April 2010 Commit Log

Number of Commits:
46
Number of Active Developers:
1
westram 2010-04-30 18:05 Rev.: 6613


- commented out 'treetool' (no longer provided?)

2 lines of code changed in 1 file:

westram 2010-04-30 15:49 Rev.: 6612


- added gcc 4.4.3

1 lines of code changed in 1 file:

westram 2010-04-29 13:46 Rev.: 6611


* IRS tree view
- enabled auto-jump (was disabled in IRS)
- tried to fix calculated cursor position (difficult, cause AW_SIZE-device acts weird
in this mode due to virtual vertical folding of tree)
- cleaned up code (unused enums/variables/parameters)
- zoom depends on canvas-width (instead of hardcoded 600 pixels)

79 lines of code changed in 3 files:

westram 2010-04-26 13:07 Rev.: 6610


* handle tree-command-modes which are common for list- and tree-views at one place
- no longer selects species when using middle-mouse-button (scroll)
- WWW mode works in all modes now
* list-view (no tree)
- perform clipping (about 30 times faster with a list of ~26000 species)
- align NDS columns (numeric columns get aligned to right side)

242 lines of code changed in 1 file:

westram 2010-04-26 11:40 Rev.: 6609


* avoid repeated dynamic casts to AWT_graphic_tree
* removed duplicated code for different tree views

34 lines of code changed in 1 file:

westram 2010-04-23 15:57 Rev.: 6608


* added GB_followingEntry and GB_following_marked
- like GB_nextEntry and GB_next_marked, but may advance any number of steps

42 lines of code changed in 5 files:

westram 2010-04-23 10:10 Rev.: 6607


- NDS text creation mode changed to enum

34 lines of code changed in 11 files:

westram 2010-04-22 17:54 Rev.: 6606


* show brackets with groupname for open groups (dendrogram only)

202 lines of code changed in 4 files:

westram 2010-04-22 13:29 Rev.: 6605


* added XmGetPixmap to ignored valgrind-errors

1 lines of code changed in 1 file:

westram 2010-04-22 13:25 Rev.: 6604


* taxonomy cache
- added define for number of chars used as group counter (in hash key)
- use 6 instead of 4 chars for counter (increases limit for groups from 2^16^ to 2^24^)
- added assertion to catch overflow

13 lines of code changed in 1 file:

westram 2010-04-21 09:31 Rev.: 6603


* re-import (GDE import, e.g. external aligner, readseq?)
- added 'skip all' and 'overwrite all species'
- added reject/accept question if checksum changed (e.g. align with filter)

67 lines of code changed in 1 file:

westram 2010-04-21 08:21 Rev.: 6602


* re-import after calling external aligner
- zero byte was not written to end of imported sequence (possible causing random data after EOS)
* AP_filter::to_string uses malloc (convention)
* use limits instead of 99999999

37 lines of code changed in 4 files:

westram 2010-04-20 11:26 Rev.: 6601


- major changes since v5

11 lines of code changed in 1 file:

westram 2010-04-19 17:20 Rev.: 6600


* if re-align failed for ALL species, ARB asked to increase alignment length to '-1'
* re-aligner unconditionally set 'codon_start' to '1'. Now it only sets it if a fixed translation_table is defined (or can be detected)

35 lines of code changed in 3 files:

westram 2010-04-19 15:45 Rev.: 6599


- do not export error in GBT_check_arb_file

3 lines of code changed in 1 file:

westram 2010-04-15 09:48 Rev.: 6598


- create species from consensus failed since [6272]. EDIT4 was always trying to add the consensus to the list of merged species, but the error was ignored before [6272]

18 lines of code changed in 1 file:

westram 2010-04-13 10:44 Rev.: 6597


- optimize hash used for suppression of repeated errors

4 lines of code changed in 1 file:

westram 2010-04-13 10:04 Rev.: 6596


- fixed crash during merge

5 lines of code changed in 1 file:

westram 2010-04-12 16:23 Rev.: 6595


* changed BOOL/TRUE/FALSE into bool/true/false
* deleted unused class MP_list

106 lines of code changed in 15 files:

westram 2010-04-12 15:59 Rev.: 6594


- error handling

1 lines of code changed in 1 file:

westram 2010-04-12 15:47 Rev.: 6593


- error handling

1 lines of code changed in 1 file:

westram 2010-04-12 15:23 Rev.: 6592


- error handling / cosmetics

22 lines of code changed in 5 files:

westram 2010-04-12 15:20 Rev.: 6591


* fixed lazy-sequence-loading for AP_sequence_protein (broken since [6238]). Parsimony+Dist should work with proteins again

24 lines of code changed in 3 files:

westram 2010-04-12 15:16 Rev.: 6590


* spelling

7 lines of code changed in 2 files:

westram 2010-04-10 18:24 Rev.: 6588

* changed default browse-url-command to 'xdg-open' ('open' on DARWIN). [thx elmar]
- renamed AWAR_WWW_BROWSER to force update in userland
* added 2 additional example URLs (SILVA + google) [thx elmar]
* parse existing URLs and force insertion of missing examples if there are unused WWW patterns
* fixed mismatched delete
* updated WWW help

