREE_WRITE: Makefile (+1), TreeWrite.cxx (+2 -2)

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

26 lines of code changed in 3 files:

• SL/TREE_WRITE: Makefile (+1), TreeWrite.cxx (+23 -23), TreeWrite.h (+2 -2)

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

2 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+2 -2)

westram 2014-04-30 13:36 Rev.: 12138

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

1 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+1 -1)

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

26 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+26 -34)

westram 2014-01-10 19:16 Rev.: 11464

- un-dummy-fied transaction (renames only)

2 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+2 -2)

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

3 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+3 -3)

westram 2013-11-18 20:23 Rev.: 11164

* overlapping strcpy -> memmove

2 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+2 -2)

westram 2013-10-31 14:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+1 -1)

westram 2013-10-30 15:58 Rev.: 10974

* renamed include variables

2 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+2 -2)

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:

• SL/TREE_WRITE: 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)

2 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+2 -2)

westram 2013-10-29 11:43 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/TREE_WRITE: 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)

2 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+2)

westram 2013-08-25 14:09 Rev.: 10482

* Tree IO (patch reintegrates branch 'tree')
- added unit test (!TreeReader, export/import consistency for most export-parameters combinations)
- refactorings: moved more behavior into !TreeReader; deny access to class internals
- improved error messages/warnings
* show error-position in input data when bailing out
* warn about unused data behind tree
* trees < 2 species produce error now
- behavior
* fixed export/import of bootstrap values (expect ':' as separator; avoiding misinterpretation of group names starting with digits)
* auto-name unnamed nodes
* supports bootstrap values specified as percent (e.g. '12.5%')
* no longer interpret {{{''}}} as escape sequence for a single {{{'}}}
* no longer remove leading '_' from leaf-/groupnames (no idea why this was done)
- fixes:
* export+import of tree using double quotes often resulted in leaf-/groupnames enclosed in double-quotes (or more often failed to load completely)
* name of root-node was lost after import.
* better support for single-node subtrees, e.g. '(leafname)'. Nodes were skipped.
* deadlock occurring when tree file was truncated somewhere in the middle.
* leaks stuffed

45 lines of code changed in 2 files:

• SL/TREE_WRITE: TreeWrite.cxx (+44 -17), TreeWrite.h (+1 -1)

westram 2013-02-13 12:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+1 -1)

westram 2013-02-09 12:52 Rev.: 9521

- updated depends for [9520]

1 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+1)

westram 2013-02-09 11:16 Rev.: 9516

- reintegrated branch 'cxx11'

1 lines of code changed in 1 file:

• SL/TREE_WRITE: Makefile (+1)

westram 2012-09-24 15:48 Rev.: 8939

* fix cppcheck warnings

1 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+1 -1)

westram 2012-03-16 17:28 Rev.: 8493

* rename

2 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+2 -2)

westram 2012-03-08 16:38 Rev.: 8453

* added new tool arb_consensus_tree
- merges multiple trees into a consensus tree (like done for ARB-NJ-Bootstrap-Tree)
* use a stable sort on generated trees to make them comparable for unit-tests
- added test merging 4 trees into one consensus tree

2 lines of code changed in 2 files:

• SL/TREE_WRITE: TreeWrite.cxx (+1 -1), TreeWrite.h (+1 -1)

westram 2011-08-08 00:01 Rev.: 7811

merge from dev [7748] [7749] [7750]
* comments (C->C++ style)
* fixed umlauts in TREEGEN

1 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+1 -1)

westram 2011-08-07 17:41 Rev.: 7801

merge from dev [7710]
* resolve some nesting in library dependencies
- allows unit tests in GENOM and GENOM_IMPORT

3 lines of code changed in 2 files:

• SL/TREE_WRITE: Makefile (+1 -1), TreeWrite.h (+2 -2)

westram 2011-03-27 17:04 Rev.: 7337

* possibility to toggle the TODO-warnings via config.makefile

1 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+1 -1)

westram 2011-03-27 14:04 Rev.: 7335

* renamed intf (global typename from /usr/include/zconf.h)
* fixed several warnings
* put some #warnings into DEVEL_RALF

2 lines of code changed in 1 file:

• SL/TREE_WRITE: TreeWrite.cxx (+2 -2)

westram 2011-03-24 18:20 Rev.: 7314

merged from dev [7300] [7301] [7309] [7310]

* move to CORE
- GBS_strstruct + old interface functions
- GB_strpartdup + GB_strndup
* templates to generate handy test-results
* removed dead code (constructSequence)

2 lines of code changed in 2 files:

• SL/TREE_WRITE: Makefile (+1), TreeWrite.cxx (+1 -1)

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