May 2003 Commit Log

Number of Commits:
123
Number of Active Developers:
3
westram 2003-05-30 14:56 Rev.: 1471

* AWT_seq_protein.cxx: - try to fix neg. branchlengths

10 lines of code changed in 1 file:

westram 2003-05-23 15:51

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8 lines of code changed in 2 files:

westram 2003-05-23 15:02 Rev.: 1468

end of test

1 lines of code changed in 1 file:

yadhu 2003-05-23 14:56

*** empty log message ***

2 lines of code changed in 2 files:

yadhu 2003-05-23 14:40 Rev.: 1465

Tips and tricks window was removed !!!! Dont panic they are available in Help files :-).

2 lines of code changed in 4 files:

westram 2003-05-23 14:10 Rev.: 1464

removed

0 lines of code changed in 2 files:

yadhu 2003-05-23 12:37 Rev.: 1463

visualization of conservation profiles using GNUPLOT was added
but not finished yet ;-(!

175 lines of code changed in 3 files:

yadhu 2003-05-23 12:34 Rev.: 1462

visualization of conservation profiles using GNUPLOT was added
but not finished yet so it works only for me ;-).

2 lines of code changed in 1 file:

yadhu 2003-05-23 12:26 Rev.: 1461

1. New feature to maintain tips and tricks that are available in ARB.
2. User can view the tips and tricks that are associated with ARB_NTREE window and
Primary Structure Editor (ARB_EDIT4) Window.
3. User can also add and change tips at his disposal and maintain the same
as local database.

269 lines of code changed in 11 files:

westram 2003-05-22 23:03 Rev.: 1460

More notes on how to install arb from source

24 lines of code changed in 1 file:

westram 2003-05-22 23:02 Rev.: 1459

- does several tests to make compiling arb more easy:
- tell sth about config.makefile
- check $ARBHOME and $PATH
- Motif skipped in 'make libs'

66 lines of code changed in 1 file:

westram 2003-05-22 23:01 Rev.: 1458

now archivates everything needed to make arb

46 lines of code changed in 1 file:

westram 2003-05-22 23:00 Rev.: 1457

removed linking to DEPOT and PERL5

4 lines of code changed in 1 file:

westram 2003-05-22 22:59 Rev.: 1456

generates some directories as well

15 lines of code changed in 1 file:

westram 2003-05-22 22:59 Rev.: 1455

- quick add does no longer set 'best parsimony' to the value
of the state when all marked species are removed

58 lines of code changed in 1 file:

westram 2003-05-22 22:58 Rev.: 1454

- fixed failed assertion (with edit marked + x relatives)

17 lines of code changed in 1 file:

westram 2003-05-22 22:58 Rev.: 1453

do not create O

0 lines of code changed in 3 files:

westram 2003-05-22 22:57 Rev.: 1452

uses mkdir -p to create directories

6 lines of code changed in 1 file:

westram 2003-05-22 22:56 Rev.: 1451

indented, debugging code

151 lines of code changed in 1 file:

westram 2003-05-22 22:54 Rev.: 1450

disabled compiler warnings

26 lines of code changed in 2 files:

westram 2003-05-21 18:01 Rev.: 1449

- uses arb_textedit to edit help files

54 lines of code changed in 15 files:

westram 2003-05-21 18:01 Rev.: 1448

- if $ARB_TEXTEDIT is undefined, then this script tries to detect a text editor

30 lines of code changed in 1 file:

westram 2003-05-21 15:07 Rev.: 1447

- fixed a bug that modified the value of ARBHOME in the environment
- when nothing was imported clicking 'suggest names' did not show any error
- when clicking again, ARB crashed (open transaction)
- all stuff printed to console depends on #define

153 lines of code changed in 1 file:

westram 2003-05-21 15:07 Rev.: 1446

*** empty log message ***

295 lines of code changed in 1 file:

westram 2003-05-21 15:06 Rev.: 1445

- removed static variables
- all stuff printed to console depends on #define
- added HELP button
- removed some casts
- fixed some memory leaks

73 lines of code changed in 1 file:

westram 2003-05-21 15:06 Rev.: 1444

- linked against each other
- corrected OCCURRENCE

14 lines of code changed in 4 files:

westram 2003-05-21 14:02 Rev.: 1443

removed backups

0 lines of code changed in 3 files:

richter 2003-05-21 13:45 Rev.: 1442

Help files for Valid Names section added

121 lines of code changed in 8 files:

westram 2003-05-21 11:12 Rev.: 1441

changed names of some (non-existing) help files

4 lines of code changed in 1 file:

westram 2003-05-21 10:17 Rev.: 1440

- added single quote (as '&apostr;')

4 lines of code changed in 1 file:

westram 2003-05-21 10:13 Rev.: 1439

*** empty log message ***

3 lines of code changed in 1 file:

westram 2003-05-21 09:03 Rev.: 1438

*** empty log message ***

2 lines of code changed in 1 file:

westram 2003-05-16 19:16 Rev.: 1437

added label for alignment input box

28 lines of code changed in 1 file:

westram 2003-05-16 19:15 Rev.: 1436

added combine label

10 lines of code changed in 1 file:

westram 2003-05-16 19:15 Rev.: 1435

- corrected path
- when resolving IUPAC: warn if incorrect alignment type

12 lines of code changed in 1 file:

westram 2003-05-16 19:14 Rev.: 1434

- added COMBINE mode to configuration extraction

40 lines of code changed in 1 file:

westram 2003-05-16 19:14 Rev.: 1433

- spelling

1 lines of code changed in 1 file:

westram 2003-05-16 19:14 Rev.: 1432

- explain COMBINE

2 lines of code changed in 1 file:

westram 2003-05-16 19:14 Rev.: 1431

- undefined TEST_BASES_TABLE

1 lines of code changed in 1 file:

westram 2003-05-16 19:13 Rev.: 1430

- set not_found_message=0 after freeing it
- valgrinded

4 lines of code changed in 1 file:

westram 2003-05-16 19:13 Rev.: 1429

- valgrinded, untabified and indented

143 lines of code changed in 1 file:

westram 2003-05-16 19:12 Rev.: 1428

- displays error if ED4_get_and_jump_to_species() is called on a species
with w/o data in current alignment
- same for ED4_get_marked_from_menu()

27 lines of code changed in 1 file:

westram 2003-05-16 19:12 Rev.: 1427

- untabified and indented
- alignment used for pt-server (next-ralative-search) configurable
- store relatives used for alignment in 'used_rels'
- gets more relatives from pt-server (cause when using DNA-Pt-Server
for Protein-Alignment, we may get species w/o protein data)

349 lines of code changed in 1 file:

westram 2003-05-16 19:12 Rev.: 1426

- removed weird typedefs

11 lines of code changed in 1 file:

westram 2003-05-16 19:11 Rev.: 1425

- valgrinded

10 lines of code changed in 2 files:

westram 2003-05-16 10:47 Rev.: 1424

*** empty log message ***

19 lines of code changed in 2 files:

westram 2003-05-16 10:47 Rev.: 1423

- renamed variable 'string' to 'str' (really ancient code)
- warns if species has no data (and does skip display of this species)
- skips SAIs that have no data in current alignment
- indented/untabified

143 lines of code changed in 1 file:

westram 2003-05-15 21:15 Rev.: 1422

*** empty log message ***

2 lines of code changed in 1 file:

westram 2003-05-15 21:00 Rev.: 1421

*** empty log message ***

2 lines of code changed in 2 files:

westram 2003-05-15 20:48 Rev.: 1420

another test file removed

0 lines of code changed in 1 file:

westram 2003-05-15 20:46 Rev.: 1419

this was only a test-file

0 lines of code changed in 1 file:

westram 2003-05-15 20:45 Rev.: 1418

checkcheck

0 lines of code changed in 1 file:

westram 2003-05-15 20:44 Rev.: 1417

beschreibung

1 lines of code changed in 1 file:

westram 2003-05-15 20:38 Rev.: 1416

changing..

0 lines of code changed in 1 file:

westram 2003-05-15 20:33 Rev.: 1415

ein test

1 lines of code changed in 1 file:

westram 2003-05-15 20:30

*** empty log message ***

2 lines of code changed in 2 files:

westram 2003-05-15 20:08 Rev.: 1412

bla

0 lines of code changed in 1 file:

westram 2003-05-15 19:53

*** empty log message ***

9 lines of code changed in 4 files:

westram 2003-05-15 19:46 Rev.: 1407

* README: - mentioned mac version

1 lines of code changed in 1 file:

westram 2003-05-15 18:12 Rev.: 1406

ok - no unknown files left :-)

16 lines of code changed in 7 files:

westram 2003-05-15 15:14 Rev.: 1405

*** empty log message ***

36 lines of code changed in 2 files:

westram 2003-05-15 13:34 Rev.: 1404

*** empty log message ***

103 lines of code changed in 19 files:

westram 2003-05-15 13:22 Rev.: 1403

*** empty log message ***

15 lines of code changed in 9 files:

westram 2003-05-15 13:11 Rev.: 1402

ignore ChangeLog

12 lines of code changed in 14 files:

westram 2003-05-15 12:58 Rev.: 1401

*** empty log message ***

3 lines of code changed in 1 file:

westram 2003-05-15 12:54 Rev.: 1400

- ignore *.hlp

1 lines of code changed in 1 file:

westram 2003-05-15 12:49 Rev.: 1399

- added get_button_length()

2 lines of code changed in 2 files:

westram 2003-05-15 12:49 Rev.: 1398

- fix

1 lines of code changed in 1 file:

westram 2003-05-15 12:49 Rev.: 1397

- menu fix

2 lines of code changed in 1 file:

westram 2003-05-15 12:48 Rev.: 1396

- removed probe_design_build_pt_server_choices()

0 lines of code changed in 1 file:

westram 2003-05-15 12:48 Rev.: 1395

- renamed pd_ptid_to_choice() -> GBS_ptserver_id_to_choice() and moved to library
- removed probe_design_build_pt_server_choices()

5 lines of code changed in 1 file:

westram 2003-05-15 12:48 Rev.: 1394

- use pop-up-selectionlists for pt-servers
- replaced probe_design_build_pt_server_choices() by awt_create_selection_list_on_pt_servers()

2 lines of code changed in 1 file:

westram 2003-05-15 12:47 Rev.: 1393

- warning fix

1 lines of code changed in 1 file:

westram 2003-05-15 12:47 Rev.: 1392

- uncommented unused variables

27 lines of code changed in 1 file:

westram 2003-05-15 12:47 Rev.: 1391

- some prototypes

40 lines of code changed in 1 file:

westram 2003-05-15 12:47 Rev.: 1390

- includes mp_proto.hxx
- added MP_cache_sonden2 (as awar callback)

6 lines of code changed in 1 file:

westram 2003-05-15 12:45 Rev.: 1389

- moved prototypes -> mp_proto.hxx

11 lines of code changed in 1 file:

westram 2003-05-15 12:45 Rev.: 1388

- renamed pd_ptid_to_choice() -> GBS_ptserver_id_to_choice() and moved to library
- uses awt_create_selection_list_on_pt_servers()

11 lines of code changed in 1 file:

westram 2003-05-15 12:45 Rev.: 1387

- use awt_create_selection_list_on_pt_servers()

38 lines of code changed in 1 file:

westram 2003-05-15 12:45 Rev.: 1386

- renamed pd_ptid_to_choice() -> GBS_ptserver_id_to_choice() and moved to library

23 lines of code changed in 1 file:

westram 2003-05-15 12:43 Rev.: 1385

- uses awt_create_selection_list_on_pt_servers()
- AWAR_PT_SERVER defaults to 0 (not -1)

3 lines of code changed in 1 file:

westram 2003-05-15 12:43 Rev.: 1384

- added awt_create_selection_list_on_pt_servers()
- untabified/indented

457 lines of code changed in 2 files:

westram 2003-05-15 12:43 Rev.: 1383

- format fix

1 lines of code changed in 1 file:

westram 2003-05-15 12:42 Rev.: 1382

- added GBS_ptserver_id_to_choice()

34 lines of code changed in 2 files:

westram 2003-05-13 16:11 Rev.: 1381

- added AW_window::get_window_id()

11 lines of code changed in 1 file:

westram 2003-05-13 16:11 Rev.: 1380

- open_default() changed
- specialized AW_root::save_default()

40 lines of code changed in 2 files:

westram 2003-05-13 16:11 Rev.: 1379

- added AW_save_specific_defaults()

3 lines of code changed in 1 file:

westram 2003-05-13 16:11 Rev.: 1378

- get_window_title() made const

3 lines of code changed in 1 file:

westram 2003-05-13 16:10 Rev.: 1377

- added AW_save_specific_defaults()
- window_awar_name is now created from internal window id (not from name).
This fixes:
* different color defaults for different alignments.
* different color defaults for second editor/ntree window

8 lines of code changed in 1 file:

westram 2003-05-13 16:09 Rev.: 1376

- added ED4_propertyName()

1 lines of code changed in 1 file:

westram 2003-05-13 16:09 Rev.: 1375

- added 'db_name' to ED4_root

1 lines of code changed in 1 file:

westram 2003-05-13 16:08 Rev.: 1374

- allows to save different specific properties
- internal window name is now 'ARB_EDIT4'

21 lines of code changed in 1 file:

westram 2003-05-13 16:08 Rev.: 1373

- tries to open different alignment-dependent properties
- added ED4_propertyName()

47 lines of code changed in 1 file:

yadhu 2003-05-13 14:24 Rev.: 1372

some changes to SAI Visualizer

58 lines of code changed in 1 file:

yadhu 2003-05-13 13:35 Rev.: 1371

Helix number duplication fixed

12 lines of code changed in 1 file:

yadhu 2003-05-13 12:09 Rev.: 1370

Fixed some bugs in Visualise SAI module

12 lines of code changed in 1 file:

westram 2003-05-13 11:33 Rev.: 1369

- ARB crashed when creating Consensus or Maxfreq SAI (proteins only)

3 lines of code changed in 1 file:

westram 2003-05-13 11:33 Rev.: 1368

- spelling

2 lines of code changed in 1 file:

westram 2003-05-13 11:32 Rev.: 1367

- warns if illegal characters were replaced by gaps

1 lines of code changed in 1 file:

westram 2003-05-13 11:31 Rev.: 1366

* AWT_asciiprint.cxx: - AWT_show_file inserts filename as default title

1 lines of code changed in 1 file:

westram 2003-05-13 11:29 Rev.: 1365

- fixed a 'devide by zero'

56 lines of code changed in 1 file:

yadhu 2003-05-09 09:56 Rev.: 1364

end of testing :)

0 lines of code changed in 1 file:

yadhu 2003-05-09 09:55 Rev.: 1363

user 'yadhu' doing some changes

1 lines of code changed in 1 file:

westram 2003-05-09 09:52 Rev.: 1362

some changes from 'westram'

1 lines of code changed in 1 file:

yadhu 2003-05-09 09:42 Rev.: 1361

yadhu again

1 lines of code changed in 1 file:

yadhu 2003-05-09 09:36 Rev.: 1360

testing as yadhu

1 lines of code changed in 1 file:

westram 2003-05-09 09:33 Rev.: 1359

ralf

3 lines of code changed in 1 file:

yadhu 2003-05-08 11:43

*** empty log message ***

325 lines of code changed in 4 files:

yadhu 2003-05-08 11:23 Rev.: 1356

*** empty log message ***

22 lines of code changed in 1 file:

westram 2003-05-06 18:17 Rev.: 1355

*** empty log message ***

1 lines of code changed in 1 file:

westram 2003-05-06 18:10 Rev.: 1354

fixed a memory bug in SAI visualization

* ed4_visualizeSAI.hxx: - changed return type of getSaiColorString() to const
* ED4_visualizeSAI.cxx: - changed return type of getSaiColorString() to const
- getSaiColorString() now returns a pointer to 'start' bytes below color string

331 lines of code changed in 4 files:

westram 2003-05-06 15:38 Rev.: 1353

* lib/import/*.ift: - commented out DONT_GEN_NAMES
* ad_transpro.cxx: - removed old version of arb_transdna()
* AWTI_import.cxx: - indented

31 lines of code changed in 11 files:

westram 2003-05-06 15:16 Rev.: 1352

removed test file

0 lines of code changed in 1 file:

westram 2003-05-06 15:14 Rev.: 1351

ok

0 lines of code changed in 1 file:

westram 2003-05-06 15:11 Rev.: 1350

hmm

1 lines of code changed in 1 file:

westram 2003-05-06 15:09 Rev.: 1349

blub

1 lines of code changed in 1 file:

westram 2003-05-06 15:04

bla

2 lines of code changed in 2 files:

westram 2003-05-06 15:03 Rev.: 1346

another test

0 lines of code changed in 1 file:

yadhu 2003-05-06 14:52

ralf testing

0 lines of code changed in 2 files:

westram 2003-05-06 14:44 Rev.: 1343

cleaned

0 lines of code changed in 1 file:

westram 2003-05-06 14:39 Rev.: 1342

* ad_transpro.cxx: - re-aligner asks to increase alignment length

23 lines of code changed in 1 file:

westram 2003-05-06 14:38 Rev.: 1341

* AWT_codon_table.cxx: - ambiguous_codons had an initialization error

1 lines of code changed in 1 file:

westram 2003-05-06 13:01 Rev.: 1340

test

0 lines of code changed in 1 file:

April 2003 »

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