February 2010 Commit Log

Number of Commits:
89
Number of Active Developers:
1
westram 2010-02-28 17:21 Rev.: 6488


- fixed includes
- added MBI-headers and wrappers

282 lines of code changed in 20 files:

westram 2010-02-28 14:14 Rev.: 6486


- fixed error in host:socket parsing (thx to elmar). bug was introduced with [5839]

1 lines of code changed in 1 file:

westram 2010-02-27 16:54 Rev.: 6485


- list of detected clusters can be sorted by different criteria

140 lines of code changed in 5 files:

westram 2010-02-27 16:40 Rev.: 6484


- fixed stack overflow in get_root_node()

1 lines of code changed in 1 file:

westram 2010-02-26 18:47 Rev.: 6483


- trace calculated distances (DEBUG)

46 lines of code changed in 2 files:

westram 2010-02-26 18:45 Rev.: 6482


- fixed width calculation (signedness?)

13 lines of code changed in 1 file:

westram 2010-02-26 17:14 Rev.: 6481


* clustersearch
- fixed crash on unnamed group in tree (just ignore such groups)
- if one sequence has no bases (caused by filter) assume its distance is zero
- collect and display min. bases used for comparison for each cluster
- cluster list detects column widths for display

134 lines of code changed in 6 files:

westram 2010-02-25 20:34 Rev.: 6480


* added filter to column stat
- chimera check uses a real filter (much faster)
- EDIT4 uses a permeable filter (for column stat)
* blowup quality-string with spaces (for filtered positions)
* changed chimera-check GUI
- added toggle for planned auto-removal

252 lines of code changed in 8 files:

westram 2010-02-25 15:05 Rev.: 6479


* assert correct awarname in ColumnStat.ctor

4 lines of code changed in 1 file:

westram 2010-02-25 15:05 Rev.: 6478


* added AP_filter.blowup_string()

18 lines of code changed in 2 files:

westram 2010-02-25 14:59 Rev.: 6477


- fixed unhandled error

4 lines of code changed in 1 file:

westram 2010-02-25 12:38 Rev.: 6476


* !ColumnStat-ctor now expects an AWAR containing an alignment (most commonly its AWAR_DEFAULT_ALIGNMENT)
- the column-stat-alignment-awar will be mapped to the provided awar
* removed all manually created column-stat awars (this is already done by !ColumnStat-ctor)
* removed all manually mapping to ali-awars

32 lines of code changed in 10 files:

westram 2010-02-25 12:16 Rev.: 6474


- define UNIT_TESTS=1 for make depends

2 lines of code changed in 1 file:

westram 2010-02-24 18:55 Rev.: 6473


- fixed array overflow, when using filter and weights together (introduced in [6252])

1 lines of code changed in 1 file:

westram 2010-02-23 19:37 Rev.: 6472


* !SummarizedLikelihoods -> !VarianceSampler
* tried to figure out what !LikelihoodRanges.generate_string() does
* sample values of t-test for each sequence and write them info into selected species field (in front of the detailed t-test results)

79 lines of code changed in 3 files:

westram 2010-02-23 19:08 Rev.: 6471


- bugfix: ARB_NT crashed when starting info window from search&query (and info window was never opened before)

3 lines of code changed in 1 file:

westram 2010-02-22 18:02 Rev.: 6470


* ST_rate_matrix was always symmetric and only contained two different values
- now only uses 2 floats (instead of 25)
- optimized matrix/vector multiplication for ST_rate_matrix
* moved some functionality into ST_base_vector and simplyfied code using ST_base_vector
* compared results with patched [6392]

151 lines of code changed in 5 files:

westram 2010-02-21 20:58 Rev.: 6469


- removed some awt prefixes

19 lines of code changed in 4 files:

westram 2010-02-21 20:22 Rev.: 6468


- cloc output splitted in code/help and ARB/ExternalTools

214 lines of code changed in 4 files:

westram 2010-02-20 19:48 Rev.: 6467


- depends updated

0 lines of code changed in 1 file:

westram 2010-02-20 19:48 Rev.: 6466


- calling 'make clean ; make depends' failed

2 lines of code changed in 2 files:

westram 2010-02-20 19:37 Rev.: 6465


- calling 'make clean' twice failed

1 lines of code changed in 1 file:

westram 2010-02-19 11:21 Rev.: 6464


- added target 'cloc' (needs cloc-1.08.pl)
- added cloc language def for arb

current output:
{{{
--------------------------------------------------------------------------------
Language files blank comment code
--------------------------------------------------------------------------------
C++ 425 40396 21779 186436
C 186 27155 11385 164714
C/C++ Header 420 8644 6494 32553
HTML 47 1404 4 23020
make 154 2069 759 11933
ARB-GUI-Layout 209 0 0 11256
ARB-Help 282 4997 1316 9246
Perl 89 1593 992 8127
Fortran 77 1 0 5425 6019
Shell 40 302 182 2202
AISC 7 184 104 1907
ARB-Import-Filters 39 635 241 1829
GDE-Menu 18 247 12 1277
XSLT 3 132 87 722
ARB-Export-Filters 14 13 5 111
DTD 3 28 45 73
--------------------------------------------------------------------------------
SUM: 1937 87799 48830 461425
--------------------------------------------------------------------------------
}}}

202 lines of code changed in 2 files:

westram 2010-02-19 10:13 Rev.: 6463


* Changed hash-size passed to GBS_create_hash etc.
- pass number of estimated elements (instead of real size)
* hashes now use size_t for size/count
* extremely slow hashes warn in release code

379 lines of code changed in 45 files:

westram 2010-02-18 19:59 Rev.: 6462


* GBS_free_hash_entries -> GBS_erase_hash
* GBS_NUMHASH now knows how many elements it contains
- added GBS_numhash_count_elems()
* more test code

153 lines of code changed in 3 files:

westram 2010-02-18 19:52 Rev.: 6461


* added test_unit.h
* completed unit test description

98 lines of code changed in 3 files:

westram 2010-02-18 17:09 Rev.: 6460


* added target 'clean' to UNIT_TESTER (and call it by main-clean)

14 lines of code changed in 3 files:

westram 2010-02-18 12:15 Rev.: 6459


- depends

1 lines of code changed in 1 file:

westram 2010-02-18 11:48 Rev.: 6458


* NDEBUG mode
- remove prototype from function name
- handle missing location correctly

6 lines of code changed in 1 file:

westram 2010-02-18 11:45 Rev.: 6457


* valgrind off by default
* fake Entering/Leaving directory messages (to make assert-messages work in emacs)
* call arb_valgrind with full path

5 lines of code changed in 1 file:

westram 2010-02-18 11:44 Rev.: 6456


* wrap everything which is needed for assertions in
{{{
#ifdef ASSERTION_USED
#endif
}}}
instead of using DEBUG
* added non-ARBDB-dependent version of ARB_SIGSEGV
* in unit tests are active, use another version of arb_assert(). It is always active (DEBUG and NDEBUG) and prints the failure like a compiler error
* added ASSERT_TRUE(expr) and ASSERT_FALSE(expr)

134 lines of code changed in 25 files:

westram 2010-02-18 09:40 Rev.: 6455


- bugfix for [6453] (parsed wrong parts)

1 lines of code changed in 1 file:

westram 2010-02-18 09:33 Rev.: 6454


* added actual unit-test for GB_HASH and GB_NUMHASH

154 lines of code changed in 1 file:

westram 2010-02-18 09:27 Rev.: 6453


- 64bit fix for symbol parser

1 lines of code changed in 1 file:

westram 2010-02-18 09:21 Rev.: 6452


- removed wrong dependency from UNIT_TESTER.a

1 lines of code changed in 1 file:

westram 2010-02-18 09:12 Rev.: 6451


* added unit-test capability

697 lines of code changed in 10 files:

westram 2010-02-17 21:29 Rev.: 6450


- removed useless return value from GBS_string_2_hashtab()

5 lines of code changed in 2 files:

westram 2010-02-17 10:47 Rev.: 6449


* SOURCE_TOOLS/needed_libs.pl
- script to handle library dependency declarations
- can print static and/or dynamic library directories or files one target depends on
- can print library part of the link command to link specific target
- can draw different dependency graphs (see [attachment:ticket:152:lib_dependency.gif example])

732 lines of code changed in 1 file:

westram 2010-02-17 10:30 Rev.: 6448


- added library dependency declarations

386 lines of code changed in 76 files:

westram 2010-02-16 19:27 Rev.: 6447


- renamed TEST_-functions

31 lines of code changed in 1 file:

westram 2010-02-16 19:14 Rev.: 6446


* compile fix for [6445]

2 lines of code changed in 1 file:

westram 2010-02-16 19:07 Rev.: 6445


* removed dependency from GLOBAL_gb_main
- was used to detect special behavior during import. Since I wasnt able to reproduce that behavior I assume the removed code (introduced with [3759]) was out-dated or wrong.

8 lines of code changed in 2 files:

westram 2010-02-16 18:54 Rev.: 6444


* fixed MG_check_alignment
- dont export error
- delete -> free
- memleak
- fixed name -> MG_copy_and_check_alignments

54 lines of code changed in 3 files:

westram 2010-02-16 17:38 Rev.: 6443


* removed dependency of MULTI_PROBE from GLOBAL_gb_main

99 lines of code changed in 10 files:

westram 2010-02-16 16:26 Rev.: 6442


* removed dependency of PRIMER_DESIGN from GLOBAL_gb_main

34 lines of code changed in 3 files:

westram 2010-02-16 16:15 Rev.: 6441


* reformatted GUI element code

53 lines of code changed in 1 file:

westram 2010-02-16 16:01 Rev.: 6440


* removed dependency of PROBE_DESIGN from GLOBAL_gb_main (finishes [6438] + [6439])

77 lines of code changed in 3 files:

westram 2010-02-16 15:07 Rev.: 6439


* continue [6438] (remove dependency of PROBE_DESIGN from GLOBAL_gb_main)

70 lines of code changed in 1 file:

westram 2010-02-16 13:15 Rev.: 6438


* started to remove dependency of PROBE_DESIGN from GLOBAL_gb_main

179 lines of code changed in 5 files:

westram 2010-02-16 11:08 Rev.: 6437


- completes [6436]

0 lines of code changed in 1 file:

westram 2010-02-16 10:51 Rev.: 6436


* PHYLO does no longer depend on SL/FILTER

6 lines of code changed in 1 file:

westram 2010-02-16 10:03 Rev.: 6435


* removed dependency of GENOM from GLOBAL_gb_main

600 lines of code changed in 17 files:

westram 2010-02-15 19:21 Rev.: 6434


* added possibility to forward user callback param to XXX_open_mask_window

23 lines of code changed in 5 files:

westram 2010-02-15 17:37 Rev.: 6433


* awt_item_type_selector/current() expects additional parameter gb_main
* itemtype implementations no longer access GLOBAL_gb_main

22 lines of code changed in 6 files:

westram 2010-02-15 17:22 Rev.: 6432


- fixed gene/experiment sensitivity masks

6 lines of code changed in 2 files:

westram 2010-02-15 13:56 Rev.: 6431


* removed dependency of RND3D from GLOBAL_gb_main

60 lines of code changed in 7 files:

westram 2010-02-15 13:28 Rev.: 6430


* removed dependency of SEQ_QUALITY from GLOBAL_gb_main

33 lines of code changed in 3 files:

westram 2010-02-13 17:13 Rev.: 6429


* moved TREE_log_action_to_tree_comment() to GBS_log_dated_action_to()

48 lines of code changed in 7 files:

westram 2010-02-13 16:11 Rev.: 6428


* replaced global (and multiple existing) AD_map_viewer() by callback which has to be passed to AWT_graphic_tree

95 lines of code changed in 16 files:

westram 2010-02-13 12:48 Rev.: 6427


* ARB_GDE
- removed dependency from GLOBAL_gb_main
- removed obsolete ARB_EDIT specials
- changed some names
* ED4_root
- renamed 'db' to 'props_db'

116 lines of code changed in 14 files:

westram 2010-02-12 21:49 Rev.: 6426


- ... and filenames

1766 lines of code changed in 19 files:

westram 2010-02-12 21:24 Rev.: 6425


- names, names, names, ...

474 lines of code changed in 13 files:

westram 2010-02-12 18:41 Rev.: 6424


* removed dependency of FAST_ALIGNER from GLOBAL_gb_main

102 lines of code changed in 5 files:

westram 2010-02-12 12:56 Rev.: 6423


* removed dependency of AWTC from GLOBAL_gb_main

13 lines of code changed in 3 files:

westram 2010-02-12 11:45 Rev.: 6422


* moved fileselection to libWINDOW (to remove dependency libWINDOW -> libAWT)
* finally removed adawcbstruct
- renamed several misused variables in db_scanner (which previously used adawcbstruct)
* added GB_is_link()
- made AW_is_.. static (cause it does special things needed for fileselection) and reimpl. using GB_is..
* fixed many includes and depends

1253 lines of code changed in 73 files:

westram 2010-02-11 15:20 Rev.: 6421


* (started to) replace adawcbstruct
- instead use classes AW_selection, AW_DB_selection (both moved into libWINDOW) and derived classes for each selection type
- itemfield reorder- and hide-/del-callbacks use AWT_itemfield_selection
- moved AW_selection_list into new module AW_select
* renamed some functions
- awt_create_selection_list_on_scandb -> awt_create_selection_list_on_itemfields
- awt_create_selection_list_on_ad -> awt_create_selection_list_on_alignments
* renamed
- AWAR_CONFIG_DATA -> CONFIG_DATA_PATH
- AWAR_CONFIG -> CONFIG_ITEM

669 lines of code changed in 46 files:

westram 2010-02-11 14:35 Rev.: 6420


* don't export error from GB_delete

1 lines of code changed in 1 file:

westram 2010-02-10 19:03 Rev.: 6418


- fix #223

4 lines of code changed in 2 files:

westram 2010-02-10 15:21 Rev.: 6417


* AW_awar
- added delete callback to AWAR origin
- rewrote unlink_from_DB()
- awars can no longer be bound to NULL, instead they automatically fall back to origin
- as soon as origin is deleted from DB, awar gets completely disfunctional

