February 2004 Commit Log

Number of Commits:
87
Number of Active Developers:
6
westram 2004-02-29 12:33 Rev.: 2444

- added optional debugging code to detect errors in huffman compression
- fixed a nasty bug in huffman compression

117 lines of code changed in 1 file:

westram 2004-02-29 12:30 Rev.: 2443

- added test code to check whether compression has an error (code is disabled)

16 lines of code changed in 1 file:

westram 2004-02-27 20:45 Rev.: 2442

generates lib/pts if not existing

2 lines of code changed in 1 file:

westram 2004-02-27 18:46 Rev.: 2441

- added parseBool

17 lines of code changed in 1 file:

westram 2004-02-27 18:46 Rev.: 2440

- now probe design may be skipped
- cosmetics

81 lines of code changed in 1 file:

westram 2004-02-27 18:45 Rev.: 2439

- reads weighted_mismatches

3 lines of code changed in 1 file:

westram 2004-02-27 18:44 Rev.: 2438

- added weighted_mismatches
- added warning

8 lines of code changed in 1 file:

westram 2004-02-27 18:43 Rev.: 2437

- added use_weighted_mismatches

4 lines of code changed in 1 file:

westram 2004-02-27 18:40 Rev.: 2436

- warnings fixed

7 lines of code changed in 1 file:

westram 2004-02-27 17:27 Rev.: 2435

increased delay

2 lines of code changed in 1 file:

yadhu 2004-02-26 14:53 Rev.: 2434

visualization of SAIs of Probe Match Results !!

254 lines of code changed in 2 files:

yadhu 2004-02-26 13:24 Rev.: 2433

Color Definitions for Visualizing SAIs of Probe Match Results.

35 lines of code changed in 1 file:

westram 2004-02-25 17:50 Rev.: 2432

- removed conditionals from gene IDP

3 lines of code changed in 2 files:

westram 2004-02-25 17:49 Rev.: 2431

- removed conditionals from gene IDP
- indented

251 lines of code changed in 5 files:

westram 2004-02-25 17:46 Rev.: 2430

removed unused (redundant) functions from gene IDP

1 lines of code changed in 3 files:

westram 2004-02-24 00:50 Rev.: 2429

- activated Juergens seq quality check for all

2 lines of code changed in 1 file:

westram 2004-02-24 00:15 Rev.: 2428

assertion fixed

1 lines of code changed in 1 file:

westram 2004-02-24 00:02 Rev.: 2427

- rewrote internal structure of probe database
(saves up to 80% of memory)
- cleanup

536 lines of code changed in 6 files:

westram 2004-02-23 23:58 Rev.: 2426

*** empty log message ***

42 lines of code changed in 2 files:

huberj 2004-02-21 12:30 Rev.: 2425

*** empty log message ***

2 lines of code changed in 2 files:

huberj 2004-02-19 17:52 Rev.: 2424

added reevaluate functionality
made evaluate() distinguish more values

164 lines of code changed in 3 files:

westram 2004-02-18 20:39 Rev.: 2423

- changed linefeeds into \n

7 lines of code changed in 1 file:

westram 2004-02-18 20:39 Rev.: 2422

- when property loading fails all ARB programs terminate with error

6 lines of code changed in 1 file:

westram 2004-02-18 20:36 Rev.: 2421

- added GB_get_quark

4 lines of code changed in 2 files:

westram 2004-02-18 20:35 Rev.: 2420

- GB_print_error flushes stdout (to avoid mixed output of stderr and stdout)

1 lines of code changed in 1 file:

westram 2004-02-18 17:59 Rev.: 2419

- changed acute

4 lines of code changed in 1 file:

meierh 2004-02-18 15:27 Rev.: 2418

workaround to avoid SIGSEGV if AP_TREE->gb_node!=0 and AP_TREE->name==0

10 lines of code changed in 1 file:

meierh 2004-02-18 15:25 Rev.: 2417

changed name written to group_name entry (was "noname")

