May 2007 Commit Log

Number of Commits:
151
Number of Active Developers:
2
westram 2007-05-30 15:57 Rev.: 4653

- depends updated

7 lines of code changed in 1 file:

westram 2007-05-30 15:57 Rev.: 4652

- 'depends' is an empty target now, .depends are generated on-the-fly

3 lines of code changed in 3 files:

westram 2007-05-30 15:20 Rev.: 4651

- ingnore generated code

1 lines of code changed in 1 file:

westram 2007-05-30 15:19 Rev.: 4650

- generate perlmain.c (now not CVS) from perlmain_source.c (CVS)
(cause it's removed by 'clean')
I can't detect where perlmain.c is used. [sic]

8 lines of code changed in 1 file:

westram 2007-05-30 14:47 Rev.: 4649

- const fixes
- gb_uncompress_by_sequence():
. const fixes
. type-punning fixes
. proper variable visability

30 lines of code changed in 1 file:

westram 2007-05-30 14:47 Rev.: 4648

- type-punning fixes
- added gbl_new_param()

41 lines of code changed in 1 file:

westram 2007-05-30 14:47 Rev.: 4647

- type-punning fix

12 lines of code changed in 2 files:

westram 2007-05-30 14:46 Rev.: 4646

- proper 'clean'
- added missing object to $(CPP_OBJECTS)

3 lines of code changed in 1 file:

westram 2007-05-30 14:46 Rev.: 4645

- added depends

2 lines of code changed in 1 file:

westram 2007-05-30 14:46 Rev.: 4644

- former code from ../Makefile

87 lines of code changed in 1 file:

westram 2007-05-30 14:46 Rev.: 4643

- forward AUTODEPENDS to AISC

1 lines of code changed in 1 file:

westram 2007-05-30 14:46 Rev.: 4642

- added 'clean'
- removed wrong target

2 lines of code changed in 1 file:

westram 2007-05-30 14:46 Rev.: 4641

- cosmetics

6 lines of code changed in 1 file:

westram 2007-05-30 14:46 Rev.: 4640

- proper 'clean'

7 lines of code changed in 2 files:

westram 2007-05-30 14:46 Rev.: 4639

- added 'clean'

6 lines of code changed in 1 file:

westram 2007-05-30 14:45 Rev.: 4638

- 'clean' does not expect (and try to build) '.depends'

4 lines of code changed in 1 file:

westram 2007-05-30 14:45 Rev.: 4637

- proper call of AISC/clean

1 lines of code changed in 1 file:

westram 2007-05-30 14:42 Rev.: 4636

- forward 'clean' to subdirs

33 lines of code changed in 4 files:

westram 2007-05-30 14:39 Rev.: 4635

- added 'clean'

169 lines of code changed in 47 files:

westram 2007-05-30 14:34 Rev.: 4634

- proper clean (avoid errors if already cleaned)

41 lines of code changed in 23 files:

westram 2007-05-30 14:29 Rev.: 4633

- added default for ARB_64

1 lines of code changed in 1 file:

westram 2007-05-30 14:28 Rev.: 4632

- added ARB_64 flag
- removed CLEAN_BEFORE_MAKE (no longer needed)
- added target-template '%.clean' (to perform proper subdir-cleaning)
- fixed setting of AUTODEPENDS (1 for '%.depends' and '%.dummy', 0 for '%.clean')
- moved commands of 'make perl' into sub-makefile (PERL2ARB/Makefile.main)
- added 'perl_clean' (called by 'clean')
- removed target 'realclean' (now 'clean' always removes everything)

90 lines of code changed in 1 file:

westram 2007-05-30 12:58 Rev.: 4631

- temporary fix for worst refresh problem (thx to Elmar)

