May 2008 Commit Log

Number of Commits:
109
Number of Active Developers:
2
westram 2008-05-30 11:36 Rev.: 5383

- warnings fixed

42 lines of code changed in 11 files:

westram 2008-05-30 11:36 Rev.: 5382

- fixed illegal access to a value which has left the visible range

3 lines of code changed in 1 file:

westram 2008-05-30 11:36 Rev.: 5381

- access to illegal position

2 lines of code changed in 1 file:

westram 2008-05-30 11:36 Rev.: 5380

- what is the advantage of an array with one element?!

17 lines of code changed in 1 file:

westram 2008-05-30 10:53 Rev.: 5379

- fixed warnings

3 lines of code changed in 2 files:

westram 2008-05-30 10:39 Rev.: 5378

- updated prototypes

65 lines of code changed in 1 file:

westram 2008-05-30 10:39 Rev.: 5377

- depends updated

14 lines of code changed in 1 file:

westram 2008-05-30 10:36 Rev.: 5376

- added strupr / strlwr comments

3 lines of code changed in 1 file:

westram 2008-05-30 10:35 Rev.: 5375

- cosmetics

1 lines of code changed in 1 file:

westram 2008-05-30 10:35 Rev.: 5374

- moved DB repair to NT_dbrepair.cxx
- fixed illegal memory access

6 lines of code changed in 1 file:

westram 2008-05-30 10:35 Rev.: 5373

- DB repair done here now
- added fix for dictionary compression bug

714 lines of code changed in 2 files:

westram 2008-05-30 10:35 Rev.: 5372

- added NT_dbrepair.o

26 lines of code changed in 1 file:

westram 2008-05-30 10:35 Rev.: 5371

- prototypes updated

15 lines of code changed in 3 files:

westram 2008-05-30 10:34 Rev.: 5370

- declared anonymous struct DictData

1 lines of code changed in 1 file:

westram 2008-05-30 10:34 Rev.: 5369

- added some comments
- cosmetics
- GB_read_pntr() now returns NULL on (decompression) error

61 lines of code changed in 1 file:

westram 2008-05-30 10:34 Rev.: 5368

- gb_load_single_key_data() does no longer raise an internal error, if an
dictionary gets deleted
- added functions to access existing directories (GB_get_dictionary,
GB_set_dictionary, GB_free_dictionary)

64 lines of code changed in 1 file:

westram 2008-05-30 10:34 Rev.: 5367

- added GBS_strforget()

5 lines of code changed in 1 file:

westram 2008-05-30 10:33 Rev.: 5366

- if alignment has length -1, do not stop with error, just print a warning
- g_b_uncompress_single_sequence_by_master(): return decompressed size
- gb_uncompress_by_sequence():
. return decompressed size
. if error reading master, return NULL and set error (instead of
returning the error message as result (sic!))

16 lines of code changed in 1 file:

westram 2008-05-30 10:33 Rev.: 5365

- cleaned up get_data_n_size()
- gb_convert_compression():
. separated copy and re-write
- gb_uncompress_by_dictionary_internal(): return decompressed size
- gb_uncompress_by_dictionary(): return NULL on error

99 lines of code changed in 1 file:

westram 2008-05-30 10:33 Rev.: 5364

- added GB_UNCOMPRESSED_SIZE()

2 lines of code changed in 1 file:

westram 2008-05-30 10:33 Rev.: 5363

- bugfix: calculate hash index according to case_sens defined in index

3 lines of code changed in 1 file:

westram 2008-05-30 10:33 Rev.: 5362

- added GBS_hash_count_value()

18 lines of code changed in 1 file:

westram 2008-05-30 10:33 Rev.: 5361

- several functions got static
- all compression functions return the new (uncompressed) size
- gb_uncompress_data():
. returns NULL in case of error
. check decompressed size vs. expected size. error on mismatch
- added GB_is_directory_compressed()

124 lines of code changed in 1 file:

westram 2008-05-30 10:32 Rev.: 5360

- added -ggdb -ggdb3

2 lines of code changed in 1 file:

baderk 2008-05-27 16:30 Rev.: 5359

Fixed multiple nodes bug in sequence quality entries (only first one was shown).

