Directory SL/TREE_WRITE/

Directory Created:
2009-06-05 20:02
Total Files:
4
Deleted Files:
0
Lines of Code:
576

[root]/SL/TREE_WRITE

Lines of Code

SL/TREE_WRITE/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
westram 81 (100.0%) 879 (100.0%) 10.8

Most Recent Commits

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)
westram 2011-02-23 13:37 Rev.: 7183


merges [7084] [7086] [7087] [7088] from refactor
* added CORE lib
- added arb_progress (unused yet)
- moved some code from ARBDB to CORE
* added tests to CORE lib
* generate_all_links.sh
- now tests link targets
- able to replace links (if link stays the same, but target changes)
* fixed perl interface
- link with libCORE
- DRYed LINUX.PL and DARWIN.PL
- added wrapper functionality (ARBDB->CORE). Functions starting with GBC_ are wrappers for code that moved into libCORE (which is NOT xsub'd)

2 lines of code changed in 1 file:

  • SL/TREE_WRITE: Makefile (+2 -1)
westram 2011-02-01 17:38 Rev.: 7111


* added export as comma-separated-values (NDS export)
* renamed enum NDS_Type-members

3 lines of code changed in 1 file:

  • SL/TREE_WRITE: TreeWrite.cxx (+3 -3)
westram 2010-09-18 16:39 Rev.: 6868


- updated prototypes and dependencies

1 lines of code changed in 1 file:

  • SL/TREE_WRITE: Makefile (+1 -1)
westram 2010-09-18 16:20 Rev.: 6866


* compiler-messages (merges [6848] [6849] [6850] [6851] [6853] [6855] [6856] [6860] from refactor)
- errors get listed before warnings
- pipe all compilations through postcompile filter
- optionally filter warnings and/or stop at 1st error (controllable by POST_COMPILE in ARB Makefile)
- no warnings for ptpan (too many; version in trunk is outdated)

2 lines of code changed in 1 file:

  • SL/TREE_WRITE: Makefile (+2 -2)
westram 2010-09-09 21:49 Rev.: 6817


- depends for [6816]

1 lines of code changed in 1 file:

  • SL/TREE_WRITE: Makefile (+1)
westram 2010-09-09 19:25 Rev.: 6814


* depends updated for [6812] + [6813]

1 lines of code changed in 1 file:

  • SL/TREE_WRITE: Makefile (+1)
westram 2010-05-13 16:43 Rev.: 6655


* struct GBS_strstruct -> GBS_strstruct

2 lines of code changed in 1 file:

  • SL/TREE_WRITE: TreeWrite.cxx (+2 -2)
westram 2010-04-23 10:10 Rev.: 6607


- NDS text creation mode changed to enum

9 lines of code changed in 3 files:

  • SL/TREE_WRITE: Makefile (+2), TreeWrite.cxx (+3 -3), TreeWrite.h (+4 -1)
westram 2010-03-03 14:00 Rev.: 6490


* moved a few types to arbdb_base.h
* only use arbdb_base.h or arbdb.h where possible
* global included cleanup
* added MBI headers to many files
* moved SQ_ambiguities.SQ_count_ambiguities() to separate object

3 lines of code changed in 2 files:

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

(19 more)

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