2 lines of code changed in 1 file:

westram 2007-05-24 13:32 Rev.: 4630

- updated

0 lines of code changed in 1 file:

westram 2007-05-24 13:32 Rev.: 4629

- avoid noreturn-warning for nt_exit

5 lines of code changed in 1 file:

westram 2007-05-24 13:32 Rev.: 4628

- ali_error / ali_fatal_error: non-inline + noreturn-attribute

10 lines of code changed in 1 file:

westram 2007-05-24 13:32 Rev.: 4627

- ali_error / ali_fatal_error: non-inline

11 lines of code changed in 1 file:

westram 2007-05-24 13:32 Rev.: 4626

- fixed main-prototype

1 lines of code changed in 1 file:

westram 2007-05-24 13:32 Rev.: 4625

- noreturn-attribute

10 lines of code changed in 6 files:

westram 2007-05-24 13:31 Rev.: 4624

- GBS_strdup -> GB_strdup

5 lines of code changed in 4 files:

westram 2007-05-24 13:31 Rev.: 4623

- removed GBS_strdup (GB_strdup is identical)

0 lines of code changed in 1 file:

westram 2007-05-23 17:18 Rev.: 4622

- gcc 2.95 fix

14 lines of code changed in 1 file:

westram 2007-05-23 17:18 Rev.: 4621

- oops, nt_exit does return in NDEBUG mode

1 lines of code changed in 2 files:

westram 2007-05-23 16:56 Rev.: 4620

- fixed type-punning

2 lines of code changed in 1 file:

westram 2007-05-23 16:55 Rev.: 4619

- updated prototypes

177 lines of code changed in 9 files:

westram 2007-05-23 16:54 Rev.: 4618

- always define GB_INLINE as inline (have to test with gcc 2.95.x)

5 lines of code changed in 1 file:

westram 2007-05-23 16:54 Rev.: 4617

- made several functions static

7 lines of code changed in 1 file:

westram 2007-05-23 16:53 Rev.: 4616

- made function static

1 lines of code changed in 1 file:

westram 2007-05-23 16:53 Rev.: 4615

- added format-attribute to TRS_export_error()
- forward filename needed for error-message
- GB_INLINE->inline
- made several functions static

39 lines of code changed in 1 file:

westram 2007-05-23 16:53 Rev.: 4614

- added struct arb_params as promotion,
because servercntrl.h is generated now

25 lines of code changed in 1 file:

westram 2007-05-23 16:53 Rev.: 4613

- now generated

15 lines of code changed in 1 file:

westram 2007-05-23 16:53 Rev.: 4612

- now always implement

0 lines of code changed in 1 file:

westram 2007-05-23 16:53 Rev.: 4611

- always implement code from probe_tree.hxx

0 lines of code changed in 1 file:

westram 2007-05-23 16:53 Rev.: 4610

- uninitialized variable

2 lines of code changed in 1 file:

westram 2007-05-23 16:52 Rev.: 4609

- removed obsolete nt_date.h

0 lines of code changed in 1 file:

westram 2007-05-23 16:52 Rev.: 4608

- removed some prototype which are already in auto-generated headers

3 lines of code changed in 1 file:

westram 2007-05-23 16:52 Rev.: 4607

- added noreturn-attribute to nt_exit()
- commented-out unused function

17 lines of code changed in 1 file:

westram 2007-05-23 16:52 Rev.: 4606

- make prototypes only if needed (using mv_if_diff).
generate nt_cb.hxx

4 lines of code changed in 1 file:

westram 2007-05-23 16:51 Rev.: 4605

- now omits main() by default
can be emitted using new switch -m
- newlines at end of EOL-C++-comments were suppressed.
As a consequence the first token after it was suppressed or
not recognized in some cases, which mislead the parser.
Nobody noticed, because of missing error-propagation. :)
- changed error-handling: writes some errors into generated code,
pointing to locations in aisc_mkpt input files.

126 lines of code changed in 1 file:

westram 2007-05-23 16:51 Rev.: 4604

- make prototypes only if needed (using mv_if_diff)

30 lines of code changed in 9 files:

westram 2007-05-23 16:51 Rev.: 4603

- new target 'proto' (makes proto in subdir CORE)

3 lines of code changed in 1 file:

westram 2007-05-23 16:51 Rev.: 4602

- new target 'proto' (makes proto in subdir C)

3 lines of code changed in 1 file:

westram 2007-05-23 16:51 Rev.: 4601

- added printf-attribute to printf_error()

1 lines of code changed in 1 file:

westram 2007-05-23 16:49 Rev.: 4600

- remove 'NO_INLINE' (obsolete)
- added target 'proto' (=regenerate all prototypes)

23 lines of code changed in 1 file:

westram 2007-05-23 13:20 Rev.: 4599

- fixed 'Auto match' position

8 lines of code changed in 1 file:

westram 2007-05-23 13:20 Rev.: 4598

- cleaned

2 lines of code changed in 1 file:

westram 2007-05-23 13:19 Rev.: 4597

- added TEMPLATES/arb_debug.h, AISC_COM/C/aisc_global.h

2 lines of code changed in 1 file:

westram 2007-05-23 13:19 Rev.: 4596

- valgrind helper function

36 lines of code changed in 1 file:

westram 2007-05-23 13:19 Rev.: 4595

- fixed SIGSEGV

9 lines of code changed in 1 file:

westram 2007-05-23 13:18 Rev.: 4594

- updated

22 lines of code changed in 4 files:

westram 2007-05-23 13:18 Rev.: 4593

- fix(?!) type-punning problems

19 lines of code changed in 2 files:

westram 2007-05-23 13:18 Rev.: 4592

- fix(?!) type-punning problems
- assertions in ptnd_get_wmismatch(), rewrote for debugging purposes,
made static
- prints received bond values in DEBUG mode

31 lines of code changed in 1 file:

westram 2007-05-23 13:18 Rev.: 4591

- attribute noreturn for names_server_shutdown()

1 lines of code changed in 1 file:

westram 2007-05-23 13:18 Rev.: 4590

- cosmetics

12 lines of code changed in 3 files:

westram 2007-05-23 13:17 Rev.: 4589

- attribute noreturn for names_server_shutdown()
- fix(?!) type-punning problems

16 lines of code changed in 1 file:

westram 2007-05-23 13:17 Rev.: 4588

- debugging code to inspect communication

68 lines of code changed in 1 file:

westram 2007-05-23 13:16 Rev.: 4587

- some defines moved to aisc_global.h

4 lines of code changed in 2 files:

westram 2007-05-23 13:16 Rev.: 4586

- typo

1 lines of code changed in 1 file:

westram 2007-05-23 13:16 Rev.: 4585

- some defines moved to aisc_global.h
- added debugging code
- type fixes (int->long)
- aisc_broadcast() avoids to send uninitialized bytes (4valgrind)
- attribute noreturn for aisc_server_shutdown_and_exit()

100 lines of code changed in 1 file:

westram 2007-05-23 13:15 Rev.: 4584

- added debugging code
- type fixes (int->long)

33 lines of code changed in 1 file:

westram 2007-05-23 13:15 Rev.: 4583

- collected duplicated global defines

30 lines of code changed in 1 file:

westram 2007-05-23 13:15 Rev.: 4582

- added -g (=promote attributes) to aisc_mkpt

1 lines of code changed in 1 file:

westram 2007-05-23 13:15 Rev.: 4581

- force -fno-strict-aliasing
Needed because code uses illegal type-punning widely.

7 lines of code changed in 1 file:

westram 2007-05-16 17:30 Rev.: 4580

- added hint for removal of duplicated species
- show tree name, where zombies are created

10 lines of code changed in 1 file:

westram 2007-05-16 16:40 Rev.: 4579

- ARB compiles with gcc 4.2.0

1 lines of code changed in 1 file:

westram 2007-05-16 12:28 Rev.: 4578

- fixed warnings

68 lines of code changed in 15 files:

westram 2007-05-16 12:27 Rev.: 4577

- removed unused variables

0 lines of code changed in 1 file:

westram 2007-05-16 12:27 Rev.: 4576

- fixed perl module warning

3 lines of code changed in 2 files:

westram 2007-05-16 12:27 Rev.: 4575

- fixed undefined value

8 lines of code changed in 1 file:

westram 2007-05-16 12:26 Rev.: 4574

- program flow + error handling fixed in gbt_write_tree()

19 lines of code changed in 1 file:

westram 2007-05-15 18:10 Rev.: 4573

- probe_pt_look_for_server -> AP_probe_pt_look_for_server

3 lines of code changed in 1 file:

westram 2007-05-15 18:10 Rev.: 4572

- probe_pt_look_for_server -> PGD_probe_pt_look_for_server

2 lines of code changed in 1 file:

westram 2007-05-15 18:10 Rev.: 4571

- probe_pt_look_for_server -> PG_probe_pt_look_for_server
- removed evil cast (fixing potential crash reason)

6 lines of code changed in 1 file:

westram 2007-05-15 18:10 Rev.: 4570

- probe_pt_look_for_server -> PD_probe_pt_look_for_server
- removed evil cast (causing probe design crash)

12 lines of code changed in 1 file:

westram 2007-05-15 18:09 Rev.: 4569

- probe_pt_look_for_server -> OC_probe_pt_look_for_server

1 lines of code changed in 1 file:

westram 2007-05-15 18:09 Rev.: 4568

- probe_pt_look_for_server -> OC_probe_pt_look_for_server
- removed evil casts

4 lines of code changed in 1 file:

westram 2007-05-15 18:09 Rev.: 4567

- fixed another reason making ARB_EDIT4 crash, when clicking
around in ARB during ARB_EDIT4-startup

9 lines of code changed in 1 file:

baderk 2007-05-15 16:15 Rev.: 4566

File dynamic_array.h removed (not used in sequence quality tool).

0 lines of code changed in 1 file:

baderk 2007-05-15 15:37 Rev.: 4565

Reformatted code (according to Kernigham&Richie), added 'Kai Bader' as coder. No changes in the program logic.

670 lines of code changed in 10 files:

baderk 2007-05-15 15:18 Rev.: 4564

- Code cleanup - reordered some type definitions for speedup.
- Specified find zombie check, added missing node check.

16 lines of code changed in 1 file:

baderk 2007-05-15 15:17 Rev.: 4563

Specified find zombie check, added missing node check.

3 lines of code changed in 1 file:

baderk 2007-05-15 15:17 Rev.: 4562

Code cleanup - removed deprecated function calls.

4 lines of code changed in 2 files:

baderk 2007-05-15 15:16 Rev.: 4561

Calc helix layout function now uses a std::map to assign filter_pos to a sequence_pos.

31 lines of code changed in 1 file:

baderk 2007-05-15 15:16 Rev.: 4560

- Tree selection widget in S.Q.-tool is now bound to AWAR_TREE.
- Specified find zombie check, added missing node check.

16 lines of code changed in 1 file:

westram 2007-05-15 14:57 Rev.: 4559

- new shortcut (make up)

5 lines of code changed in 1 file:

westram 2007-05-15 14:56 Rev.: 4558

*** empty log message ***

1 lines of code changed in 1 file:

westram 2007-05-15 14:56 Rev.: 4557

- const fix

2 lines of code changed in 2 files:

westram 2007-05-15 14:56 Rev.: 4556

- tweaked interface of add_timed_callback..()

8 lines of code changed in 1 file:

westram 2007-05-15 14:56 Rev.: 4555

- renamed modifier defs (AW_KEY_... -> AW_KEYMODE_...)
- added AW_KEYMODE_NUMLOCK

6 lines of code changed in 1 file:

westram 2007-05-15 14:56 Rev.: 4554

- depends updated

2 lines of code changed in 2 files:

westram 2007-05-15 14:56 Rev.: 4553

- META key translated to ALT
- rewrote aw_xkey_2_awkey():
now ignores NUMLOCK generally.
clean program flow.

126 lines of code changed in 1 file:

westram 2007-05-15 14:56 Rev.: 4552

- use AWT_edit

4 lines of code changed in 3 files:

westram 2007-05-15 14:56 Rev.: 4551

- callback tool (used to send notification when some external program finishes)

46 lines of code changed in 1 file:

westram 2007-05-15 14:56 Rev.: 4550

- added arb_notify

7 lines of code changed in 1 file:

westram 2007-05-15 14:55 Rev.: 4549

- use AWT_edit
- made some functions static

4 lines of code changed in 1 file:

westram 2007-05-15 14:55 Rev.: 4548

- fixed bug in arb_start_server() - sometimes caused broken system call
when a server was started

5 lines of code changed in 1 file:

westram 2007-05-15 14:55 Rev.: 4547

- program flow, allocation issues

38 lines of code changed in 1 file:

westram 2007-05-15 14:55 Rev.: 4546

- changed calls to GBS_ptserver_id_to_choice()

4 lines of code changed in 2 files:

westram 2007-05-15 14:55 Rev.: 4545

- changed calls to GBS_ptserver_id_to_choice()
- changed messages when killing servers
- write to ptserver log
- added arb_tcp_dat_changed_cb(), catches changes to arb_tcp.dat
when edited using the 'Configure' button.
- use AWT_edit with cb

45 lines of code changed in 1 file:

westram 2007-05-15 14:55 Rev.: 4544

- write to ptserver log
- raise message in ARB when ptserver build has finished

15 lines of code changed in 1 file:

westram 2007-05-15 14:55 Rev.: 4543

- write to ptserver log

4 lines of code changed in 1 file:

westram 2007-05-15 14:55 Rev.: 4542

- true->AW_TRUE

1 lines of code changed in 1 file:

westram 2007-05-15 14:55 Rev.: 4541

- added warning

3 lines of code changed in 1 file:

westram 2007-05-15 14:54 Rev.: 4540

- use ALT, only mention META

16 lines of code changed in 2 files:

westram 2007-05-15 14:54 Rev.: 4539

- removed ED4_create_all_awars (now static)

0 lines of code changed in 1 file:

westram 2007-05-15 14:54 Rev.: 4538

- separated awar callbacks for main-DB awars from AWAR creation
- install these callbacks later (it was possible to crash the editor
during startup, by clicking around in ARB_NTREE)
- made some functions static

39 lines of code changed in 1 file:

westram 2007-05-15 14:54 Rev.: 4537

- renamed AW_KEY_... into AW_KEYMODE_...
Removed META (ALT is now synonym for both)

4 lines of code changed in 1 file:

westram 2007-05-15 14:54 Rev.: 4536

- renamed AW_KEY_... into AW_KEYMODE_...

4 lines of code changed in 2 files:

westram 2007-05-15 14:53 Rev.: 4535

- uses AWT_edit

4 lines of code changed in 2 files:

westram 2007-05-15 14:53 Rev.: 4534

- added awt_refresh_all_pt_server_selection_lists()

2 lines of code changed in 1 file:

westram 2007-05-15 14:53 Rev.: 4533

- awt_edit -> AWT_edit

2 lines of code changed in 1 file:

westram 2007-05-15 14:53 Rev.: 4532

- added awt_refresh_all_pt_server_selection_lists()
- track ptserver log -> if changed, update selection lists
- wrote AWT_edit (replacement for GB_edit and awt_edit):
Can install callback called whenever edited file changes.
- removed awt_edit()

184 lines of code changed in 1 file:

westram 2007-05-15 14:53 Rev.: 4531

- pass type to GB_find_sub_by_quark()

1 lines of code changed in 1 file:

westram 2007-05-15 14:53 Rev.: 4530

- uses AWT_edit
- still needs work to automatically reload input mask

3 lines of code changed in 1 file:

westram 2007-05-15 14:52 Rev.: 4529

- updated

12 lines of code changed in 3 files:

westram 2007-05-15 14:52 Rev.: 4528

- GB_TYPE and GB_TYPE_TS return type now GB_TYPES (was int - whyever)

4 lines of code changed in 1 file:

westram 2007-05-15 14:52 Rev.: 4527

- type change

3 lines of code changed in 1 file:

westram 2007-05-15 14:52 Rev.: 4526

- added general notification mechanism:
GB_generate_notification() to install a notification callback.
GB_notify() to trigger the notification callback (called by arb_notify)

213 lines of code changed in 1 file:

westram 2007-05-15 14:52 Rev.: 4525

- added GBS_ptserver_logname()
- PT-server selection shows build date, hide localhost and port, display
'building..' during build.

94 lines of code changed in 1 file:

westram 2007-05-15 14:52 Rev.: 4524

- 'cannot read data' more verboose
- use gbcm_write_long() where appropriate
- added gbcm_write_long / gbcm_read_long
- removed GB_edit (use AWT_edit now)

35 lines of code changed in 1 file:

westram 2007-05-15 14:52 Rev.: 4523

- added gb_find_value_equal() - used by GB_find_sub_by_quark() to compare values
- pass type to GBCMC_find()
- GB_find -> gb_find_internal
- new functions GB_find und GB_find_int
- gb_search() takes type as GB_TYPES (not long)

77 lines of code changed in 1 file:

westram 2007-05-15 14:51 Rev.: 4522

- fixed call to GB_find_sub_by_quark()

5 lines of code changed in 1 file:

westram 2007-05-15 14:51 Rev.: 4521

- several const fixes
- GBCMC_find() now sends estimated type of DB field to server.
Fails on missing implementation.
Added parameter 'type'.
- gbcms_talking_find() receives estimated type of DB field from client.
Fails on missing implementation or type mismatch..
- commented comm-functions table with corresponding IDs
- use gbcm_write_long() where appropriate

93 lines of code changed in 1 file:

baderk 2007-05-11 16:19 Rev.: 4520

Added a 'temporary workaround' warning concerning the display of GB_INT and GB_FLOAT types in EDIT4.

3 lines of code changed in 1 file:

westram 2007-05-11 13:03 Rev.: 4519

- fixed segfault (when merging similar species)

2 lines of code changed in 1 file:

westram 2007-05-11 12:46 Rev.: 4518

*** empty log message ***

3 lines of code changed in 1 file:

westram 2007-05-11 12:46 Rev.: 4517

- added storage for prefix_hash

12 lines of code changed in 1 file:

westram 2007-05-11 12:46 Rev.: 4516

- changes server-timeout in DEBUG version

4 lines of code changed in 1 file:

westram 2007-05-11 12:45 Rev.: 4515

- renamed an_find_shrt -> an_find_shrt_prefix and rewrote it using a prefix_hash.
prefix_hash is kept up-to-date by an_add_short and an_remove_short.
- added nameModHash (used to speed up modification of existings names)
- These changes speedup name-generation, if names for unknown species are
generated: factor 1.5 for 1000, factor 4.7 for 10000, increasing..

70 lines of code changed in 1 file:

westram 2007-05-11 12:36 Rev.: 4514

- updated

2 lines of code changed in 1 file:

westram 2007-05-11 12:36 Rev.: 4513

- added GB_strpartdup + GB_strndup

33 lines of code changed in 1 file:

westram 2007-05-11 12:36 Rev.: 4512

- increase hash-size earlier

1 lines of code changed in 1 file:

baderk 2007-05-11 11:06 Rev.: 4511

Fixes 'unknown data type' assertion when displaying quality checked species data in arb_edit4.

9 lines of code changed in 1 file:

westram 2007-05-10 11:16 Rev.: 4510

- updated

2 lines of code changed in 1 file:

westram 2007-05-10 11:16 Rev.: 4509

- less information when testing for duplicated species. Internal buffer was
to small and information is not really useful. Generate new names should
fix the problem.

12 lines of code changed in 1 file:

westram 2007-05-10 11:15 Rev.: 4508

- if internal buffer for GBS_global_string overflows -> print message

3 lines of code changed in 1 file:

westram 2007-05-10 11:15 Rev.: 4507

- added GBS_optimize_hash (resizes a hash if it's getting slow).
Has to be called manually.
- changed size variables of gbs_hash_struct to size_t (was long)

98 lines of code changed in 1 file:

westram 2007-05-10 11:14 Rev.: 4506

- mentioned profile_annotate.pl

15 lines of code changed in 1 file:

westram 2007-05-10 11:14 Rev.: 4505

- typo

1 lines of code changed in 1 file:

westram 2007-05-03 10:20 Rev.: 4504

- fixed some evil casts which caused essential warnings to be skipped
and leaded to the segfault
- fixed 2nd potential segfault in AP_probe_design_event()

17 lines of code changed in 1 file:

baderk 2007-05-02 15:34 Rev.: 4503

Removed Segfault: The char* servername is a substring fetched by get_ATD_entry(...) from the environment settings and therefore should not be freed.

2 lines of code changed in 1 file:

April 2007 »

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