- fixed includes
- added MBI-headers and wrappers
282 lines of code changed in 20 files:
- fixed error in host:socket parsing (thx to elmar). bug was introduced with [5839]
1 lines of code changed in 1 file:
- list of detected clusters can be sorted by different criteria
140 lines of code changed in 5 files:
- fixed stack overflow in get_root_node()
1 lines of code changed in 1 file:
- trace calculated distances (DEBUG)
46 lines of code changed in 2 files:
- fixed width calculation (signedness?)
13 lines of code changed in 1 file:
* 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:
* 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:
* assert correct awarname in ColumnStat.ctor
4 lines of code changed in 1 file:
* added AP_filter.blowup_string()
18 lines of code changed in 2 files:
- fixed unhandled error
4 lines of code changed in 1 file:
* !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:
- define UNIT_TESTS=1 for make depends
2 lines of code changed in 1 file:
- fixed array overflow, when using filter and weights together (introduced in [6252])
1 lines of code changed in 1 file:
* !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:
- 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:
* 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:
- removed some awt prefixes
19 lines of code changed in 4 files:
- cloc output splitted in code/help and ARB/ExternalTools
214 lines of code changed in 4 files:
- depends updated
0 lines of code changed in 1 file:
- calling 'make clean ; make depends' failed
2 lines of code changed in 2 files:
- calling 'make clean' twice failed
1 lines of code changed in 1 file:
- 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:
* 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:
* 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:
* added test_unit.h
* completed unit test description
98 lines of code changed in 3 files:
* added target 'clean' to UNIT_TESTER (and call it by main-clean)
14 lines of code changed in 3 files:
- depends
1 lines of code changed in 1 file:
* NDEBUG mode
- remove prototype from function name
- handle missing location correctly
6 lines of code changed in 1 file:
* 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:
* 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:
- bugfix for [6453] (parsed wrong parts)
1 lines of code changed in 1 file:
* added actual unit-test for GB_HASH and GB_NUMHASH
154 lines of code changed in 1 file:
- 64bit fix for symbol parser
1 lines of code changed in 1 file:
- removed wrong dependency from UNIT_TESTER.a
1 lines of code changed in 1 file:
* added unit-test capability
697 lines of code changed in 10 files:
- removed useless return value from GBS_string_2_hashtab()
5 lines of code changed in 2 files:
* 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:
- added library dependency declarations
386 lines of code changed in 76 files:
- renamed TEST_-functions
31 lines of code changed in 1 file:
* compile fix for [6445]
2 lines of code changed in 1 file:
* 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:
* 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:
* removed dependency of MULTI_PROBE from GLOBAL_gb_main
99 lines of code changed in 10 files:
* removed dependency of PRIMER_DESIGN from GLOBAL_gb_main
34 lines of code changed in 3 files:
* reformatted GUI element code
53 lines of code changed in 1 file:
* removed dependency of PROBE_DESIGN from GLOBAL_gb_main (finishes [6438] + [6439])
77 lines of code changed in 3 files:
* continue [6438] (remove dependency of PROBE_DESIGN from GLOBAL_gb_main)
70 lines of code changed in 1 file:
* started to remove dependency of PROBE_DESIGN from GLOBAL_gb_main
179 lines of code changed in 5 files:
- completes [6436]
0 lines of code changed in 1 file:
* PHYLO does no longer depend on SL/FILTER
6 lines of code changed in 1 file:
* removed dependency of GENOM from GLOBAL_gb_main
600 lines of code changed in 17 files:
* added possibility to forward user callback param to XXX_open_mask_window
23 lines of code changed in 5 files:
* 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:
- fixed gene/experiment sensitivity masks
6 lines of code changed in 2 files:
* removed dependency of RND3D from GLOBAL_gb_main
60 lines of code changed in 7 files:
* removed dependency of SEQ_QUALITY from GLOBAL_gb_main
33 lines of code changed in 3 files:
* moved TREE_log_action_to_tree_comment() to GBS_log_dated_action_to()
48 lines of code changed in 7 files:
* 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:
* 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:
- ... and filenames
1766 lines of code changed in 19 files:
- names, names, names, ...
474 lines of code changed in 13 files:
* removed dependency of FAST_ALIGNER from GLOBAL_gb_main
102 lines of code changed in 5 files:
* removed dependency of AWTC from GLOBAL_gb_main
13 lines of code changed in 3 files:
* 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:
* (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:
* don't export error from GB_delete
1 lines of code changed in 1 file:
- fix #223
4 lines of code changed in 2 files:
* 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:
* 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:
* removed two exported errors from GBT_rename_alignment
2 lines of code changed in 1 file:
* 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:
- moved advice.fig
33 lines of code changed in 4 files:
- simple rename
7 lines of code changed in 1 file:
* removed unused vectorfont
7 lines of code changed in 19 files:
* replaced stupid name 'selection_box' with 'fileselection'
101 lines of code changed in 27 files:
* 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:
* moved AWT/AWT_advice to WINDOW/AW_advice
316 lines of code changed in 18 files:
* 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:
* moved parts of WINDOW/AW_status.cxx to WINDOW/AW_modal.cxx
743 lines of code changed in 4 files:
* 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:
* 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:
* removed MostLikelySeq from ST_ml.hxx
- removes dependency from AP_Tree.hxx
180 lines of code changed in 5 files:
* 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:
* disabled CHECK_TREE_STRUCTURE
1 lines of code changed in 1 file:
* 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:
* fixed wrong status counter (never reached 100%)
1 lines of code changed in 1 file:
* fixed small hash size
6 lines of code changed in 1 file:
* 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: