root/trunk/CONSENSUS_TREE

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Rev Chgset Date Author Log Message
(edit) @8585 [8585] 6 weeks westram * moved code from arb_consensus_tree -> class ConsensusTreeBuilder
(edit) @8574 [8574] 6 weeks westram * [8567] failed on WCs where shared libs were up-to-date, but not yet …
(edit) @8507 [8507] 2 months westram * use double for weights ([0..1] instead of [0..10000]) * added tests …
(edit) @8506 [8506] 2 months westram * correctly round branch probabilities
(edit) @8505 [8505] 2 months westram * replaced hash+list by set+vector * weight parts via ctor
(edit) @8490 [8490] 2 months westram * elim last global from CT_rbtree.cxx - now multiple ConsensusTree …
(edit) @8489 [8489] 2 months westram * moved globals from CT_hash.cxx into class PartRegistry * increased …
(edit) @8488 [8488] 2 months westram * move globals from CT_part.cxx into class PartitionSize * class PART …
(edit) @8482 [8482] 2 months westram * new class ConsensusTree - moved globals from CT_ctree.cxx there …
(edit) @8481 [8481] 2 months westram * define a strict order on partitions. criteria are - partition-freq …
(edit) @8478 [8478] 2 months westram * avoid crash @calcbootstraptree when no species were marked (but 'marked' …
(edit) @8476 [8476] 2 months westram * fix for NDEBUG mode (broken by [8473])
(edit) @8475 [8475] 3 months westram * insert all childs at multifurcations with more than 2 subtrees - now …
(edit) @8473 [8473] 3 months westram * minor refactorings
(edit) @8472 [8472] 3 months westram * partition tree now fulfills stricter requirements: - tree is …
(edit) @8471 [8471] 3 months westram * part_key generated negative hash keys - that caused several lost …
(edit) @8470 [8470] 3 months westram * various refactorings (performed while digging for non-determinism) - …
(edit) @8469 [8469] 3 months westram * added test which generates an invalid tree (as intended by [8455])
(edit) @8468 [8468] 3 months westram * branch-order (but not topology) of CONSENSUS_TREE depends on the order …
(edit) @8465 [8465] 3 months westram * added most simple test (create consensus tree of 1 tree) - …
(edit) @8463 [8463] 3 months westram * made PART-params const AFAP * renamed part-query-functions * check …
(edit) @8461 [8461] 3 months westram * do not use 0 as value in Name_hash (did not harm) * moved debug flags …
(edit) @8460 [8460] 3 months westram * added explicit init/cleanup functions for each module in CONSENSUS_TREE …
(edit) @8459 [8459] 3 months westram * add debug code dumping drops
(edit) @8458 [8458] 3 months westram * added second test (which drops some tree nodes) - deactivated 1st …
(edit) @8455 [8455] 3 months westram * document a case where CONSENSUS_TREE generates an invalid tree (one …
(edit) @8454 [8454] 3 months westram - fix memleak
(edit) @8451 [8451] 3 months westram * added GBT_is_invalid (check tree and return error if invalid) * check …
(edit) @8313 [8313] 5 months westram * removed dead code
(edit) @8309 [8309] 5 months westram * moved much code into static scope
(edit) @7812 [7812] 10 months westram merge from dev [7751] [7752] * updated many old-style typedefs (typedef …
(edit) @7811 [7811] 10 months westram merge from dev [7748] [7749] [7750] * comments (C->C++ style) * fixed …
(edit) @7803 [7803] 10 months westram merge from dev [7716] [7732] [7733] [7734] [7735] * script to add+remove …
(edit) @7800 [7800] 10 months westram merge from dev [7687] [7692] [7693] [7694] [7695] [7697] [7706] [7707] …
(edit) @7183 [7183] 15 months westram merges [7084] [7086] [7087] [7088] from refactor * added CORE lib - …
(edit) @6912 [6912] 20 months westram - printf -> assert
(edit) @6866 [6866] 21 months westram * compiler-messages (merges [6848] [6849] [6850] [6851] [6853] [6855] …
(edit) @6817 [6817] 21 months westram - depends for [6816]
(edit) @6814 [6814] 21 months westram * depends updated for [6812] + [6813]
(edit) @6659 [6659] 2 years westram * free() - removed unneeded casts of argument - removed unneeded …
(edit) @6527 [6527] 2 years westram - ignore *.gcda *.gcno
(edit) @6506 [6506] 2 years westram [static check] * stuffed one leak in test-code * excluded test-code from …
(edit) @6490 [6490] 2 years westram * moved a few types to arbdb_base.h * only use arbdb_base.h or arbdb.h …
(edit) @6463 [6463] 2 years westram * Changed hash-size passed to GBS_create_hash etc. - pass number of …
(edit) @6448 [6448] 2 years westram - added library dependency declarations
(edit) @6385 [6385] 2 years westram - removed trailing whitespace
(edit) @6383 [6383] 2 years westram - removed void
(edit) @6381 [6381] 2 years westram - fixed includes - added MBI headers - removed unused files
(edit) @6374 [6374] 2 years westram * fixed doxygen-alike comments - either use explicit qt-style triggers …
(edit) @6366 [6366] 2 years westram * fixed whitespace (scripted)
(edit) @6347 [6347] 2 years westram Moved a lot of dead code to where it belongs: into the depths of SVN. I …
(edit) @6332 [6332] 2 years westram - GB_BOOL -> bool
(edit) @6331 [6331] 2 years westram * removed GB_strdup * moved freeset, nulldup, etc to own header …
(edit) @6325 [6325] 2 years westram * ARBDB - hide internal structures (GBDATA etc.) inside ARBDB. Fixed …
(edit) @6318 [6318] 2 years westram * ARBDB - compiles as C++ (no longer compiled as plain C) - removed …
(edit) @6141 [6141] 3 years westram * spellchecked all (phew)
(edit) @5725 [5725] 3 years westram * removed useless macros: - GB_STRDUP (easily taken for GB_strdup) …
(edit) @5709 [5709] 3 years westram - made depends for [5708]
(edit) @5702 [5702] 3 years westram - dead "code"
(edit) @5471 [5471] 4 years westram - ignore Makefile.bak and TAGS
(edit) @5468 [5468] 4 years westram Ignore links and generated files
(edit) @5390 [5390] 4 years westram - TAB-Ex
(edit) @5356 [5356] 4 years westram - fixed calls to GBS_create_hash
(edit) @5225 [5225] 4 years westram - changed names of linker commands
(edit) @5129 [5129] 4 years westram - depends updated
(edit) @4634 [4634] 5 years westram - proper clean (avoid errors if already cleaned)
(edit) @2338 [2338] 8 years westram fixed and reformatted dependencies (using fix_depends.pl)
(edit) @1617 [1617] 9 years westram - updated dependencies for all Makefiles - rewrote dependency generation …
(edit) @1258 [1258] 9 years westram * CONSENSUS_TREE/CT_part.cxx: - untabified, indented and valgrinded
(edit) @1257 [1257] 9 years westram * CONSENSUS_TREE/CT_mem.cxx: - getmem() returns 0 if memory couldn't be …
(edit) @887 [887] 10 years westram make depend
(edit) @866 [866] 10 years westram changed assert macros (see arb_assert.h)
(edit) @149 [149] 11 years westram *** empty log message ***
(edit) @142 [142] 11 years westram gene search and query (hopefully everything changed)
(edit) @83 [83] 11 years westram *** empty log message ***
(edit) @80 [80] 11 years meierh haralds checkin
(edit) @68 [68] 11 years westram Updated dependencies
(add) @2 [2] 12 years oldcode Initial revision
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