May 2012 Commit Log

Number of Commits:
78
Number of Active Developers:
2
westram 2012-05-31 09:14 Rev.: 8774


* replaced global abort flag by return value
* removed default params from Generation::calcFitness

74 lines of code changed in 4 files:

westram 2012-05-31 08:26 Rev.: 8773


* calculate at least 1 generation
- failed when number of possible probe-combis was between MAXINITPOPULATION and 3*MAXPOPULATION (wanted to calculate 0 populations)

1 lines of code changed in 1 file:

westram 2012-05-30 18:48 Rev.: 8772


* removed label and mnemonic params from create_selection_list
- labels do not make much sense anyway (and were hidden behind the list up to now)
- added assertion versus using labels with selection lists

45 lines of code changed in 18 files:

westram 2012-05-30 18:25 Rev.: 8771


* multi probe
- use generic sellist collect buttons
* removed now unused collect-code
- cleaned up layout of main- and result-window
- removed unused defines
- moved manual probe input field into main window

307 lines of code changed in 8 files:

westram 2012-05-30 18:23 Rev.: 8770


- make awt_create_collect_buttons() independent of currently set button_length

1 lines of code changed in 1 file:

westram 2012-05-30 14:58 Rev.: 8769


* removed default params from create_option_menu calls

18 lines of code changed in 10 files:

westram 2012-05-30 14:54 Rev.: 8768


* avoid empty label at option-menu

6 lines of code changed in 4 files:

westram 2012-05-30 14:54 Rev.: 8767


* layout fix

19 lines of code changed in 1 file:

westram 2012-05-30 14:49 Rev.: 8766


* init_Advisor from add_common_property_menu_entries

7 lines of code changed in 4 files:

westram 2012-05-30 14:10 Rev.: 8765


* option menus
- attach widget in update_option_menu
- resolved several incompatibilities between menus with and w/o label
- moved menu-align-code from refresh_option_menu -> update_option_menu
- effects
* corrects X-misalignment (compared with other widget types)
* corrects Y-misalignment for Y-attached menues
* fixes partial visibility for attached menues
* most likely several misplaced option-menus (wherever xfig-label has been adjusted to compensate wrong menu-alignment)

51 lines of code changed in 1 file:

westram 2012-05-30 13:52 Rev.: 8764

* renamed refresh-functions for option_menu, toggle_field and selection_list

13 lines of code changed in 3 files:

westram 2012-05-30 10:10 Rev.: 8763


* when attaching a widget
- collect all changes in aw_xargs and send them in one step
- reduces the chances of hitting motif bug http://bugs.motifzone.net/long_list.cgi?buglist=1169 (which does a double free causing application termination)

23 lines of code changed in 1 file:

westram 2012-05-29 13:44 Rev.: 8762


* load/save for selection lists
- generic code can be configured by class !StorableSelectionList
* defines extension used for fileboxes
- all fileboxes bound to the same extension use the same awars, i.e. changing directory etc. in one of the boxes, also changes all others
* defines "what" is loaded/saved to provide proper title for popup windows
* allows to pass converter-functions to convert between selection-list-content and file-content
- default converter-functions do the job for most selection boxes
- handling for all LF types (uses !FileBuffer)
- added 'Append'-switch (append to sellist vs. overwrite)
- attached filebox to window borders
* multi-probes
- when loading saved probe-design results, multi-probe used the 'probe'-sequence, but the code internally works with the target-sequence. fixed
* it only worked when 'check complement' was checked (which was the default)
- wrote converter-functions to load old and new formats from probe-design and multi-probe
* automatically reverse-complement old-multi-probe format
* added unit tests for all supported formats
- removed 'value_equal_display'-hack from AW_selection_list (introduced by multi-probe-coders)
* probe-design
- added function to load saved probes (fixes #204)

821 lines of code changed in 23 files:

westram 2012-05-29 12:41 Rev.: 8761


- free/delete mismatch

1 lines of code changed in 1 file:

westram 2012-05-29 12:40 Rev.: 8760


- added CharPtrArray::clear()

2 lines of code changed in 2 files:

westram 2012-05-29 08:43 Rev.: 8759


- clear reused PT_LOCS handles

3 lines of code changed in 2 files:

westram 2012-05-26 10:19 Rev.: 8758


* refactored some locals

92 lines of code changed in 2 files:

westram 2012-05-26 09:17 Rev.: 8757


* probe match no longer calculates different results depending on whether PT_PDC-object was generated or not
- bonds and split are members of PT_LOCS now
* now they always exist, so several conditional calculations concerning weighted mismatches are done unconditionally now
- removed hacks (see [8755], [8741])
* probe match also depended on split-threshold (as specified in probe-design export window)
- made that value as well available in probe-match-expert-window
- renamed awar

150 lines of code changed in 9 files:

westram 2012-05-25 15:43 Rev.: 8756

formatting only (see [8755:8756])

10 lines of code changed in 1 file:

westram 2012-05-25 15:41 Rev.: 8755


* adjust probe match called from arb_probe (CL tool) to work like probe match called from GUI
- use same hack as added for multi probe in [8741]
- adjusted test results

24 lines of code changed in 1 file:

westram 2012-05-25 10:50 Rev.: 8754


- clear repeatedly used AISC object

1 lines of code changed in 1 file:

westram 2012-05-25 10:14 Rev.: 8753


* moved all prototypes/externDecls to headers (removed them from .cxx)
* fixed includes/include wrappers

60 lines of code changed in 9 files:

westram 2012-05-25 09:56 Rev.: 8752


- removed possibility to generate prototypes for static/inline functions

5 lines of code changed in 1 file:

westram 2012-05-25 09:31 Rev.: 8751


* guided by clang static checker:
- fix or at least comment many assigned but never used values

197 lines of code changed in 41 files:

epruesse 2012-05-24 19:19 Rev.: 8750

document that libmotif4 is needed/ok on Ubuntu 12.04 (and above I guess)

1 lines of code changed in 1 file:

westram 2012-05-24 11:05 Rev.: 8749


- more warnings fixed (shadow, noreturn)

7 lines of code changed in 3 files:

westram 2012-05-24 10:59 Rev.: 8748


- use simpler way to declare attributed static/inline functions

52 lines of code changed in 16 files:

westram 2012-05-24 09:23 Rev.: 8747


- fixed a few more warnings

17 lines of code changed in 4 files:

westram 2012-05-24 09:06 Rev.: 8746


- fixed NULL pointer conversions (gcc 4.6 warnings)

27 lines of code changed in 5 files:

westram 2012-05-23 07:26 Rev.: 8745


- format string fixes (32bit compile complained)

4 lines of code changed in 1 file:

westram 2012-05-22 17:11 Rev.: 8744


* AISC clients
- client-handles for server-side objects are distinguishable types now (esp. can no longer be confounded w/o compiler messages)
- main server object has to be passed to aisc_close

293 lines of code changed in 23 files:

westram 2012-05-22 16:25 Rev.: 8743


* probe_struct_global
- use setup/cleanup instead of memset-crap
* DRYed probe_statistic_struct

115 lines of code changed in 2 files:

westram 2012-05-22 10:29 Rev.: 8742


* commented AISC server side callbacks with command tokens (as used on client side)

20 lines of code changed in 1 file:

westram 2012-05-18 10:24 Rev.: 8741


- hack to fix multi-probe generation (was broken by [7276]; originating from [7263])

6 lines of code changed in 1 file:

westram 2012-05-17 09:36 Rev.: 8740


* script to edit .fig w/o specifying path

38 lines of code changed in 1 file:

westram 2012-05-17 09:35 Rev.: 8739


* progress.done on abort

1 lines of code changed in 1 file:

westram 2012-05-17 09:33 Rev.: 8738


* AW_selection_list::clear
- added flag whether to clear default entry (defaults to true, which was old hardcoded behavior)
* do not clear default entry in move_content_to
- fixes bug introduced by [8723] (move all left->right in multiprobes failed assertion)

5 lines of code changed in 2 files:

westram 2012-05-15 12:28 Rev.: 8737


* RegExpr::match returns NULL if didMatch returns false
* few simple tests for regexpr (as place to tdd complicated regular expressions)

42 lines of code changed in 3 files:

westram 2012-05-13 14:31 Rev.: 8736


* add pointers to regexpr format

4 lines of code changed in 2 files:

westram 2012-05-13 14:21 Rev.: 8735


* fixed sections in help file

3 lines of code changed in 1 file:

westram 2012-05-12 15:57 Rev.: 8734


* rename

7 lines of code changed in 2 files:

westram 2012-05-12 15:51 Rev.: 8733


* deactivated debug code in primer design (added toggle)

49 lines of code changed in 3 files:

westram 2012-05-12 13:32 Rev.: 8732


* avoid crash in !FileBuffer (when accidentally reading binary files)

4 lines of code changed in 1 file:

westram 2012-05-12 11:49 Rev.: 8731


* added CharPtrArray::resize()

17 lines of code changed in 2 files:

westram 2012-05-11 15:39 Rev.: 8730


* more renames

17 lines of code changed in 3 files:

westram 2012-05-11 15:17 Rev.: 8729


* [readability]
- renamed most selection lists still called 'id' or similar
- renamed some globals (aw_help_global->HELP, pd_gl->PD)
* removed a few more obsolete AW_window*

348 lines of code changed in 20 files:

westram 2012-05-11 14:02 Rev.: 8728


- fix wrong use of GB_strduplen

1 lines of code changed in 1 file:

westram 2012-05-11 13:03 Rev.: 8727


* updated

25 lines of code changed in 1 file:

westram 2012-05-11 12:04 Rev.: 8726


* help (mouse wheel)

34 lines of code changed in 7 files:

westram 2012-05-11 11:32 Rev.: 8725


* comments cleanup

174 lines of code changed in 62 files:

westram 2012-05-11 11:07 Rev.: 8724


* moved leftover functionality from AW_window into AW_selection_list
* removed now useless, passed around AW_window*
* AW_selection
- removed AW_window* member
- protected modifying member functions

304 lines of code changed in 29 files:

westram 2012-05-10 16:45 Rev.: 8723


* moved functionality from AW_window into AW_selection_list
* removed
- AW_selection_list::first_element/next_element (using AW_selection_list_iterator)
- removed AW_root param from selection list interface

425 lines of code changed in 34 files:

westram 2012-05-10 11:27 Rev.: 8722


* replaced old-style selection list iteration functions by AW_selection_list_iterator

103 lines of code changed in 20 files:

westram 2012-05-10 11:06 Rev.: 8721


* renames
* remove unused params

7 lines of code changed in 1 file:

westram 2012-05-10 10:11 Rev.: 8720


* support for mouse wheel
- selection lists

37 lines of code changed in 2 files:

westram 2012-05-10 10:04 Rev.: 8719


* added header arb_algo.h (idioms based on <algorithm>)
- added force_in_range
* use in DI_view_matrix

31 lines of code changed in 4 files:

westram 2012-05-10 08:49 Rev.: 8718


* change type of selection lists to XmBROWSE_SELECT
- allows scrolling through list with pressed mouse button, select on release
- when using keyboard, the element under cursor gets selected instantly

2 lines of code changed in 1 file:

westram 2012-05-09 09:29 Rev.: 8717


* support for mouse wheel
- scrolling (vertical; horizontal with ALT/META)
* for all standard canvases (NTREE, SECEDIT, ...)
* for special displays (EDIT4, DIST)
- zoom (with CTRL)
* for on all standard canvases

171 lines of code changed in 7 files:

westram 2012-05-09 09:27 Rev.: 8716


* removed redundant AW_window* param from AWT_canvas::scroll

16 lines of code changed in 5 files:

westram 2012-05-09 07:21 Rev.: 8715


* mouse button-defs
- moved from AWT -> AW (where AW_event is)
- renamed values (AWT_M_ -> AW_BUTTON_)
- use them in EDIT4

102 lines of code changed in 13 files:

westram 2012-05-08 16:10 Rev.: 8714


* DRYed mouse click event code (press/release)

16 lines of code changed in 1 file:

westram 2012-05-08 16:01 Rev.: 8713


* forward modifier state (shift, ctrl + alt/meta) to mouse events

14 lines of code changed in 1 file:

westram 2012-05-08 15:56 Rev.: 8712


* canvas zoom
- parametrized zoom-percent
- fixed zoom center position

10 lines of code changed in 2 files:

westram 2012-05-08 08:31 Rev.: 8711


- rename only

261 lines of code changed in 21 files:

westram 2012-05-07 18:11 Rev.: 8710


* fix 'Fit' for secedit (broken by [7668], came from dev/[7616])

2 lines of code changed in 1 file:

westram 2012-05-07 17:42 Rev.: 8709


* AWT_graphic_exports
- separated mixed concepts (fit vs. zoom) and get rid of several poor names
- removed redundant initialization to default values (in classes derived from AWT_graphic)
* fixes
- book-style/vertical gene-map now zoom proportional, but fit smaller width

154 lines of code changed in 8 files:

westram 2012-05-07 13:07 Rev.: 8708


* if none of 'dont_fit_...' is set, do not fit x, instead fit larger
* ignore width/height for fitting larger/smaller - instead consider scaling
* center in smaller direction (i.e. in direction not used for fitting)

23 lines of code changed in 2 files:

westram 2012-05-07 12:01 Rev.: 8707


- marked suspicious 32/64bit incompatibility
- fix test for 32bit

13 lines of code changed in 3 files:

westram 2012-05-07 11:58 Rev.: 8706


merge from saiali [8705]

4 lines of code changed in 7 files:

westram 2012-05-05 06:57 Rev.: 8704


- fix test-result changed by [8699]

6 lines of code changed in 1 file:

westram 2012-05-04 19:21 Rev.: 8703


- allow progress with zero elements (happens often, when something does not exist at all)
- force progress.done in gbt_insert_character

6 lines of code changed in 2 files:

westram 2012-05-04 19:10 Rev.: 8702


- missing IDs in calls to aw_question (all params shifted by 1; thx to gcc 4.6 for proper warnings)

3 lines of code changed in 2 files:

westram 2012-05-04 18:55 Rev.: 8701


- rename

9 lines of code changed in 4 files:

westram 2012-05-04 18:39 Rev.: 8700


- clear unused error when invalid sort tree specified

3 lines of code changed in 1 file:

westram 2012-05-04 18:26 Rev.: 8699


- add new trees to bottom of list (as done till [8552])
(breaks tests - see [8704])

10 lines of code changed in 2 files:

westram 2012-05-04 13:58 Rev.: 8698


- use most recent window for events injected by secedit

1 lines of code changed in 1 file:

westram 2012-05-04 13:55 Rev.: 8697


- removed assertion '!filled' from generic_box (fails when filled circle/rectangle is "drawn" by click-device)

2 lines of code changed in 1 file:

westram 2012-05-02 19:21 Rev.: 8696


* merge from saiali log:branches/saiali@8635-8695
- unalign center (blockop)
- modify SAI range (using ACI/SRT)
- align ranges defined by SAI
- refactorings
* block ops
* selection lists

2089 lines of code changed in 71 files:

April 2012 »

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