Directory SL/NEIGHBOURJOIN/

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

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

24 lines of code changed in 3 files:

• SL/NEIGHBOURJOIN: Makefile (+2), NJ.cxx (+21 -11), neighbourjoin.hxx (+1 -1)

westram 2021-11-12 14:47 Rev.: 18841

* add progress to {{{neighbourjoining()}}}-phase (this may be really long running)
- add one extra progress to {{{di_calculate_tree_cb()}}} encapsulating matrix-calculation + {{{neighbourjoining()}}}-phase.
- progress inside {{{di_calculate_matrix()}}} now counts 2 steps: loading data + matrix-calculation.

13 lines of code changed in 2 files:

• SL/NEIGHBOURJOIN: Makefile (+1), NJ.cxx (+12 -2)

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

* directly use {{{OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: 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/NEIGHBOURJOIN: Makefile (+1 -4)

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

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

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: Makefile (+1 -3)

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

* eliminate unused {{{C_OBJECTS}}}.

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: Makefile (+1 -2)

westram 2020-11-10 17:24 Rev.: 18634

* reintegrates 'root' into 'trunk'
- implements #449
* adds: log:branches/root@18451:18633

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: Makefile (+1)

westram 2019-09-17 20:52 Rev.: 18099

* mark loop failing with 4.9.2

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: NJ.cxx (+1 -1)

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

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

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: NJ.cxx (+1 -1)

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

2 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: NJ.cxx (+2 -2)

westram 2017-11-28 19:22 Rev.: 16766

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

7 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: NJ.cxx (+7 -14)

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

2 lines of code changed in 2 files:

• SL/NEIGHBOURJOIN: NJ.cxx (+1 -1), NJ.hxx (+1 -1)

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

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

3 lines of code changed in 2 files:

• SL/NEIGHBOURJOIN: Makefile (+1), NJ.cxx (+2 -2)

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

18 lines of code changed in 3 files:

• SL/NEIGHBOURJOIN: Makefile (+1), NJ.cxx (+16 -11), neighbourjoin.hxx (+1 -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/NEIGHBOURJOIN: Makefile (+2 -2)

westram 2014-08-27 12:21 Rev.: 12783

* publish TESTs for which nm 2.24 fails to export source location

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: NJ.cxx (+1)

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/NEIGHBOURJOIN: NJ.hxx (+1 -1)

westram 2014-03-19 15:40 Rev.: 11824

- document differences between 32- and 64bit versions of ARB NJ (neighbourjoin)
- difference is somehow related to effect of toggling TEST_FORWARD_ORDER

12 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: NJ.cxx (+12 -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

4 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: NJ.cxx (+4 -4)

westram 2014-01-09 19:52 Rev.: 11455

* use is_nan etc

0 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: NJ.cxx (-2)

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

191 lines of code changed in 5 files:

• SL/NEIGHBOURJOIN: Makefile (+3), NJ.cxx (+171 -67), NJ.hxx (+15 -5), needs_libs (+1 -1), neighbourjoin.hxx (+1 -1)

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

* 'class { public' -> struct

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: NJ.hxx (+1 -2)

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

* use cflags before cxxflags

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: Makefile (+1 -1)

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

* renamed include variables

2 lines of code changed in 1 file:

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

westram 2013-09-09 16:36 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/NEIGHBOURJOIN: Makefile (+2)

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

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: Makefile (+1 -1)

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

- updated depends for [9520]

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: Makefile (+1)

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

- reintegrated branch 'cxx11'

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: 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/NEIGHBOURJOIN: NJ.cxx (changed), NJ.hxx (changed)

westram 2012-04-11 13:19 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:

• SL/NEIGHBOURJOIN: needs_libs (+1 -1)

westram 2011-06-10 15:50 Rev.: 7623

- merge from dev [7450] [7452] [7456] [7457] [7458] [7459] [7460] [7461] [7464] [7465] [7466] [7467] [7468] [7469] [7482]
* tweaked compiler options
- activated -Weffc++
* postfilter warnings where Scott Meyers' advices are too general.
- base classes should not always have virtual destructors, since that renders tiny classes useless and
- members should not always be initialized via initialization list, since that often violates the DRY principle
* fix gcc's inability to detect that Noncopyable implements a private copy-ctor and op=
* this slows down complete ARB recompilation by ~5%
- added -Wold-style-cast (inactive)
- removed -Wno-non-template-friend added in [7447]
* postcompile.pl
- added option --original to show unmodified compiler output
* declared op= for classes which had a copy-ctor
* moved op= macros to arbtools.h
* derived classes containing pointers from Noncopyable (use Noncopyable virtually) or
* made them copyable if needed (awt_mask_item, KnownDB, Code, AWT_registered_itemtype, GEN_gene, !PosGene, !PartialSequence, !PlugIn, Range, Convaln_exception)
* other related changes
- user mask destruction working now

4 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: NJ.hxx (+4 -1)

westram 2011-02-23 14:37 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/NEIGHBOURJOIN: Makefile (+2 -1)

westram 2010-09-18 17:20 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/NEIGHBOURJOIN: Makefile (+2 -2)

westram 2010-09-09 22:49 Rev.: 6817

- depends for [6816]

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: Makefile (+1)

westram 2010-09-09 20:25 Rev.: 6814

* depends updated for [6812] + [6813]

1 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: Makefile (+1)

westram 2010-05-14 13:58 Rev.: 6659

* free()
- removed unneeded casts of argument
- removed unneeded if-clauses

2 lines of code changed in 1 file:

• SL/NEIGHBOURJOIN: NJ.cxx (+2 -2)

westram 2010-03-03 15:00 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 3 files:

• SL/NEIGHBOURJOIN: NJ.cxx (+1), neighbourjoin.hxx (new)

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