20 lines of code changed in 1 file:

westram 2008-05-26 12:06 Rev.: 5358

- replaced call to gbs_stricmp
- fixed calls to GBS_create_hash

7 lines of code changed in 1 file:

westram 2008-05-26 12:05 Rev.: 5357

- replaced calls to GBS_stricmp etc.

4 lines of code changed in 2 files:

westram 2008-05-26 12:04 Rev.: 5356

- fixed calls to GBS_create_hash

72 lines of code changed in 42 files:

westram 2008-05-26 12:01 Rev.: 5355

- prototypes updated

1 lines of code changed in 2 files:

westram 2008-05-26 12:00 Rev.: 5354

- uses GB_CALC_HASH_INDEX_CASE_IGNORED instead of own macro

3 lines of code changed in 1 file:

westram 2008-05-26 12:00 Rev.: 5353

- defines hash-index macros (now used by adhash.c and adindex.c)

32 lines of code changed in 1 file:

westram 2008-05-26 11:58 Rev.: 5352

- removed gbs_stricmp, GBS_stricmp and gbs_strnicmp (use strcasecmp and strncasecmp)
- fixed GBS_create_hash calls

4 lines of code changed in 1 file:

westram 2008-05-26 11:58 Rev.: 5351

- hash uses GB_CASE instead of bool flag
- hash-index macros: moved to adlocal.h
- added find_hash_entry to avoid duplicated code
- added write_hash (used by GBS_write_hash and GBS_write_hash_no_strdup)

89 lines of code changed in 1 file:

westram 2008-05-26 09:39 Rev.: 5350

- fixed use of GBS_strstruct functions

156 lines of code changed in 28 files:

westram 2008-05-26 09:38 Rev.: 5349

- prototypes updated

11 lines of code changed in 2 files:

westram 2008-05-26 09:38 Rev.: 5348

- changed void* to GBS_strstruct*

31 lines of code changed in 1 file:

westram 2008-05-26 09:37 Rev.: 5347

- define incomplete type GBS_strstruct

1 lines of code changed in 1 file:

westram 2008-05-23 15:32 Rev.: 5346

- bool/GB_BOOL/AW_BOOL-fixes
- replaced some casts

14 lines of code changed in 1 file:

westram 2008-05-23 15:31 Rev.: 5345

- bool/GB_BOOL/AW_BOOL-fixes

43 lines of code changed in 15 files:

westram 2008-05-23 15:28 Rev.: 5344

- gde_filter_weights: one return point
- replaced GBS_string_cmp by GBS_stricmp and GBS_string_matches

23 lines of code changed in 1 file:

westram 2008-05-23 15:27 Rev.: 5343

- use GB_CASE param for client->server-search

9 lines of code changed in 1 file:

westram 2008-05-23 15:26 Rev.: 5342

- prototypes updated

9 lines of code changed in 2 files:

westram 2008-05-23 15:26 Rev.: 5341

- changed GBS_string_cmp
- convert GB_CASE to int for perl interface

2 lines of code changed in 1 file:

westram 2008-05-23 15:25 Rev.: 5340

- use GB_CASE parameter
- changed GBS_string_[s]cmp

94 lines of code changed in 28 files:

westram 2008-05-23 15:19 Rev.: 5339

- GB_create_index:
. specify case-sensitivity when creating
. single return point
- gb_index_find:
. specify case-sensitivity (much match with created index)

54 lines of code changed in 1 file:

westram 2008-05-23 15:19 Rev.: 5338

- increased map file version to 5 (due to case-sensitivity flag
in indices)

1 lines of code changed in 1 file:

westram 2008-05-23 15:19 Rev.: 5337

- all functions with case-sensitivity flag now use GB_CASE,
so it's obvious at caller whether case is ignored or not

24 lines of code changed in 1 file:

westram 2008-05-23 15:19 Rev.: 5336

- GBS_string_cmp -> GBS_string_matches
. was working like strcmp, but this does not make sense, since
2nd parameter can contain wildcards, so it wasn't and won't
ever be used for sorting
. result changed (before: 0=="equal", now: GB_TRUE==matches)
- GBS_string_scmp -> GBS_string_matches_regexp
. result changed (before: 0=="equal", now: GB_TRUE==matches)
- added GBS_stricmp (case insensitive strcmp)

61 lines of code changed in 1 file:

westram 2008-05-23 15:18 Rev.: 5335

- added GB_CASE
- GB_BOOL is enum now

14 lines of code changed in 1 file:

westram 2008-05-23 15:18 Rev.: 5334

- added case_sensitivity to gb_index_files_struct
- new type GB_CASE

4 lines of code changed in 1 file:

westram 2008-05-23 15:17 Rev.: 5333

- MG_transfer_fields_cb: due to wrong compare, sequences were not
realigned when they were transfered using Transfer fields.

2 lines of code changed in 1 file:

westram 2008-05-22 15:01 Rev.: 5332

- simplified code

9 lines of code changed in 1 file:

westram 2008-05-22 14:59 Rev.: 5331

- fixed a bug in GBS_hash_next_element (it stopped iteration at first
hash index conflict). Maybe fixes random strange behavior with cached
taxonomies and possible, unrecognized problems with add partial
sequences in ARB_PARS.

15 lines of code changed in 1 file:

westram 2008-05-21 21:18 Rev.: 5330

- mostly const fixes

167 lines of code changed in 35 files:

westram 2008-05-21 21:17 Rev.: 5329

- depends updated

2 lines of code changed in 1 file:

westram 2008-05-21 21:16 Rev.: 5328

- avoid writing into const memory

7 lines of code changed in 1 file:

westram 2008-05-21 21:16 Rev.: 5327

- fixed illegal free of DB-memory

1 lines of code changed in 1 file:

westram 2008-05-21 21:16 Rev.: 5326

- call ./arb_valgrind not arb_valgrind

1 lines of code changed in 1 file:

westram 2008-05-21 21:15 Rev.: 5325

- prototypes updated

33 lines of code changed in 3 files:

westram 2008-05-21 21:15 Rev.: 5324

- rewrote GBS_eval_env(), now it does no longer modify const memory
and it does no rekursive expansion (if this is really used/needed
somewhere, it should be called several times instead)
- GBS_string_eval:
. do not write to const data
. removed very strange frees/dups
- several functions now return GB_CSTR:
. GBS_find_string
. GBS_regsearch
. gb_compile_regexpr
. GBS_regsearch
regexp-stuff is not test-compiled with undefined NO_REGEXPR;
have no such system.

52 lines of code changed in 1 file:

westram 2008-05-21 21:14 Rev.: 5323

- GB_login:
. only one return-point
. changes due to constness

124 lines of code changed in 1 file:

westram 2008-05-21 21:14 Rev.: 5322

- gb_findExtension gets unconst argument, cause its used
to modify writeable strings
- fixed some buffer-sizes

20 lines of code changed in 1 file:

westram 2008-05-21 21:14 Rev.: 5321

- several functions now return GB_CSTR:
. GB_read_pntr
. GB_read_char_pntr
. GB_read_link_pntr
. GB_read_bits_pntr
. GB_read_bytes_pntr
. gb_read_pntr_ts

25 lines of code changed in 1 file:

westram 2008-05-21 21:14 Rev.: 5320

- replaced strange typename GB_CPNTR (sounds const but isnt)
by GB_BUFFER and GB_CBUFFER
- added non-const wrapper for GBS_find_string (c++ only)

16 lines of code changed in 1 file:

westram 2008-05-21 20:57 Rev.: 5319

- cosmetics

1 lines of code changed in 1 file:

westram 2008-05-19 13:49 Rev.: 5318

- replacement was wrong if parent directory contained 'ARB.o' (e.g. 'ARB.openGL')

3 lines of code changed in 1 file:

westram 2008-05-19 12:14 Rev.: 5317

- now not _only_ auto-generated

65 lines of code changed in 1 file:

westram 2008-05-19 12:14 Rev.: 5316

- added target 'proto', put GDE_proto.h into CVS and updated
broken depends

9 lines of code changed in 1 file:

westram 2008-05-19 12:14 Rev.: 5315

- removed GDE_proto.h

0 lines of code changed in 1 file:

westram 2008-05-19 12:14 Rev.: 5314

- added ARB_GDE to proto

2 lines of code changed in 1 file:

westram 2008-05-19 12:05 Rev.: 5313

- prototypes updated

16 lines of code changed in 3 files:

westram 2008-05-19 12:04 Rev.: 5312

- depends updated

0 lines of code changed in 3 files:

westram 2008-05-19 12:04 Rev.: 5311

- search for '@name' is now case-sensitive!
(fixes a serious DB bug, where directories were overwritten during
DB optimization, resulting in data corruption)

9 lines of code changed in 1 file:

westram 2008-05-19 12:03 Rev.: 5310

- shorten displayed name for db in DB viewer

28 lines of code changed in 1 file:

westram 2008-05-19 11:48 Rev.: 5309

- replaced calls to GB_find with new find-functions

1092 lines of code changed in 111 files:

westram 2008-05-19 11:45 Rev.: 5308

- TEST_SOME now allows to specify the keys

15 lines of code changed in 1 file:

westram 2008-05-19 11:45 Rev.: 5307

- show key index

9 lines of code changed in 1 file:

westram 2008-05-19 11:44 Rev.: 5306

- fixed non-working 'skip newline'

3 lines of code changed in 1 file:

westram 2008-05-19 11:44 Rev.: 5305

- added POST_COMPILE
- explicit rules (avoids deleting objects after compile)
- compile arb_test + arb_perf_test only in DEBUG mode

5 lines of code changed in 1 file:

westram 2008-05-19 11:44 Rev.: 5304

- test program using different case for field names

167 lines of code changed in 1 file:

westram 2008-05-19 11:43 Rev.: 5303

- pass DEBUG flag to sub-Makefiles

2 lines of code changed in 1 file:

westram 2008-05-19 11:42 Rev.: 5302

- changed predefined prototype for P2A_find

2 lines of code changed in 1 file:

westram 2008-05-19 11:38 Rev.: 5301

- added GB_has_key()

16 lines of code changed in 1 file:

westram 2008-05-19 11:37 Rev.: 5300

- added GB_expect_error

8 lines of code changed in 1 file:

westram 2008-05-19 11:37 Rev.: 5299

- gbcms_talking_find/GBCMC_find use GB_NONE to search unspecific child

15 lines of code changed in 1 file:

westram 2008-05-19 11:37 Rev.: 5298

- added case-sensitivity parameter to functions searching for childs
with specific content
- added several replacement functions for GB_find:
GB_find_string,
GB_child, GB_nextChild,
GB_entry, GB_nextEntry,
GB_brother.
GB_find should now only be used is special cases!

80 lines of code changed in 1 file:

westram 2008-05-16 12:20 Rev.: 5297

- fix dependency paths

2 lines of code changed in 1 file:

westram 2008-05-15 18:32 Rev.: 5296

- removed test code

15 lines of code changed in 1 file:

westram 2008-05-15 09:08 Rev.: 5294

- removed adseqcompr.h

0 lines of code changed in 1 file:

westram 2008-05-13 14:43 Rev.: 5293

- prototypes updated

3 lines of code changed in 2 files:

westram 2008-05-13 14:42 Rev.: 5292

- depends updated

0 lines of code changed in 3 files:

westram 2008-05-13 14:42 Rev.: 5291

- fixed DEBUG+RELEASE compile

4 lines of code changed in 3 files:

westram 2008-05-13 14:42 Rev.: 5290

- align tree selection box to longest tree name

7 lines of code changed in 1 file:

westram 2008-05-13 14:41 Rev.: 5289

- type fix

4 lines of code changed in 1 file:

westram 2008-05-13 14:41 Rev.: 5288

- comment

2 lines of code changed in 1 file:

westram 2008-05-13 14:41 Rev.: 5287

- renamed 2 globals (size,low)

16 lines of code changed in 1 file:

westram 2008-05-13 14:40 Rev.: 5286

- added comments for GB_warning, GB_information, GB_status, GB_status2
- added GBS_readable_size (show size info in human readable form)

42 lines of code changed in 1 file:

westram 2008-05-13 14:40 Rev.: 5285

- GBT_link_tree_using_species_hash skips generation of "seen species"-hash
if duplicate-counting and status-display is off.
Else, it detects size of "seen species"-hash by counting nodes in tree,
not by counting existing species (fixes slow link on huge "zombie"-trees
in DBs with much less species)
- new parameter maxTreeNameLen to GBT_tree_info_string (used for proper text-alignment)
- comments on GBT_message

58 lines of code changed in 1 file:

westram 2008-05-13 14:40 Rev.: 5284

- Status trace now has 2 levels of detail
- Renamed 'Kill' into 'Abort' in status window
- After timeout w/o aborting, the popup-window shows
a new option 'Continue' -> Encourage user to mail to devel.
- in aw_status_timer_listen_event, one read did not update 'gaugeValue'.
Therefore some status updates where skipped, which was no problem in
most cases, but if a zero-gaugeValue (which is interpreted as "Reset
starting time") was ignored, estimated time went completely wrong.
- avoid sending int 0 to status process for low (but non-zero) gauge values

87 lines of code changed in 1 file:

westram 2008-05-13 14:40 Rev.: 5283

- nni_rek() only opens and updates status if flag is set;
before it updated always.
abort now also works if flag is cleared.

23 lines of code changed in 1 file:

westram 2008-05-13 14:39 Rev.: 5282

- added status-flag to struct isits.
when set, update status for each single species
when cleared, update status for progress over multiple species
- global optimization now abortable

40 lines of code changed in 1 file:

westram 2008-05-13 14:39 Rev.: 5281

- added functions to mark deep and degenerated branches

105 lines of code changed in 2 files:

westram 2008-05-13 14:39 Rev.: 5280

- global optimize: single status windows for optimizing sequence and
non-sequence data
- added functions to mark deep and degenerated branches

43 lines of code changed in 1 file:

westram 2008-05-13 14:37 Rev.: 5279

- GB_CTREE moved into adseqcompr.c

0 lines of code changed in 1 file:

westram 2008-05-13 14:33 Rev.: 5278

- sequence compression
. allow up to 50 sequences per master
. removed header adseqcompr.h (types were local)
. can be aborted now
. much better master distribution, to support compression trees with
degenerated branches. I had one DB where more than 300 decompression steps
where necessary to get the data of one sequence - impossible to work with.
. added test code to save tree with master-locations as groups
. much code now static
. warns if used tree is very degenerated
. displays correct status for different phases of optimization
. localized variable-scopes
. fixed compression statistic
. fixed missing frees

462 lines of code changed in 1 file:

westram 2008-05-13 14:33 Rev.: 5277

removed (types only used locally in adseqcompr.c)

0 lines of code changed in 1 file:

westram 2008-05-11 10:09 Rev.: 5276

- comment on GB_STRING_SHRT

14 lines of code changed in 1 file:

westram 2008-05-11 10:08 Rev.: 5275

- added debug code to gb_read_bin_rek_V2()
- open files in binary mode

21 lines of code changed in 1 file:

westram 2008-05-11 10:08 Rev.: 5274

- gb_write_bin_rek:
. auto-change db-type back to GB_STRING (when size is too big)
. test GB_STRING_SHRT for correct size and final zero-byte.
if test fails -> fallback to GB_STRING
Before corrupt databases where saved to disk, whenever
the string data contained a zero-byte, resulting in
unloadable databases ("Unknown DB type 0")
. added assertion to catch unknown DB types

50 lines of code changed in 1 file:

April 2008 »

Generated by StatSVN 0.7.0