December 2009 Commit Log

Number of Commits:
35
Number of Active Developers:
2
westram 2009-12-31 11:12 Rev.: 6322


- object order changed in [6321] => affects automatic prototype order

490 lines of code changed in 6 files:

westram 2009-12-31 11:01 Rev.: 6321


- renamed *.c -> *.cxx
- removed AD_MOBJECTS.h

32411 lines of code changed in 78 files:

westram 2009-12-30 20:58 Rev.: 6320


- fixed bug in arb_proto_2_xsub (strangely not reported by valgrind)

1 lines of code changed in 1 file:

westram 2009-12-30 20:47 Rev.: 6319


- [6318] broke PTPan - fixed

3 lines of code changed in 4 files:

westram 2009-12-30 19:56 Rev.: 6318


* ARBDB
- compiles as C++ (no longer compiled as plain C)
- removed ARBDB2 + ARBDBS
- removed rotten C++-wrappers (ARBDBPP)
- generates special header for perl-interface to reduce dependencies (ad_p_prot.h)
* removed (ARBDB)
- gb_search_enum (merged with GB_TYPES)
* renamed (ARBDB)
- gbs_malloc_copy -> GB_memdup
- gb_search_types -> GB_SEARCH_TYPE + renamed enum-members
* tweaked perl interface
- code in ARBDB is now able to 'die' correctly (see GBP_croak_function)
- compiles as C++
- wrote generic functions for enum <-> string conversion (perl uses strings for enum values)
- added needed conversion functions
- removed handcoded xsubs (now all are generated by arb_proto_2_xsub - nevertheless, it's still possible to define xsubs manually)
- ARB::find and ARB::find_string (3rd parameter needs different values, only one file affected: PERL_SCRIPTS/GENOME/GI.pm - fixed)
- removed all functions using GBQUARK from perl interface
* perl interface generator (arb_proto_2_xsub)
- completely rewritten
- does automatic type conversion (expecting that the needed functions are defined in ARBDB/adperl.c)
* prototype generator
- compiles as C++
- switch -F accept's '!^' as beginning-of-name expression
* removed ARB_EDIT
- moved naligner interface code to EDIT4

7189 lines of code changed in 149 files:

westram 2009-12-23 13:08 Rev.: 6317


* CONVERTALN: indent

3883 lines of code changed in 17 files:

westram 2009-12-23 12:34 Rev.: 6316


* CONVERTALN: *.c -> *.cxx

8071 lines of code changed in 34 files:

westram 2009-12-23 12:22 Rev.: 6315


* CONVERTALN
- converted K&R prototypes to ANSI (using protoize)
- compile as C++ (+fixed compile errors)
- 'make proto' creates ANSI header
- deleted unused files (swissprot.c + vaxdate.c)

415 lines of code changed in 19 files:

westram 2009-12-22 12:51 Rev.: 6314


- missed some calls in [6313]

9 lines of code changed in 3 files:

westram 2009-12-21 17:05 Rev.: 6313


- renamed SmartPtr.Null() into SmartPtr.isNull() (got a strange clash in perl XS code)

32 lines of code changed in 10 files:

westram 2009-12-20 15:26 Rev.: 6312


* made use of aw_status_counter simpler
- automatically updates status every 0.25%
- tracks user abort flag
- restartable

36 lines of code changed in 4 files:

westram 2009-12-19 16:48 Rev.: 6311


* cleaned up
- insert_species_in_tree
- moveTo
* corrected methods moveTo and insert of AP_tree_nlen
- virtual method does DOWNCAST and calls overloaded method
- virtual uses AP_tree*-params, overload AP_tree_nlen*-params. This speeds up normal operation, which does direct instead of virtual-calls. It also slows down virtual-calls, but since they are not called it does slow down nothing and it's impossible now to call AP_tree/moveTo by mistake.
* this fixes
- 'quick add marked'. SIGSEGV caused by calling AP_tree/moveTo instead of AP_tree_nlen/moveTo?
- 'remove + add all!' (assertion concerning deletion of tree-DB-entry failed)
* marked GB_print_error deprecated (fixed two calls in parsimony)
* fixed mixTree (debug function)
* removed parameter defaults from nn_interchange_rek

230 lines of code changed in 10 files:

baderk 2009-12-18 15:11 Rev.: 6310

Small fix for gcc 4.4.1

1 lines of code changed in 1 file:

westram 2009-12-18 08:49 Rev.: 6309


- compile fix

1 lines of code changed in 1 file:

westram 2009-12-17 13:00 Rev.: 6308


- db browser crashed when two consecutive parts of a db-path contained bracket-qualifier

5 lines of code changed in 1 file:

westram 2009-12-16 17:45 Rev.: 6307


- refactored AISC (data parsing and error handling)

1150 lines of code changed in 7 files:

westram 2009-12-16 15:55 Rev.: 6306


- added dependency on aisc_include.header

7 lines of code changed in 4 files:

westram 2009-12-16 12:36 Rev.: 6305


* autogenerated AISC interface depends on prototyper (and so does AISC generation in general)
* AISC prototypes no longer generate empty argument tables for 'func(void)' (because AISC prototyper will warn about that in near future)

17 lines of code changed in 4 files:

westram 2009-12-15 17:25 Rev.: 6304


- do not store empty blocks (does not change generated code, only affects dumps)

12 lines of code changed in 1 file:

westram 2009-12-15 16:53 Rev.: 6303


* write_aisc
- print key names in quotes
- print !'' instead '(null)' (like it's interpreted internally)

2 lines of code changed in 1 file:

westram 2009-12-15 16:04 Rev.: 6302


* AISC
- renamed command 'DBG' into 'DUMPDATA'
- 'DUMPDATA' accepts optional argument 'filename'
- dump loaded data structure to DUMP subdirectory (needed for tests)

38 lines of code changed in 7 files:

westram 2009-12-11 12:19 Rev.: 6301

- fix link bug (suse64?)

1 lines of code changed in 1 file:

westram 2009-12-10 17:42 Rev.: 6300


* create/delete groups for found clusters
* new tree type ARB_countedTree (knows its number of leafs)
* debug version no longer displays group data address

692 lines of code changed in 11 files:

westram 2009-12-10 17:20 Rev.: 6299


- depends + prototype

3 lines of code changed in 2 files:

westram 2009-12-10 15:00 Rev.: 6298


- print exported error when calling missing help-file

12 lines of code changed in 1 file:

westram 2009-12-10 14:50 Rev.: 6297


- removed hard coded awar names

31 lines of code changed in 1 file:

westram 2009-12-10 13:10 Rev.: 6296

* changed AP_tree to AP_tree_nlen at many places
* use usual tree downcast accessors in AP_tree_nlen


181 lines of code changed in 6 files:

westram 2009-12-10 09:16 Rev.: 6295


* added macros to overwrite accessor functions in classes derived from ARB_tree or ARB_tree_root
* renamed
- is_root -> is_root_node
- get_root -> get_root_node (AP_tree/get_root really walked up the tree, now it uses AP_tree_root, i.e. behavior changed for subtrees unlinked from main tree. Checked/fixed usage)
* removed unused member 'kl_marked'

58 lines of code changed in 16 files:

westram 2009-12-08 17:13 Rev.: 6294


* added macro ASSERT_NO_ERROR
- asserts no error occurs
- allows to drop an error result, which is known to be NULL
* fixed error handling for
- gbcm_unfold_client
- gbcmc_send_undo_commands
- GB_request_undo_type
- GB_undo
* "Cannot send data to Server" errors handled by macro using __LINE__ as error-code

210 lines of code changed in 8 files:

westram 2009-12-08 16:37 Rev.: 6293


- fixed "uninitialized" warnings

4 lines of code changed in 3 files:

westram 2009-12-03 10:04 Rev.: 6292


- free calculated clusters on_hide()

20 lines of code changed in 4 files:

westram 2009-12-03 10:03 Rev.: 6291


* added AW_window::on_hide()
- called back when window is closed
- intended use: free static data generated by functions called from window

6 lines of code changed in 2 files:

baderk 2009-12-01 16:52 Rev.: 6290

Added gcc version 4.3.4

1 lines of code changed in 1 file:

westram 2009-12-01 11:53 Rev.: 6288


* include ALL arb_*.txt into release tarball
* renamed arb_README_gcc.txt
* fixed executable flag for arb_OS_X_MacPorts.txt

59 lines of code changed in 5 files:

westram 2009-12-01 10:36 Rev.: 6286


- koala 32bit does not like homegrown getline(); renamed to GetLine()

34 lines of code changed in 1 file:

November 2009 »

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