4 lines of code changed in 1 file:

spanfeln 2004-02-16 06:47 Rev.: 2416

IDP changes of probe_match event were correctet

18 lines of code changed in 1 file:

westram 2004-02-13 18:01 Rev.: 2415

solaris changes

14 lines of code changed in 3 files:

westram 2004-02-13 18:01 Rev.: 2414

uint is not std C

1 lines of code changed in 1 file:

westram 2004-02-13 17:59 Rev.: 2413

define OWTOOLKIT_WARNING_DISABLED

250 lines of code changed in 25 files:

richter 2004-02-13 17:04 Rev.: 2412

solaris changes

5 lines of code changed in 3 files:

westram 2004-02-13 11:30 Rev.: 2411

*** empty log message ***

3 lines of code changed in 1 file:

westram 2004-02-13 11:29 Rev.: 2410

- removes result files [was commented out]

1 lines of code changed in 1 file:

westram 2004-02-13 11:29 Rev.: 2409

- new parameter 'exact'; possible values: 0|1
- forwards different commands to workers (getexactprobes|getnonexactprobes)

4 lines of code changed in 1 file:

westram 2004-02-13 11:29 Rev.: 2408

- right click distinguishes between exact and other matches

1 lines of code changed in 1 file:

westram 2004-02-13 11:28 Rev.: 2407

- retrieveNodeInformation has to specify whether
exact or non-exact probes are desired

2 lines of code changed in 1 file:

westram 2004-02-13 11:28 Rev.: 2406

- updateNodeInformation(): new parameter 'exactMatches'

2 lines of code changed in 1 file:

westram 2004-02-13 11:28 Rev.: 2405

- command 'getprobes' changed into 'getexactprobes' and 'getnonexactprobes'
- extracts compressed probes

105 lines of code changed in 1 file:

westram 2004-02-13 11:28 Rev.: 2404

- merges all lines (not only different lines)
(even for identical lines "exact matches" need to get summarized)

78 lines of code changed in 1 file:

westram 2004-02-13 11:27 Rev.: 2403

- expects all probes of one group in one string
- update of 'exact' entry was skipped if probe design
had no results [fixed]

111 lines of code changed in 1 file:

westram 2004-02-13 11:27 Rev.: 2402

- writes all probes of one group into one string
- disabled undo for all used databases

25 lines of code changed in 1 file:

westram 2004-02-13 11:26 Rev.: 2401

- tests whether servers are running

17 lines of code changed in 1 file:

westram 2004-02-13 11:24 Rev.: 2400

- tweaked cleanup

5 lines of code changed in 1 file:

westram 2004-02-13 11:21 Rev.: 2399

*** empty log message ***

8 lines of code changed in 2 files:

westram 2004-02-13 11:16 Rev.: 2398

- changed names of define
- added template saveProbeContainerToString

51 lines of code changed in 1 file:

meierh 2004-02-12 15:28 Rev.: 2397

errno --> err_no, include errno.h

7 lines of code changed in 1 file:

westram 2004-02-06 17:08 Rev.: 2396

do not define output encoding (solaris knows nothing about them)

4 lines of code changed in 2 files:

westram 2004-02-06 17:07 Rev.: 2395

fixed sed call

1 lines of code changed in 1 file:

westram 2004-02-06 17:06 Rev.: 2394

added math lib to SYSLIBS

1 lines of code changed in 1 file:

westram 2004-02-06 16:50 Rev.: 2393

fixed sed calls

6 lines of code changed in 1 file:

westram 2004-02-06 16:38 Rev.: 2392

dos->unix

0 lines of code changed in 1 file:

richter 2004-02-06 16:28 Rev.: 2391

wrong newline removewrong newline removedd

1 lines of code changed in 1 file:

westram 2004-02-06 15:53 Rev.: 2390

Solaris changes

15 lines of code changed in 1 file:

westram 2004-02-06 14:46 Rev.: 2389

Solaris gcc uses linux part

29 lines of code changed in 2 files:

westram 2004-02-05 15:50 Rev.: 2388

toggle to write 'transl_table' and 'codon_start'

17 lines of code changed in 1 file:

westram 2004-02-05 15:48 Rev.: 2387

depends

0 lines of code changed in 1 file:

westram 2004-02-05 15:48 Rev.: 2386

- moved code to read and transform 'transl_table' entry to findTranslationTable()
- re-aligner uses 'transl_table' entry if found
- overwrites existing 'codon_start' entries with "1"
- added new awars AWAR_TRANSPRO_XSTART and AWAR_TRANSPRO_WRITE (+toggles)
- writes used translation table and start position into fields
'transl_table' and 'codon_start' (if AWAR_TRANSPRO_WRITE != 0)
- awt_pro_a_nucs_convert adds a 'X' at start of translated protein sequence
if the nucleotide sequence contains nucleotides before the ORF start