102 lines of code changed in 6 files:

westram 2010-04-09 16:39 Rev.: 6587


* species/SAI-references for alignment adaption
- added buttons to move, delete and test references
- changed formatting of candidate list

227 lines of code changed in 3 files:

westram 2010-04-09 13:43 Rev.: 6586


- fixed unit-test broken by [6584]
- added additional unit-tests for GBT_names_move and GBT_names_add

22 lines of code changed in 1 file:

westram 2010-04-09 13:18 Rev.: 6585


* memleak

1 lines of code changed in 1 file:

westram 2010-04-09 12:50 Rev.: 6584


* GBT_names_move() wraps around if dest index is out of bounds
* AW_selection_list
- added method size() and use it
- removed now obsolete AW_window/get_no_of_entries()
* AW_window
- added selection_list_to_array(); "opposite" of init_selection_list_from_array()
- init_selection_list_from_array() internally copies the passed defaultEntry
- get_element_at_index() now returns 'const char *'
- save_selection_list() no longer exports or aw_message's any errors - it just returns them
* NT_concatenate
- rewrote shiftAlignment using GBT_names_...-functions
- removed dummy awar used to fake temporary selection list (omg)

181 lines of code changed in 10 files:

westram 2010-04-09 10:27 Rev.: 6583


* moved some local prototypes to headers
* rename
- check_status -> MP_check_status
* rewrote MP_Comment
- uses move_selection() instead of leaking memory with get_element_at_index()
- removed bulky code for spaced output
* added unit-tests for and rewrote MP_get_comment + MP_get_probes

157 lines of code changed in 5 files:

westram 2010-04-08 15:51 Rev.: 6582


* moved AW_selection_list methods to AW_select.cxx
* renamed
- get_index_of_current_element -> get_index_of_selected_element
- get_element_of_index -> get_element_at_index
* removed awar_name parameter from some AW_window functions (cause AW_selection_list knows to which awar it is bound)
- get_index_of_selected_element
- select_element_at_index (former select_index). Now does fallback to default value if index is out of bounds. If no default is defined it fallbacks to "" like before.
- move_selection
* added new methods to AW_selection_list
- get_awar_value
- set_awar_value
- get_default_value

118 lines of code changed in 8 files:

westram 2010-04-08 14:41 Rev.: 6581


* added AW_window/init_selection_list_from_array()
* AW_selection_list/first_selected returned NULL if default-selection was selected. Fixed.
* added some broken-design-warnings

69 lines of code changed in 3 files:

westram 2010-04-08 09:53 Rev.: 6580


* added new flavour of GBT_split_string (acting analogous to strtok)
- uses multiple separators
- optionally drops empty tokens
- implemented old flavour using new one
- both use size_t ref for result-param (instead of int). fixed occurrances.
* added GBT_count_names(), GBT_names_index_of(), GBT_names_erase(), GBT_names_add() and GBT_names_move()
* added unit-tests for new and changed functions

204 lines of code changed in 3 files:

westram 2010-04-07 13:39 Rev.: 6579


- use TEST_ASSERT_EQUAL instead of strcmp

4 lines of code changed in 1 file:

westram 2010-04-07 13:28 Rev.: 6577


- depends/prototypes updated

6 lines of code changed in 4 files:

westram 2010-04-07 13:25 Rev.: 6576


- fixed usage of undefined locations

4 lines of code changed in 1 file:

westram 2010-04-07 13:14 Rev.: 6575


- corrected include

1 lines of code changed in 1 file:

westram 2010-04-07 13:11 Rev.: 6574


- added valgrind.h (from valgrind 3.4.1)
- if running under valgrind, skip callback in GBK_raises_SIGSEGV() and always assume it does raise SIGSEGV

3946 lines of code changed in 3 files:

westram 2010-04-07 09:14 Rev.: 6573


- added missing lib (TRANSLATE)

1 lines of code changed in 1 file:

westram 2010-04-07 09:13 Rev.: 6572


- execute tests in same order as defined in code (you cannot rely on that order, there's no guarantee that nm reports locations for symbols)

13 lines of code changed in 1 file:

westram 2010-04-06 13:27 Rev.: 6571


- typefix

2 lines of code changed in 1 file:

westram 2010-04-06 12:17 Rev.: 6570


- test for GBT_split_string() and GBT_join_names()

55 lines of code changed in 1 file:

westram 2010-04-06 12:16 Rev.: 6569


- replaced TEST_ASSERT_STRINGRESULT by generic test TEST_ASSERT_EQUAL
- specialized for char*, int and size_t

24 lines of code changed in 3 files:

westram 2010-04-03 11:58 Rev.: 6568


- name change

5 lines of code changed in 3 files:

westram 2010-04-01 12:27 Rev.: 6567


* class MG_remaps
- fixed resources in ctor/dtor
- made independent from AWARs

31 lines of code changed in 3 files:

westram 2010-04-01 08:56 Rev.: 6566


- separated alignment adaption from MG_species.cxx

1111 lines of code changed in 4 files:

March 2010 »

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