70 lines of code changed in 2 files:

westram 2010-02-10 10:37 Rev.: 6416


* mapped AWARs auto-unmap when trying to map them to NULL (fixes crash, if ARB was closed when any AWAR was mapped to NULL, e.g. when alignment '????' was selected in alignment-admin)

25 lines of code changed in 1 file:

westram 2010-02-10 10:18 Rev.: 6415


* removed two exported errors from GBT_rename_alignment

2 lines of code changed in 1 file:

westram 2010-02-09 14:08 Rev.: 6414


* WINDOW/AW_preset.cxx is no longer compiled into AWT/AWT_preset.o (this was only an unnecessary hack for vectorfont file selector)

11 lines of code changed in 6 files:

westram 2010-02-09 13:33 Rev.: 6413


- moved advice.fig

33 lines of code changed in 4 files:

westram 2010-02-09 13:33 Rev.: 6412


- simple rename

7 lines of code changed in 1 file:

westram 2010-02-09 13:32 Rev.: 6411


* removed unused vectorfont

7 lines of code changed in 19 files:

westram 2010-02-09 11:51 Rev.: 6410


* replaced stupid name 'selection_box' with 'fileselection'

101 lines of code changed in 27 files:

westram 2010-02-08 18:10 Rev.: 6409


* aw_root::open_default no longer uses AWT_announce_db_to_browser
* now done by AWT_open_properties() which is used instead of open_default() in all cases except
- aw_status no longer announces its properties (they were not accessible anyway)
- EDIT4 announces it manually (cause of alignment specific properties)

68 lines of code changed in 14 files:

westram 2010-02-08 17:02 Rev.: 6408


* moved AWT/AWT_advice to WINDOW/AW_advice

316 lines of code changed in 18 files:

westram 2010-02-08 15:16 Rev.: 6407


* renamed libAW.so into libWINDOW.so (to get same DIR/FILE-name-scheme as other shared ARB libs)

5 lines of code changed in 2 files:

westram 2010-02-08 14:56 Rev.: 6406


* moved parts of WINDOW/AW_status.cxx to WINDOW/AW_modal.cxx

743 lines of code changed in 4 files:

westram 2010-02-08 11:40 Rev.: 6405


* moved parts of WINDOW/AW_status.cxx to WINDOW/AW_help.cxx
* moved AWT/AWT_www.cxx/awt_openURL to WINDOW/AW_help.cxx/AW_openURL

573 lines of code changed in 6 files:

westram 2010-02-08 09:52 Rev.: 6404


* move AWT/AWT_sel_boxes.cxx/AWT_edit to WINDOW/AW_edit.cxx/AW_edit (removes a bit cross-reference between libs AWT and WINDOW)

220 lines of code changed in 19 files:

westram 2010-02-03 18:32 Rev.: 6403


* removed MostLikelySeq from ST_ml.hxx
- removes dependency from AP_Tree.hxx

180 lines of code changed in 5 files:

westram 2010-02-03 15:38 Rev.: 6402


* made several params const
* use ST_FLOAT instead of float for ST_base_vector, ST_rate_matrix and all their calculations (for easy change to double for experiments).
* use size_t instead of int for start/end pos of range, alignment_len
* ST_sequence_ml
- renamed into !MostLikelySeq
- some functions renamed
- ST_ML is no longer a friend
- removed protected/virtual specifiers (nothing derives from it)
- made some members private (still needs work)

244 lines of code changed in 6 files:

westram 2010-02-02 18:43 Rev.: 6401


* disabled CHECK_TREE_STRUCTURE

1 lines of code changed in 1 file:

westram 2010-02-02 18:37 Rev.: 6400


* fixed error handling in
- st_ml_add_quality_string_to_species
- st_ml_check_sequence_quality
* fixed a buffer overflow in st_ml_add_quality_string_to_species() - occurred only with small buckets or long sequences
* added class !SummarizedLikelihoods (collects likelihoods for one bucket)
* renamed other classes in st_quality
* use aw_status_counter to provide more fine-grained status during quality calculation

217 lines of code changed in 3 files:

westram 2010-02-02 18:31 Rev.: 6399


* fixed wrong status counter (never reached 100%)

1 lines of code changed in 1 file:

westram 2010-02-02 18:30 Rev.: 6398


* fixed small hash size

6 lines of code changed in 1 file:

westram 2010-02-01 14:10 Rev.: 6397


* renamed AWT_csp -> !ColumnStat
* renamed many other !ColumnStat related functions/awars/etc.
* ColumnStat::go/exit -> calculate/forget

1194 lines of code changed in 30 files:

January 2010 »

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