January 2010 Commit Log

Number of Commits:
70
Number of Active Developers:
2
westram 2010-01-31 08:49 Rev.: 6396


* prefixed all STAT.a interface functions with 'STAT_'
* class ST_ML
- all members made private
- renamed several members
- new member function get_matrix_for(distance)
- new member containing former friends code. friend now declared enemy

232 lines of code changed in 13 files:

westram 2010-01-29 14:09 Rev.: 6395


* made some tree functions use 'const GBT_TREE*'
* GBT_count_nodes -> GBT_count_leafs
* removed gbt_sum_leafs (dup of GBT_count_leafs)
* renamed some functions

30 lines of code changed in 8 files:

westram 2010-01-29 13:45 Rev.: 6394


* added const version of ARB_tree::get_gbt_tree

1 lines of code changed in 1 file:

westram 2010-01-29 11:41 Rev.: 6393


* minor clean up (comments, formatting)
* use dynaval hash for st_cq_info
* fixed wrong usage of delete/delete[]
* removed unused functions
* made some functions static
* made get_ml_vectors-bug workarounds more obvious
* ST_sequence_ml::unbind_from_species does no longer try to unbind, if no species was bound

201 lines of code changed in 8 files:

westram 2010-01-29 11:40 Rev.: 6392


* display "quality" entries compressed

5 lines of code changed in 1 file:

westram 2010-01-28 16:11 Rev.: 6391


* fixed old ARB_EDIT help references
- reused help for functions available in ARB_EDIT4
- removed outdated help files
* resurrected tr_export.hlp from @5845 (has been deleted by mistake)

182 lines of code changed in 26 files:

westram 2010-01-28 13:53 Rev.: 6390


- aw_ref_to_title did not clear exported error

3 lines of code changed in 1 file:

westram 2010-01-28 12:43 Rev.: 6389


- fixed manual hyphenation

10 lines of code changed in 5 files:

westram 2010-01-28 12:42 Rev.: 6388


- reduced GDE doc to GDE-menus
- fixed links

281 lines of code changed in 5 files:

westram 2010-01-28 11:50 Rev.: 6387


- spelling

4 lines of code changed in 3 files:

westram 2010-01-28 11:49 Rev.: 6386


- check_TODO did not catch all occurrances. fixed

5 lines of code changed in 1 file:

westram 2010-01-27 09:48 Rev.: 6385


- removed trailing whitespace

2634 lines of code changed in 379 files:

westram 2010-01-27 09:42 Rev.: 6384


- excluded some generated files from TAB-check

14 lines of code changed in 1 file:

westram 2010-01-27 09:08 Rev.: 6383


- removed void

574 lines of code changed in 155 files:

westram 2010-01-27 09:05 Rev.: 6382


- updated prototypes

59 lines of code changed in 1 file:

westram 2010-01-27 08:05 Rev.: 6381


- fixed includes
- added MBI headers
- removed unused files

2253 lines of code changed in 326 files:

westram 2010-01-25 16:50 Rev.: 6380


- link against libGLU (needed for ARB/OPENGL on SuSE 11.2)

1 lines of code changed in 1 file:

westram 2010-01-25 13:16 Rev.: 6379


- added gcc 4.4 (SuSE 11.2)

1 lines of code changed in 1 file:

westram 2010-01-25 12:08 Rev.: 6378


- 'redo_links' also deleted 'lib/nas' or 'lib/pts' if they were links since [6359]. fixed

1 lines of code changed in 1 file:

westram 2010-01-25 11:39 Rev.: 6377


- 'clean' now deletes dependencies in XXX_COM (even 'rebuild' failed to refresh depends)

1 lines of code changed in 1 file:

westram 2010-01-24 18:14 Rev.: 6376


- comments
- converted c->c++
- made some doxygen-comments

256 lines of code changed in 9 files:

westram 2010-01-24 18:13 Rev.: 6375


- fixed some typos in descriptions

4 lines of code changed in 1 file:

westram 2010-01-24 16:05 Rev.: 6374


* fixed doxygen-alike comments
- either use explicit qt-style triggers (/*! and //!)
- or made them simple comments
* converted several "normal" comments into doxygen-comments
* moved many comments inside the function/struct to which they (seemed) to belong (otherwise function and comments tend to get separated over the years)
* deleted several comments
- obvious things like paraphrases of the function name
- spammy things like repeating the function prototype
* reduced comments for vertical seperation

1622 lines of code changed in 126 files:

westram 2010-01-24 12:48 Rev.: 6373


- removed unused files

0 lines of code changed in 3 files:

westram 2010-01-22 15:22 Rev.: 6372


* SECEDIT
- hackaround for out-of-sync xstrings - error message about which helix needs refolding
(related to #159)

27 lines of code changed in 3 files:

westram 2010-01-22 11:46 Rev.: 6371


* more ws fixes

13 lines of code changed in 4 files:

westram 2010-01-22 11:29 Rev.: 6370


* comments C->C++

138 lines of code changed in 1 file:

westram 2010-01-21 19:41 Rev.: 6369


* removed NOOPs

28 lines of code changed in 22 files:

westram 2010-01-21 19:33 Rev.: 6368


* prototype generation
- added depends in AISC_COM (generator+Makefile)
- generator creates same whitespace as applied with [6366]

43 lines of code changed in 2 files:

westram 2010-01-21 17:29 Rev.: 6367


* manual whitespace fix (some broken by script, some already broken b4)

521 lines of code changed in 13 files:

westram 2010-01-21 16:49 Rev.: 6366


* fixed whitespace (scripted)

20654 lines of code changed in 521 files:

westram 2010-01-21 13:42 Rev.: 6365


- changed very uncommon multiline-string format (never seen that :)

5 lines of code changed in 1 file:

westram 2010-01-20 18:05 Rev.: 6364


- use less useless comments

62 lines of code changed in 17 files:

westram 2010-01-20 17:25 Rev.: 6363


- unused file

0 lines of code changed in 1 file:

westram 2010-01-20 13:45 Rev.: 6362


* fix for [6359] + [6361]
- don't always warn about links pointing to nowhere (happens in make 'rebuild')

14 lines of code changed in 1 file:

westram 2010-01-20 13:30 Rev.: 6361


- more tests for links
- remove 3 more outdated links

24 lines of code changed in 1 file:

westram 2010-01-20 12:58 Rev.: 6360


- remove SUN tags generation
- removed wrong name CTAGS

7 lines of code changed in 1 file:

westram 2010-01-20 12:55 Rev.: 6359


* target 'clean' removes obsolete symlinks now (using new target 'redo_links')
* when generating symlinks
- distinguish between links to dirs and files
- test whether target has expected type
- error location now based on link name where possible (it's unique; link target may occur multiple)
- removed outdated links 'NALIGNER/LIBLINK' and 'TOOLS/LIBLINK'

151 lines of code changed in 2 files:

westram 2010-01-19 13:50 Rev.: 6357


- fixed type of 'not_found_counter'
- corrected format specifiers

7 lines of code changed in 4 files:

westram 2010-01-19 13:01 Rev.: 6356


* remove useless local prototypes
* made several functions static and removed prefix 'AWT_'

30 lines of code changed in 2 files:

westram 2010-01-18 15:12 Rev.: 6355


- trim spaces after AISC_MKPT_PROMOTE

4 lines of code changed in 1 file:

westram 2010-01-14 15:55 Rev.: 6354


* message about unknown species in configurations

14 lines of code changed in 1 file:

westram 2010-01-14 15:10 Rev.: 6353


* removed useless variable 'species_read'
* fixed overflow if too many missing species in configuration
- shortened error message (show only first 200 missing species)
* moved some duplicated code into ED4_init_notFoundMessage / ED4_finish_and_show_notFoundMessage

69 lines of code changed in 7 files:

westram 2010-01-13 19:15 Rev.: 6352


- condensed several comments

504 lines of code changed in 63 files:

westram 2010-01-13 17:37 Rev.: 6350


- accept arb.tgz as file (not only as link). Needed if you install ARB from source, because this creates arb.tgz (not arb.32/64.tgz)

8 lines of code changed in 1 file:

westram 2010-01-13 17:19 Rev.: 6349


- prototype updated

0 lines of code changed in 1 file:

westram 2010-01-13 16:38 Rev.: 6348


- continues [6347]

48 lines of code changed in 31 files:

westram 2010-01-13 14:41 Rev.: 6347


Moved a lot of dead code to where it belongs: into the depths of SVN.
I didn't care much: If there was no obvious reason (e.g. some coment explaining why it's still there), it has been deleted


830 lines of code changed in 274 files:

westram 2010-01-13 10:55 Rev.: 6346


* NALIGNER
- removed unused files
- removed commented out code
- fixed include-wrappers and includes
- added MBI headers

375 lines of code changed in 34 files:

westram 2010-01-12 19:00 Rev.: 6345


- fixed hard readable '} else {'

1746 lines of code changed in 162 files:

westram 2010-01-12 17:10 Rev.: 6344


- comments (c->c++). finishes [6328]

1075 lines of code changed in 24 files:

westram 2010-01-12 15:37 Rev.: 6343


* fixed an old bug in AISC client code (illegal free)
- occurred e.g. when doing probeMatch+stopPtServer+probeMatch

8 lines of code changed in 2 files:

westram 2010-01-12 13:12 Rev.: 6342


* AISC memory tester
- replaced unportable usage of SUN signal internas by a simple flag (as always, KISS)
- added longjmp to recover from possible SEGV (caused by client sending illegal address)
- rewrote client memory tester in ARBDB in the same way (gbcm_test_address). Moved to GBK_install_SIGSEGV_handler and implemented signal suppression there
* made several functions in AISC server static
* made several functions in ARBDB static
- relocated some functions in adcomm.cxx
* globally removed leftover SUN-specific code
* increased available memory (default fallback) from 512 Mb to 1 Gb
* ARBDB no longer overwrites already installed SIGSEGV handlers
- prints a warning in DEBUG mode
* signal handlers
- renamed type (SIG_PF -> SigHandler)
- removed casts and corrected wrong function types (signal handlers do not return any values - they either return or not)
- added assertions to all signal-handler installations (assert that no handler has been installed before)
* AISC clients now store/restore previously installed SIGPIPE handlers
- ARB_NTREE for example, disabled it's own handler (used by DB server to detect disconnected clients) by connecting to any AISC server (pt_server, nameserver)
* make depends did not update depends in PROBE_COM and NAMES_COM

796 lines of code changed in 26 files:

westram 2010-01-11 13:15 Rev.: 6340


- greyed out parsimony weights in novice mode (#214)

2 lines of code changed in 1 file:

westram 2010-01-11 12:42 Rev.: 6338


- updated arb build instructions (LD_LIBRARY_PATH, make tarfile, etc.)

29 lines of code changed in 1 file:

westram 2010-01-08 17:33 Rev.: 6337


- minor comment fix (!signal)

7 lines of code changed in 2 files:

westram 2010-01-08 13:59 Rev.: 6336


- do not export error in arb_look_and_start_server()

4 lines of code changed in 1 file:

westram 2010-01-07 17:17 Rev.: 6335


- simplified several boolean expressions

62 lines of code changed in 18 files:

westram 2010-01-07 16:21 Rev.: 6334


- AP_BOOL -> bool

98 lines of code changed in 9 files:

westram 2010-01-07 15:50 Rev.: 6333


- removed old ARB editor (#51)

0 lines of code changed in 25 files:

westram 2010-01-07 15:21 Rev.: 6332


- GB_BOOL -> bool

372 lines of code changed in 87 files:

westram 2010-01-07 14:07 Rev.: 6331


* removed GB_strdup
* moved freeset, nulldup, etc to own header (dupstr.h)
* added freenull
- replacement for freeset(var,NULL)
- freeset is a template now and does no longer work with NULL/0
- replaced all occurrances

565 lines of code changed in 125 files:

westram 2010-01-07 11:38 Rev.: 6330


* ARBDB structs
- removed typedef (and type synonyms caused by them)
- renamed several local types

176 lines of code changed in 8 files:

westram 2010-01-07 10:04 Rev.: 6329


* ARBDB enums
- removed typedefs (enums are already types). fixed type synonyms
- changed enum values to UPPERCASE

178 lines of code changed in 21 files:

westram 2010-01-06 18:52 Rev.: 6328


* comments
- converted C->C++
- cleanup
* GB_is_directory_compressed -> GB_is_dictionary_compressed :)

923 lines of code changed in 28 files:

westram 2010-01-06 14:28 Rev.: 6327


picky!

2 lines of code changed in 1 file:

westram 2010-01-06 14:15 Rev.: 6326

- fixed format strings (from 64bit warnings)

5 lines of code changed in 4 files:

westram 2010-01-06 14:03 Rev.: 6325


* ARBDB
- hide internal structures (GBDATA etc.) inside ARBDB. Fixed all layer violations
- splitted up big header files into many. Did not reduce much internal dependencies, but at least there's some kind of semantic separation now.
- moved many decls right into the .cxx file (if only used in one)
- removed several duplicated type-names like
{{{
typedef struct gb_main_type {
...
} GB_MAIN_TYPE;
}}}
- GB_HASHI -> GB_NUMHASH + functions renamed
- gb_assert no longer globally visible. replaced
- fixed includes
- local (ARBDB internal) headers all start with prefix 'gb_'

3892 lines of code changed in 132 files:

westram 2010-01-06 12:27 Rev.: 6324


- formatting
- GB_INLINE -> inline

76 lines of code changed in 4 files:

baderk 2010-01-04 09:30 Rev.: 6323

gcc v4.4.1 patches.

5 lines of code changed in 5 files:

December 2009 »

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