May 2009 Commit Log

Number of Commits:
83
Number of Active Developers:
3
westram 2009-05-30 17:28 Rev.: 5969


* removed parameter 'ntw' from concatenate window - just used for one not really necessary refresh

16 lines of code changed in 3 files:

westram 2009-05-30 17:13 Rev.: 5968


* new flag -w to aisc_mkpt (add include wrapper)
* uniform style for several include wrappers
* removed duplicated includes
* removed useless nt_concatenate.hxx

706 lines of code changed in 74 files:

westram 2009-05-29 18:32 Rev.: 5967


- 64bit (int -> size_t)

8 lines of code changed in 1 file:

westram 2009-05-29 18:25 Rev.: 5966


* fixed 64bit format warnings

5 lines of code changed in 1 file:

westram 2009-05-29 18:20 Rev.: 5965


* changed (gb_data_base_type_union) i from long to int32_t
- int32_t is all GB_INT may ever handle
- int32_t has same range as long in arb32
* arb64 fails with error if int passed to GB_write_byte is outside int32_t-range.
* "fixes" #132

24 lines of code changed in 2 files:

westram 2009-05-29 15:46 Rev.: 5964


- dont display tree move buttons in release (see #71)

5 lines of code changed in 1 file:

westram 2009-05-29 15:23 Rev.: 5963


Note: Still ongoing work..

* macro feature was broken, because the used ids were not unique. Which callbacks were executed, depended on the order in which some windows were opened. This patch fixes many of them, but this patch as well breaks with most existing macro-code - sorry there's really no way how this could have been avoided.
* create unique window ids for different input masks
* accept duplicate remote commands, if only parent window differs (used for duplicated menus)
* unique 'query_id' does no longer depend on order in which query-boxes were opened (instead it's passed by caller)
* create unique menu-entry-ids for querybox submenus
* changed querybox awar names
* id "RADIAL_DISPLAY_TYPE" was used 3 times
* unique ids in NDS config
* added (AW_window) local_id()
* use local_id() to create unique ids for ARB_NTREE clone window
* callallcallbacks handles some callbacks special
- if id begins with '!' callback is skipped
- if id begins with '-' callback is delayed
* excluded several callbacks calling external tools to speed up things

363 lines of code changed in 16 files:

westram 2009-05-29 13:21 Rev.: 5962


* deleting callback structs was a really bad idea - introduced by [5948]
* fixes #177
* added warning-message for DEBUG mode

5 lines of code changed in 1 file:

westram 2009-05-29 12:16 Rev.: 5961


* more robust linefeed-handling in TreeReader (fixes #176)

41 lines of code changed in 1 file:

baderk 2009-05-29 11:59 Rev.: 5960

Additional check when deleting a database field from a species entry. (Ticket #123)
A container field cannot be removed before all its children have been removed as well.

13 lines of code changed in 1 file:

westram 2009-05-29 11:09 Rev.: 5959


* fixed crash with long tree comments (see #176)

14 lines of code changed in 1 file:

westram 2009-05-29 10:53 Rev.: 5958


* assertion if rewind fails

5 lines of code changed in 1 file:

westram 2009-05-29 09:34 Rev.: 5957


* fixes #174
* tests for overflow and terminates with error

26 lines of code changed in 1 file:

baderk 2009-05-28 17:48 Rev.: 5956

Logfile permissions set to rw-rw-rw (needed for multi-user environments).

3 lines of code changed in 1 file:

baderk 2009-05-28 16:25 Rev.: 5955

Added missing include 'algorithm'.

2 lines of code changed in 1 file:

westram 2009-05-28 15:45 Rev.: 5954


* disabled termination on duplicate id

2 lines of code changed in 1 file:

westram 2009-05-28 11:47 Rev.: 5953


* awt_create_selection_list_on_scand
- pass label for popup button - currently there are multiple buttons with same remote-command-id in query window, this offers a way to fix it.
- packed two bool params ('add_all_fields_pseudo_field' and 'include_hidden_fields') into enum 'awt_selected_fields'
* moved awt_changekey.hxx to (empty) awt_item_sel_list.hxx

150 lines of code changed in 36 files:

westram 2009-05-28 11:43 Rev.: 5952


* new target 'modified' rebuilds local modifications in svn workdir

54 lines of code changed in 2 files:

westram 2009-05-27 15:29 Rev.: 5951


* debug tool: call all callbacks

119 lines of code changed in 6 files:

westram 2009-05-27 14:26 Rev.: 5950


* patch for OSX (thx Matt)

2 lines of code changed in 1 file:

westram 2009-05-27 13:27 Rev.: 5949


* some special widgets (buttons,selections,...) appear in Expert mode only (thx elmar)

22 lines of code changed in 9 files:

westram 2009-05-27 13:10 Rev.: 5948


* now it is possible to set the sens mask for any widget (buttons, selections in radio-buttons, etc..).
* added AWT_create_debug_menu (encapsulates db browser)
* reverted order of sens-list (aka AW_buttons_struct)
* replaced AW_INSERT_BUTTON_IN_SENS_LIST by AW_root::make_sensitive(). Now only adds to sens-list, if mask != AWM_ALL
* removed unused IDs from
- insert_sub_menu
- create_menu
- create_mode
- insert_help_topic
- AW_option_menu_struct
- AW_buttons_struct
- AW_at
* removed
- (AW_window) id() - only used once in old editor (seems useless; removed there)
- (AW_root) set_sensitive and set_insensitive (those using id as param; were not used)
- (AW_root) enable_execute_macro (outdated)
* renamed
- (AW_root) set_sensitive -> apply_sensitivity
- (AW_window) mask() -> sens_mask()
- (AW_root_Motif) get_last_button_widget -> get_last_widget (because it always returns the last widget regardless whether it was a button or not). Now every call to make_sensitive sets the widget as "last-one".
* new functions
- (AW_root) define_remote_command (fails if remote-command is redefined with different callback)
- (AW_cb_struct) is_equal (used by define_remote_command)
* fixed duplicated remote commands
- all GDE duplicated resolved by [5940]
- create_trees_window (all move buttons used same id)
- Each user mask menu created "new_mask" (now they generate "new_Species_mask", "new_Gene_mask" etc.)
- species- and gene-color-submenu used same id

454 lines of code changed in 37 files:

westram 2009-05-27 12:40 Rev.: 5947


* less output on target 'rmbak'
* new target 'save_test' (called automatically for developer 'SAVETEST')

12 lines of code changed in 1 file:

arb_build 2009-05-27 11:32 Rev.: 5946

Auto version upgrade to 4.33 by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2009-05-27 11:32 Rev.: 5945


* added export2sub to list of packed sources
* fixed perl warnings

3 lines of code changed in 1 file:

westram 2009-05-26 13:32 Rev.: 5944


* one more warning

1 lines of code changed in 1 file:

westram 2009-05-26 13:28 Rev.: 5943


* fixed some warnings

23 lines of code changed in 9 files:

westram 2009-05-26 13:14 Rev.: 5942


* added AW_window::activate (activates window using show() and sending _NET_ACTIVE_WINDOW to WM)
* use activate in
- standard popups (all menu/button popups using AW_POPUP)
- special popup functions that don't bind window to menu/button
- small requesters (aw_input, aw_question, ...)
- in popup-functions of information windows. But not if info-window is minimized and user just selects a new result in search window.
- popup message window on each new message
* no-exit-shells now popdown when X-Button is pressed (e.g. MESSAGE BOX)
* fixed several special popup functions
* renamed AW_window::get_show() -> is_shown()

473 lines of code changed in 45 files:

baderk 2009-05-26 11:17 Rev.: 5941

Fix for a segfault (a 'free' fails) during pt-server creation process.

5 lines of code changed in 1 file:

westram 2009-05-26 08:36 Rev.: 5940


* removed class AWwindowinfo
* directly linked each GmenuItem to its parent Gmenu
* provide GmenuItem as callback client data (instead of AWwindowinfo)
* this avoids
- unneccessary allocation of class AWwindowinfo
- multiple AWwindowinfo's if a GDE menuitems is added multiple (most of the are added multiple times).
- the callbacks bound to the menu-topics can be identified as identical (patch using that will follow)
* Popup windows opened by GDE menuitem callbacks are stored in GmenuItem. Calling the same menuitem from different menus now re-uses the window.
* removed prototypes from GDE.cxx (and include GDE_proto.h)

263 lines of code changed in 5 files:

westram 2009-05-24 10:29 Rev.: 5939


* moved non-GUI parts from AWT/AWT_changekey.cxx to ARBDB/adChangeKey.c
* added GBT_convert_changekey
* added 'Convert fields ...' to 'Fields'-menu

thx to Elmar

528 lines of code changed in 26 files:

westram 2009-05-23 15:22 Rev.: 5938


* patch http://bugs.arb-home.de/attachment/ticket/167/adlang_sizet from Elmar (thx)
* fixes #167


4 lines of code changed in 1 file:

westram 2009-05-23 15:02 Rev.: 5937


* patch http://bugs.arb-home.de/attachment/ticket/172/gb_multi_perl from Elmar (thx)
* fixes #172


1 lines of code changed in 1 file:

westram 2009-05-23 14:53 Rev.: 5936


* patch http://bugs.arb-home.de/attachment/ticket/157/treeimport from Elmar (thx)
* fixes #157

1 lines of code changed in 1 file:

westram 2009-05-23 14:42 Rev.: 5935


* changed format for floats from '%.4g' to '%g' in GB_read_as_string ('%.4g' prints 4567.8 as "4567"). Now editing float values does sth useful - before it often seemed to have no effect.
* rewrote GB_atof using strtod. put assertion into GB_atof (fails if not completely converted) and added GB_safe_atof

22 lines of code changed in 2 files:

westram 2009-05-23 13:13 Rev.: 5934


* added GBS_trim()

11 lines of code changed in 2 files:

westram 2009-05-23 12:06 Rev.: 5933


- fixed wrong usage of AW_awar::read_string on non-string awars (thx Elmar)

10 lines of code changed in 1 file:

westram 2009-05-22 10:32 Rev.: 5932


- avoid removing callback (while running)

5 lines of code changed in 1 file:

westram 2009-05-19 15:12 Rev.: 5931


* callbacks may be nested, so we need to count nesting-level. bugfix for [5928]

4 lines of code changed in 2 files:

westram 2009-05-19 06:58 Rev.: 5930


* new func SEC_exit free's memory and unlinks callbacks from database (called as GB_atclose-callback)
* stuffed more leaks

56 lines of code changed in 9 files:

westram 2009-05-18 20:29 Rev.: 5929


* added AW_awar::read_char_pntr()
* stuffed several memory leaks

63 lines of code changed in 10 files:

westram 2009-05-18 20:08 Rev.: 5928


* cleaned GB_.._callback-mechanism
- remove callback does no longer return an error - instead GB_add_callback asserts that the callback is not already there (atm just for me, cause it failes often)
- added GB_remove_all_callbacks_to (replacing functionality of GB_remove_callback with clientdata==0 (didn't work anyway), which is a legal normal value as well.).
- added a flag 'running' to callbacks, to avoid/detect removal of callbacks while they are runnning. This can only happen in "no transaction mode". Does GBK_terminate atm
- GB_remove_callback should run w/o open transaction (and even when GB_MAIN_TYPE already is not accessible).
* fixed those rare locations where a GB_remove_callback-error was handled
* changed some GB_remove_callback's into GB_remove_all_callbacks_to

122 lines of code changed in 12 files:

westram 2009-05-18 18:23 Rev.: 5927


* added GB_atclose (instanciate callbacks called directly before GB_close deletes all data). No callback instanciated atm - still testing whether this leads somewhere.

57 lines of code changed in 4 files:

westram 2009-05-18 17:29 Rev.: 5926


* no warnings in READSEQ

3 lines of code changed in 1 file:

westram 2009-05-17 11:53 Rev.: 5925


* GBT_get_next_tree_name
- fixed a bug introduced in [5309] (always returned NULL when a name was given). Only caused tree to be deselected when deleted in Tree-Admin.
- now returns first tree when called for last tree
* use GBT_get_tree where reasonable
* rewrote a few functions (GBT_get_tree, GBT_get_next_tree_name, GBT_existing_tree)

52 lines of code changed in 7 files:

westram 2009-05-16 12:46 Rev.: 5924


* added AWT_browser_forget_db
- call it in exit functions
* corrected CLI for arb_phylo
* add new DB (import) to browser

45 lines of code changed in 9 files:

westram 2009-05-16 12:22 Rev.: 5923


* stuffed 2 small leaks

2 lines of code changed in 1 file:

westram 2009-05-16 10:40 Rev.: 5922


* renamed macros (now it's hopefully more difficult to trick myself)

50 lines of code changed in 1 file:

westram 2009-05-16 10:31 Rev.: 5921


* ignore invalid access in _XSend (motif bug)

6 lines of code changed in 2 files:

westram 2009-05-16 10:17 Rev.: 5920

* fixes #166 (free'd data already transferred to outstream)

0 lines of code changed in 1 file:

westram 2009-05-16 00:39 Rev.: 5919


* PT-server
- DEVEL_JB -> ARB_64
- save information block (containing magic and db-version)
- fail on 32bit when trying to load big database (>4Gb) created with 64-bit version

132 lines of code changed in 4 files:

westram 2009-05-15 23:10 Rev.: 5918


* PT-Server
- count mismatches vs '.' as N-mismatch (previously it used a invalid value from distance matrix depending on base compared with). This occurred when leaf in pos-tree is reached and rest of probe is matched vs. plain sequence data.
- fixed illegal memory access in probe_compress_sequence (caused by code reading over gaps using uint32_t). Most-likely caused no problems.
- removed duplicated read of sequence (one to calculate checksum and one to store sequence). Unfortunately no performance gain (result cached)
- use GB_checksum instead GBS_checksum (size of sequence is already known)

119 lines of code changed in 8 files:

westram 2009-05-15 22:51 Rev.: 5917


* depends

1 lines of code changed in 1 file:

westram 2009-05-15 22:42 Rev.: 5916


* removed unused result

2 lines of code changed in 2 files:

westram 2009-05-15 22:39 Rev.: 5915


* dump_POS_TREE - show apos and rpos

1 lines of code changed in 1 file:

westram 2009-05-15 22:22 Rev.: 5914


* debug function to dump a prefix-(sub-)tree

61 lines of code changed in 1 file:

westram 2009-05-15 20:09 Rev.: 5913


* added switch -D (debug)

14 lines of code changed in 1 file:

baderk 2009-05-15 17:31 Rev.: 5912

Added gcc 4.3.3 to the list of supported GNU compiler collections.

1 lines of code changed in 1 file:

westram 2009-05-15 13:04 Rev.: 5911


* -O2 for callgring

1 lines of code changed in 1 file:

westram 2009-05-15 13:02 Rev.: 5910


* avoid assertion for intentionally overfilled hash

16 lines of code changed in 1 file:

westram 2009-05-15 09:29 Rev.: 5909


* use strchr and strstr from standard lib

5 lines of code changed in 2 files:

westram 2009-05-14 19:30 Rev.: 5908


* source files with identical names are really a pain when using valgrind

7946 lines of code changed in 27 files:

westram 2009-05-14 17:58 Rev.: 5907


* removed GBS_free_hash_free_pointer()
- added GBS_create_dynaval_hash() providing free-function to hash
* removed GBS_hash_first_element/GBS_hash_next_element() and hash-members needed for them
- added GBS_hash_next_element_that()
* GBS_hash_do_sorted_loop writes back result of loop-function (as GBS_hash_do_loop does)
* GBS_hash_do_loop and GBS_hash_do_sorted_loop now delete elements from hash if loop-function returns 0

120 lines of code changed in 6 files:

westram 2009-05-14 15:06 Rev.: 5906


* Search&Query
- if 'any field' or 'all fields' is involved -> automatically sort by hit
- display _which_ field has '<no data>'

18 lines of code changed in 1 file:

westram 2009-05-14 12:11 Rev.: 5905


* renaming species in info window caused a zombie

2 lines of code changed in 1 file:

westram 2009-05-12 17:04 Rev.: 5904


* fixed some illegal memory access in FastAligner (ClustalV-part)

44 lines of code changed in 1 file:

westram 2009-05-12 15:05 Rev.: 5903


* default input mask written w/o tabs
* added AWT_destroy_input_masks(). Call in nt_exit before closing DB
* some safety belts in tree callbacks
* fixes crash on GB_close when input masks have been used. (crashed since [5894])

54 lines of code changed in 4 files:

westram 2009-05-12 13:16 Rev.: 5902


* added AW_root::label_is_awar replacing several code-parts doing different awar-detection
* this fixes the crash in 'ARB_NTREE/Species/Set Colors'

34 lines of code changed in 4 files:

westram 2009-05-11 17:31 Rev.: 5901


- AW_BOOL -> bool

820 lines of code changed in 92 files:

westram 2009-05-11 16:33 Rev.: 5900


- fixed senseless warning

4 lines of code changed in 3 files:

westram 2009-05-11 16:25 Rev.: 5899


* Tweaked BugReport/Registration
- system information now put into window, to let user see it
- more info from /proc (if available)

142 lines of code changed in 2 files:

westram 2009-05-08 16:17 Rev.: 5898

* default button height may be defined using AW_window::button_height()
* detect_text_size -> aw_detect_text_size (global). optimized using strcspn()
* AW_window::create_autosize_button()
- sets height of button
- asserts button is no graphical button
- asserts awar contains more than "" (otherwise autosizing makes no sense)
* AW_window::create_button uses default height (if set)
* aw_question works with questions containing linefeeds (fixed some wrong sized popups)

67 lines of code changed in 6 files:

westram 2009-05-08 13:49 Rev.: 5897

- generally added -fPIC (thx Elmar)

1 lines of code changed in 1 file:

westram 2009-05-08 13:48 Rev.: 5896

- removed undefined variable

1 lines of code changed in 1 file:

westram 2009-05-08 11:57 Rev.: 5895


* played a bit with arb_perf_test

148 lines of code changed in 1 file:

westram 2009-05-07 19:24 Rev.: 5894

* reactivated original GB_close
* removed GB_exit (use GB_close)
* gb_delete_entry now takes and invalidates a GBDATA** (to avoid further undetected usage)
* gb_do_callback_list called with GB_MAIN_TYPE (instead of possibly already deleted gb_main)
* added some missing transactions
* moved declaration of GBDATA into arbdb_base.h (and include where needed)
* GB_MAIN_TYPE is no longer void
* AW_default is no longer void
* replaced the 3 differing ways to exit EDIT4 by ED4_exit()
* added AW_root::unlink_awars_from_DB() and call in arb_ntree, arb_dist, arb_edit4, arb_pars and arb_phylo
* rewrote arb_2_ascii, arb_2_bin, arb_perf_test, arb_read_tree (single exit point, error handling)
* unlinked AWARs now return "" not "?????"
* AW_awar::read_string works only with awars of type AW_STRING. Added assertion + fixed one wrong usage.
* inlined AW_awar::get()
* added AW_awar::remove_all_callbacks() and AW_awar::remove_all_target_vars()

603 lines of code changed in 45 files:

westram 2009-05-07 09:06 Rev.: 5893


* prefix rename only ('ap'->'ph')

91 lines of code changed in 5 files:

westram 2009-05-06 14:20 Rev.: 5892


* use xmllint instead of rxp

46 lines of code changed in 6 files:

westram 2009-05-06 12:54 Rev.: 5891


* build tools differ between DEBUG/NDEBUG versions. As consequence dependencies differ as well. Force DEBUG=1 to build dependencies, to ensure DEBUG-independent dependencies.

4 lines of code changed in 1 file:

westram 2009-05-05 20:05 Rev.: 5890


* 'clean' now removes .o

6 lines of code changed in 1 file:

westram 2009-05-05 19:49 Rev.: 5889


* do NOT tar files, that reside in directories called 'unused'

1 lines of code changed in 1 file:

westram 2009-05-05 19:44 Rev.: 5888


* also test-compile macros in lib/macros

7 lines of code changed in 1 file:

westram 2009-05-05 18:08


* added resource tester (make ressource_check)
* Each ARB application has one default icon now
- if icon is missing, no fallback exists - instead the application raises an error
- all windows created under one AW_root use the same icon
- it's still possible to define special icons for special windows (but it's not used atm)
* class AW_window
- create_toggle now expects that names of toggle-graphics start with '#' (previously it accepted with and without '#')
- moved code from set_icon to aw_create_shell
- added code setting small titlebar/taskbar-icon. Works in GNOME (please report whether it works in KDE as well)
- .xpm possible for icons
* class AW_root
- renamed init() to init_root() to make function name unique for resource testing. Removed default-value for 2nd parameter
- init_root() stores 'programmname' in class member (used as name for default icon)
* fixed/removed calls to changed/removed functions
* moved all unused resources into 'unused' subfolders

3106 lines of code changed in 224 files:

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