- commented out 'treetool' (no longer provided?)
2 lines of code changed in 1 file:
- added gcc 4.4.3
1 lines of code changed in 1 file:
* 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:
* 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:
* avoid repeated dynamic casts to AWT_graphic_tree
* removed duplicated code for different tree views
34 lines of code changed in 1 file:
* 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:
- NDS text creation mode changed to enum
34 lines of code changed in 11 files:
* show brackets with groupname for open groups (dendrogram only)
202 lines of code changed in 4 files:
* added XmGetPixmap to ignored valgrind-errors
1 lines of code changed in 1 file:
* 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:
* 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:
* 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:
- major changes since v5
11 lines of code changed in 1 file:
* 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:
- do not export error in GBT_check_arb_file
3 lines of code changed in 1 file:
- 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:
- optimize hash used for suppression of repeated errors
4 lines of code changed in 1 file:
- fixed crash during merge
5 lines of code changed in 1 file:
* changed BOOL/TRUE/FALSE into bool/true/false
* deleted unused class MP_list
106 lines of code changed in 15 files:
- error handling
1 lines of code changed in 1 file:
- error handling
1 lines of code changed in 1 file:
- error handling / cosmetics
22 lines of code changed in 5 files:
* 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:
* spelling
7 lines of code changed in 2 files:
* 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:
* 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:
- 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:
* memleak
1 lines of code changed in 1 file:
* 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:
* 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:
* 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:
* 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:
* 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:
- use TEST_ASSERT_EQUAL instead of strcmp
4 lines of code changed in 1 file:
- depends/prototypes updated
6 lines of code changed in 4 files:
- fixed usage of undefined locations
4 lines of code changed in 1 file:
- corrected include
1 lines of code changed in 1 file:
- 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:
- added missing lib (TRANSLATE)
1 lines of code changed in 1 file:
- 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:
- typefix
2 lines of code changed in 1 file:
- test for GBT_split_string() and GBT_join_names()
55 lines of code changed in 1 file:
- 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:
- name change
5 lines of code changed in 3 files:
* class MG_remaps
- fixed resources in ctor/dtor
- made independent from AWARs
31 lines of code changed in 3 files:
- separated alignment adaption from MG_species.cxx
1111 lines of code changed in 4 files: