- mark all species with distance to selected failed when any species in DB was missing data in the selected alignment
18 lines of code changed in 1 file:
- fix predefined ranges (broken by [11267])
1 lines of code changed in 1 file:
* fix #439 and #440
- rename refresh_matrix_display -> matrix_changed_cb
* force a setup there (needed since the matrix has changed)
- when calculating compressed matrix
* always forget matrix - otherwise !MatrixDisplay does not adapt to changed tree-folding
* do refresh AFTER compressing the matrix (was done before, causing setup to wrong size)
- adapt_to_canvas_size:
* reset page_size if no matrix
* force NEED_CLEAR on next draw()
28 lines of code changed in 2 files:
* !MatrixDisplay
- different possible update-levels are now driven by flags
- should not change behavior
82 lines of code changed in 3 files:
* DI_dmatrix -> !MatrixDisplay
- renamed instances
72 lines of code changed in 3 files:
* eliminate unused, but confusing member di_matrix from DI_dmatrix
- useless since [8450] (guessed)
9 lines of code changed in 3 files:
- avoid using uninitialized value if the line has no length (i.e. is a point)
4 lines of code changed in 1 file:
- typed callbacks in DIST
100 lines of code changed in 4 files:
- mark test as slow
1 lines of code changed in 1 file:
* use correct type for MutableItemSelector::selection_list_rescan_cb
35 lines of code changed in 8 files:
* typed some more globally used callbacks
- AW_create_gc_window
- popup_select_species_field_window
- AWT_create_nds_window
- AWT_popup_select_srtaci_window
* typed callbacks in
- SL/NDS
- SL/ITEMS (except one more complicated in !MutableItemSelector)
43 lines of code changed in 15 files:
* no deprecation warning for GB_export_errorf atm; reactivate when deprecated callbacks are gone
* added {{{__ATTR__DEPRECATED_LATER}}}
* remove disfunctional deprecation code from cb.h
6 lines of code changed in 4 files:
* typed callback for
- uses of COLSTAT_create_selection_window()
- inside STAT
9 lines of code changed in 3 files:
* use awt_create_select_filter_win() as typed callback
* removed superfluous struct keyword
* renamed some variables ('cd'-ex)
24 lines of code changed in 10 files:
- detect interrupted tests and show early in compile log
25 lines of code changed in 1 file:
* create_hierarchy: check if any sequence terminal has been created
- if none created => terminate editor
- may happen @ startup or when loading new config
- fixes #351
10 lines of code changed in 1 file:
- remove matrix-changed-callback before exiting (fixes #423)
2 lines of code changed in 2 files:
- fix more failing macro-recording assertions
3 lines of code changed in 2 files:
* cleanup merge_scheme (esp. close databases on error or cancel)
13 lines of code changed in 1 file:
* use typed callbacks in mergetool startup code
21 lines of code changed in 2 files:
* cleanup callback interface of awt_create_load_box
44 lines of code changed in 5 files:
- need cb.h in awt_sel_boxes.hxx
6 lines of code changed in 21 files:
* publish makeWindowPopper
* added similar makeWindowReplacer (popup new window, popdown caller window)
* moved window creation/registration into separate function find_or_createAndRegisterWindow
21 lines of code changed in 2 files:
- removed unused function (relict from [11240])
0 lines of code changed in 1 file:
* use typed callbacks in MERGE
* removed MG_popup_if_renamed (using [11242] instead)
221 lines of code changed in 11 files:
* use typed callbacks in TREE_ADMIN
24 lines of code changed in 4 files:
* accept that !CreateWindowCallback returns NULL
- interpreted as "cant create window (yet)"
14 lines of code changed in 1 file:
* eliminate PARS_export_cb
- 'mode & 1' was always false
4 lines of code changed in 1 file:
* pars_check_size:
- distinguish between error and warning
* error -> show message + return to intro window, instead of loading "no tree"
26 lines of code changed in 1 file:
* inlined PH_matr.cxx
11 lines of code changed in 4 files:
- no need to save in properties (overwritten anyway)
1 lines of code changed in 1 file:
* eliminate unneeded includes
2 lines of code changed in 2 files:
* eliminated dead AWARs
3 lines of code changed in 2 files:
* eliminated GLOBAL_gb_main
111 lines of code changed in 6 files:
* removed debug code
0 lines of code changed in 2 files:
* fixed format strings
2 lines of code changed in 1 file:
* ARB_PHYLO alignment selection
- made window resizable
- added 'Abort' button (needed for gtk-close action)
- fixed resource handling in ph_exit (to support 'Abort' button)
* eliminated now unused callback parameters
38 lines of code changed in 2 files:
* remove unnecessary cb param
8 lines of code changed in 1 file:
* fix assertion failure if no valid alignment selected in startup window
- show error and stay in alignment selection
* alignment selection starts with default-alignment selected
38 lines of code changed in 1 file:
* typed callbacks
15 lines of code changed in 2 files:
- wrong placed comment
2 lines of code changed in 1 file:
- reduce diff between trunk<>gtk
6 lines of code changed in 3 files:
- use simple interface for AW_preset_window and AW_save_properties
21 lines of code changed in 9 files:
- one awar forgotten in [11215]
6 lines of code changed in 2 files:
* adapt to gtk
8 lines of code changed in 1 file:
* define explicit typedefs for simplest flavours of !RootCallback, !WindowCallback and !CreateWindowCallback
* add convenience wrappers to AW_window
- insert_menu_topic() and callback() accept !CreateWindowCallbackSimple and !WindowCallbackSimple
16 lines of code changed in 3 files:
* removed last "usage" of AW_Window_Creator (in NT_global; was not used)
* removed obsolete callback types (AW_Window_Creator, AW_PPP, AWC_CB)
18 lines of code changed in 6 files:
* replaced magic AWAR names
* marked possibly obsolete AWARs
129 lines of code changed in 6 files:
* merge [11187] from 'tree' into 'trunk':
108 lines of code changed in 1 file:
- remove dummy awars (relict?!)
1 lines of code changed in 2 files:
* fix double-delete of aw_root (happened by: run arb_ntree with invalid DB; press EXIT)
* dont show stupid 'User abort' popups before terminating ARB_NTREE
* set !NullTracker for startup-popups
8 lines of code changed in 1 file:
- expired as expected
0 lines of code changed in 1 file:
* fix issues documented in [11208]
- GB_canonical_path does now a fallback to '.' (instead of failing an assertion)
- GB_split_full_path does special handling for '.', '..' and '/' (rootdir)
* may now return only directory
25 lines of code changed in 1 file:
* added some unittests
- provokes same assertion failure as running 'arb_ntree blubb' (commented out)
- GB_split_full_path:
* document some unwanted behavior
* test reversibility via GB_concat_path/GB_append_suffix
87 lines of code changed in 2 files:
* redo [11145]; was undone in [11205] for gtk_only
2 lines of code changed in 1 file:
* DRYed window-local awarname-generation (for scrollbars; see also aw_size_awar_name 4 further DRY)
40 lines of code changed in 4 files:
* fixes for [11199]
- compilation failed for DEBUG=1/UNITTEST=0
- savetest failed
9 lines of code changed in 2 files:
* test action ids present at end of main-window-setup
- in ARB_NTREE and ARB_EDIT4
- will help fixing #428
743 lines of code changed in 11 files:
- fix savetest
1 lines of code changed in 2 files:
* move wrong placed userland-files (fixing effects of #425)
147 lines of code changed in 8 files:
* fixes #425
20 lines of code changed in 1 file:
* use EXISTING(!) faked homedir for unittests
- otherwise code behaves different, e.g. tries to create /fakehome (which fails), ...