190 lines of code changed in 1 file:

westram 2004-02-05 15:42 Rev.: 2385

unused

0 lines of code changed in 1 file:

westram 2004-02-05 15:42 Rev.: 2384

- added missing help for re-aligner

42 lines of code changed in 1 file:

westram 2004-02-05 15:42 Rev.: 2383

- link to realign_dna.hlp

34 lines of code changed in 1 file:

westram 2004-02-05 15:41 Rev.: 2382

- added AWT_allowedCode::forbidAllBut

7 lines of code changed in 1 file:

westram 2004-02-05 14:07 Rev.: 2381

new toggle

26 lines of code changed in 1 file:

westram 2004-02-05 12:18 Rev.: 2380

- call SQ_clear_group_dictionary after calculation
- changed call to SQ_evaluate
- added re-evaluate toggle (no effect yet!)

21 lines of code changed in 1 file:

westram 2004-02-05 12:17 Rev.: 2379

- SQ_calc_helix_layout
+ calculates BI_helix only once per alignment
+ ignores right helix positions
+ ignores gap-gap in helix regions

71 lines of code changed in 1 file:

westram 2004-02-05 12:17 Rev.: 2378

- added SQ_clear_group_dictionary
- pass weights as 'ref to struct'
- spelling (SQ_GROUPDATA_H)
- corrected prototype of SQ_mark_species
- made some parameters/functions const

32 lines of code changed in 1 file:

westram 2004-02-05 12:17 Rev.: 2377

- added SQ_clear_group_dictionary
- changed weights parameter(s) for SQ_evaluate
- replaced dynamic variables with static variables

37 lines of code changed in 1 file:

westram 2004-02-05 12:17 Rev.: 2376

- avoiding multiple include of <iostream>
- spelling (SQ_GROUPDATA_H)
- made some parameters/functions const

22 lines of code changed in 1 file:

westram 2004-02-05 12:17 Rev.: 2375

- made some parameters/functions const

5 lines of code changed in 1 file:

huberj 2004-02-04 12:02 Rev.: 2374

*** empty log message ***

4 lines of code changed in 2 files:

huberj 2004-02-04 11:48 Rev.: 2373

rewrote notree functions

119 lines of code changed in 2 files:

huberj 2004-02-03 14:50 Rev.: 2372

*** empty log message ***

18 lines of code changed in 5 files:

huberj 2004-02-03 14:32 Rev.: 2371

*** empty log message ***

58 lines of code changed in 3 files:

westram 2004-02-02 19:06 Rev.: 2370

- filter comments after 'DO NOT DELETE' line

1 lines of code changed in 1 file:

westram 2004-02-02 19:06 Rev.: 2369

- removed auto-duplicated comments

0 lines of code changed in 3 files:

westram 2004-02-02 18:55 Rev.: 2368

- 'RALF' -> 'RALFX'
- replaced '-fenum-int-equiv' by variable

4 lines of code changed in 1 file:

westram 2004-02-02 18:53 Rev.: 2367

*** empty log message ***

3 lines of code changed in 1 file:

westram 2004-02-02 18:53 Rev.: 2366

- fixed formatting
- Changed description of 'Consensus' and general description

42 lines of code changed in 1 file:

westram 2004-02-02 18:52 Rev.: 2365

- conditionalized usage of gene_str

5 lines of code changed in 1 file:

westram 2004-02-02 18:51 Rev.: 2364

added toggle pos + text for marking of species

188 lines of code changed in 1 file:

westram 2004-02-02 18:50 Rev.: 2363

- added a toggle and awar to en/disable marking feature
- SQ_mark_species is only called if marking is requested

25 lines of code changed in 1 file:

westram 2004-02-02 18:49 Rev.: 2362

- simplified string generation for consensus_deviation
- species below threshold get marked, all other unmarked

59 lines of code changed in 1 file:

huberj 2004-02-01 12:16 Rev.: 2361

*** empty log message ***

1 lines of code changed in 1 file:

huberj 2004-02-01 12:12 Rev.: 2360

first ver of help

49 lines of code changed in 1 file:

huberj 2004-02-01 08:45 Rev.: 2359

*** empty log message ***

21 lines of code changed in 1 file:

huberj 2004-02-01 08:44 Rev.: 2358

added marking of bad sequences

64 lines of code changed in 3 files:

January 2004 »

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