7 lines of code changed in 3 files:
* added test showing what's broken in #425
* use faked environment values in that test and in another interfering test
- there's still a general problem with functions like GB_getenvHOME; added test showing that hook is ignored there
30 lines of code changed in 4 files:
* merge [11183] from 'tree' into 'trunk':
66 lines of code changed in 2 files:
* added some often used test-scopes
5 lines of code changed in 1 file:
* allow to restrict test-scope to test-functions matching a given regexpr (no recompile needed)
38 lines of code changed in 4 files:
- fix for svn client 1.8.4 (suse 13.1)
8 lines of code changed in 1 file:
* mention library needed for compilation under SuSE 13.1
1 lines of code changed in 1 file:
* fixes compilation with COVERAGE!=0 (was broken by [10956])
1 lines of code changed in 1 file:
- disable old aligner (crashing)
1 lines of code changed in 1 file:
* removed reference to old aligner (relict from [6333])
0 lines of code changed in 1 file:
* prefer lines over text for rotate-, length- and spread-mode (fixes #415)
34 lines of code changed in 3 files:
* inline AW_getBestClick in AWT_graphic_event::best_click
- replace only other use in ARB_DIST by explicitely creating an AWT_graphic_event
15 lines of code changed in 3 files:
- move AW_getBestClick from WINDOW -> AWT
38 lines of code changed in 4 files:
- leak stuffed
1 lines of code changed in 1 file:
- let valgrind fail external valgrinded calls done from inside unittests with exitcode!=0 (if it detects errors)
- if caller does not check the exitcode (or if test-success does not rely on exitcode==0) the whole testsuite still may succeed, even if some valgrind errors were reported (in external call)
1 lines of code changed in 1 file:
* stuffed leak in "rename species"
* Note: atm all unittests pass with valgrind activated
4 lines of code changed in 3 files:
* overlapping strcpy -> memmove
2 lines of code changed in 1 file:
* avoid code signaling SEGV is called when running under valgrind
2 lines of code changed in 2 files:
* avoid sending uninitialized bytes over comm-interface (not harmful, but valgrind complains)
40 lines of code changed in 3 files:
* use new/delete for gb_callback and gb_callback_list, ensuring dynamic data bound to callbacks gets deleted
60 lines of code changed in 4 files:
* potential bugfixes
- always initialize Main->keys[].compression_mask (not only when increasing key-array-size)
- first call to gb_create_key_array with index>1000 would have allocated wrong array-size (possible to happen in clients if server provides more than 1000 keys)
5 lines of code changed in 1 file:
* dynamically allocate table for N-match->mismatch calculation
- fixes #410 (buffer-overflow)
Thanks to Paavo Jumppanen
25 lines of code changed in 3 files:
* reproduce #410 in unittest
32 lines of code changed in 1 file:
- run assertion-failing test in NDEBUG version (i guess, it's not a real buffer-overflow for the example used here - just a possible overflow)
7 lines of code changed in 1 file:
- document buffer overflow in ptserver (as detected by paavo)
19 lines of code changed in 1 file:
* probe match
- specify mismatches using inputfield (implements #411)
- slight layout changes (longer probe input field)
33 lines of code changed in 2 files:
* remove AWAR_MIN_MISMATCHES
- no such functionality provided by ptserver (maybe it was planned but not implemented?)
- use local awar following common naming scheme in EDIT4
1 lines of code changed in 3 files:
- use runtime assertion (expression not detected as const by older gcc/clang)
2 lines of code changed in 1 file:
- add AW_awar::set_min
1 lines of code changed in 1 file:
- implement AW_awar::get_min/get_max (were added in gtk)
28 lines of code changed in 2 files:
* allow to use vertical branch-parts and bootstrap-text as drag&drop elements
- draw vertical parts of branches as "branch-lines" (defines orientation node->tip)
- changed some predefined filters
* vert_line_filter + remark_text_filter (+ AW_CLICK + AW_CLICK_DROP)
* root_filter (not clickable; afaik not intended)
* new filter bs_circle_filter (for bootstrap circles; not clickable)
* made all filters const
30 lines of code changed in 3 files:
* updated resource-checker
* force detection of undetected helpfiles
* remove unused fig (since [10120])
43 lines of code changed in 3 files:
* use makeHelpCallback
12 lines of code changed in 9 files:
* unified names of mode-pixmaps and -helpfiles
* renamed modes (using separate enum values for distinct modes)
* sorted modes according to their usage in arb applications
871 lines of code changed in 56 files:
* separate AWT_MODE_EDIT and AWT_MODE_INFO
- afaik there is no need to use consecutive mode code-numbers
9 lines of code changed in 6 files:
* warn if command mode is inappropriate for tree display type
* remove unused member
18 lines of code changed in 2 files:
- DRYed help for modes
28 lines of code changed in 11 files:
- removed reset-mode (useless since [11126])
0 lines of code changed in 8 files:
* provide reference to AWT_graphic_exports of treedisplay to every Dragged
- remove all AWT_graphic_exports-parameters
* fixes leftover drag indicator in gtk-version by forcing refresh
72 lines of code changed in 1 file:
* mostly only code-moves (adapting to code-moves in gtk_only)
* else
- stole some comments from gtk
- added same diff-syncs as in [11134]
- made get_window_title const
827 lines of code changed in 2 files:
don't try accessing awar if awar_tree_name is NULL (fixes #407)
4 lines of code changed in 1 file:
* reintegrates 'redev' into 'trunk':
- fixed tree key-bindings (mark, fold, ...)
- improved several tree-commands (move, rotate, spread, length, width)
- fixed #68
* adds:
- log:branches/dev@7912,7914,7938,7942:7943
- log:branches/redev@11088:11119,11122:11125
1672 lines of code changed in 47 files:
* merge (11120 11121) from 'redev' into 'trunk':
- fixes a bug in K.L. optimizer
* adds:
- log:branches/redev@11120:11121
11 lines of code changed in 2 files:
* 'TEST_gpt.arb' is generated by another test
- under some conditions it was missing, causing the test to fail
- use not-generated file instead
1 lines of code changed in 1 file:
- get rid of {{{declaration of 'Mask' shadows a global declaration}}}
5 lines of code changed in 2 files:
- depends for [11092]
37 lines of code changed in 12 files:
- redo another useless codemove to allow merging click device changes
84 lines of code changed in 6 files:
- fix gcc 4.8.1 compile (was broken by [10956])
1 lines of code changed in 1 file:
* ptserver failed to build when species w/o data in the selected alignment existed
- PT_prepare_species_sequence no longer reports an error for missing data (that error was ignored anyway)
- delete species w/o data during '-build_clean' phase
18 lines of code changed in 1 file:
- do NOT fail '-build_clean'-phase with error if DB already has been prepared
19 lines of code changed in 1 file:
- push security while preparing db for ptserver
- fixes failures caused by data security of common databases
9 lines of code changed in 1 file:
- do not fail progress-assertion in error-case
4 lines of code changed in 1 file:
* reintegrates meaningless branch 'aci' into 'trunk':
* adds:
- log:branches/aci@10846:11080
26 lines of code changed in 4 files:
* merge (10844 10845) from 'aci' into 'trunk':
* adds:
- log:branches/aci@10844:10845
- log:branches/dev@7288:7291,7294:7296,7824:7828,7830,7833:7834,7837:7838,7841:7843,7845:7848,7939
1374 lines of code changed in 8 files:
* species config window
- attach sellist to XY
- attach buttons to X
16 lines of code changed in 1 file:
- revert [10881] (see #399)
11 lines of code changed in 1 file:
* truncate strings used for display in selection lists
- fixes
{{{
X Error of failed request: BadLength (poly request too large or internal Xlib length error)
Major opcode of failed request: 74 (X_PolyText8)
}}}
for strings larger than ~750k
32 lines of code changed in 2 files:
* typed callbacks
10 lines of code changed in 2 files:
* tested 'arb' script with EMPTY environment. sets defaults for
- $HOME ('~'; seems to work; might be problematic, but i have no better idea how to get a default)
- $DISPLAY (':0')
10 lines of code changed in 1 file:
* '~/.arb_prop' replaced by environmentvariable ARB_PROP
- define/accept $ARB_PROP in 'arb' script
- replaced all hardcoded occurrences
- corrected several help files
* fixed two conditions in 'arb'-script (broken by [11064])
@elmar '-u' = fail early = good idea :)
57 lines of code changed in 13 files:
fix ARB not launching if ARBHOME unset or if no parameter supplied
was broken by r11064 -- is "-u" really a good idea?
2 lines of code changed in 1 file:
* use GBS_static_string
2 lines of code changed in 1 file:
* arb startup script
- now fails on undefined variables
- fix tests for unset variables
8 lines of code changed in 1 file:
* use member initializers in Hs_struct-ctor
10 lines of code changed in 1 file:
* stop using malloc.h
4 lines of code changed in 8 files:
* reintegrates 'ptsfix' into 'trunk':
* adds:
- log:branches/ptsdump@8966:9000
- log:branches/ptsfix@8965:9012,9014:9017,9019:9023,9025:9046,9048:9089,9091:9114,9116:9132,9134:9139,9141:9145,9147:9151,9153:9158,9160:9379,9381:11059
- log:branches/ptsstartup@9160:9235,9237:9278,9280:9336,9339:9361,9363:9446
- log:branches/ptsundef@9061:9358
13004 lines of code changed in 116 files:
- predefine and use common GB_CB_TYPE combinations
39 lines of code changed in 12 files:
* remove deprecated !TypedDatabaseCallback interface
1 lines of code changed in 2 files:
* remove deprecated DB callback interface
0 lines of code changed in 2 files:
* include ad_cb.h in arbdb.cxx
- deprecates old callback interface
* use typed callbacks in callback tests
25 lines of code changed in 2 files:
* use AWT_expose_cb as typed DB callbacks (completes [10906])
2 lines of code changed in 2 files:
* use typed DB callbacks (rest)
73 lines of code changed in 14 files:
* use typed DB callbacks (AWT)
17 lines of code changed in 4 files:
* use typed DB callbacks (infowin+searchtool)
9 lines of code changed in 2 files:
* use typed DB callbacks (ARBDB)
16 lines of code changed in 2 files:
* use typed DB callbacks (tree related)
14 lines of code changed in 3 files:
* link cb_base.h
3 lines of code changed in 2 files:
* use typed DB callbacks (in EDIT4/SECEDIT)
35 lines of code changed in 6 files:
* use typed DB callbacks (in WINDOW)
18 lines of code changed in 5 files:
* untabified
9 lines of code changed in 1 file:
* depends for [11033]
199 lines of code changed in 42 files:
* added a bunch of callback signature accepted by makeDatabaseCallback
- allow 1st parameter of type UNFIXED (allows to use same function for !DatabaseCallback and Window/RootCallback)
- allow to skip 3rd parameter (GB_CB_TYPE)
- allow callbacks w/o arguments
* added cb_base.h (allows to use UNFIXED in interfaces)
* removed cyclic include cbtypes.h <-> cb.h
46 lines of code changed in 3 files:
* declare old DB-callback interface deprecated
14 lines of code changed in 4 files:
* gb_cb_spec -> !TypedDatabaseCallback
27 lines of code changed in 4 files:
* gb_cb_spec
- store callback as !DatabaseCallback
- get_info() prints readable GB_CB_TYPE (affects DB-browser)
* added overloads expecting !DatabaseCallback for
- GB_add_callback
- GB_remove_callback
- GB_ensure_callback
- use each of them in one example (tested each; work fine)
* added same_function_as() comparator to callback-templates
93 lines of code changed in 7 files:
* print readable callback function names in DB-browser
- not much value added because it only works for non-static function and most callbacks are static functions :(
- example of non-static callback:
* start NT, open SAI/ManageSAIs
* open DB-browser, goto node '/extended_data'
20 lines of code changed in 5 files:
* gb_cb_spec: made members private
55 lines of code changed in 4 files:
* hide gb_cb_spec + gb_callback
29 lines of code changed in 5 files:
* publish DB callback interface separately from rest of DB interface
183 lines of code changed in 58 files:
* allow '+' for simple AND-match (-F and -S)
34 lines of code changed in 1 file:
* remove class init via memset (arb_prm_struct + AW_xfig)
34 lines of code changed in 4 files:
- added compatibility wrapper for unordered_map (arb_unordered_map)
- use arb_unordered_map somewhere
43 lines of code changed in 5 files: