November 2004 Commit Log

Number of Commits:

63

Number of Active Developers:

3

westram 2004-11-26 13:33 #63 Rev.: 3411

- missing tick

3 lines of code changed in 1 file:

• Makefile (+3 -3)

westram 2004-11-18 20:32 #62 Rev.: 3410

- C fix

14 lines of code changed in 1 file:

• ARBDB: adGene.c (+14 -10)

westram 2004-11-18 20:19 #61 Rev.: 3409

- added 'Refresh fields' to 'Species Information/Fields'

9 lines of code changed in 1 file:

• NTREE: ad_spec.cxx (+9 -7)

westram 2004-11-18 20:18 #60 Rev.: 3408

- database is scanned for and cleaned from empty gene_data containers
- added class CheckedConsistencies (helper class to perform one-time-tasks like the above one)

89 lines of code changed in 1 file:

• NTREE: NT_main.cxx (+89 -1)

westram 2004-11-18 20:17 #59 Rev.: 3407

- added 'Refresh fields' to 'Experiment Information/Fields'

9 lines of code changed in 1 file:

• GENOM: EXP_interface.cxx (+9 -8)

westram 2004-11-18 20:17 #58 Rev.: 3406

- uses new gene_data access functions
- added 'Refresh fields' to 'Gene Information/Fields'

11 lines of code changed in 1 file:

• GENOM: GEN_interface.cxx (+11 -12)

westram 2004-11-18 20:16 #57 Rev.: 3405

- uses new gene_data access functions

1 lines of code changed in 1 file:

• GENOM: GEN_gene.cxx (+1 -1)

westram 2004-11-18 20:16 #56 Rev.: 3404

- splitted GEN_get_gene_data into GEN_find_gene_data, GEN_findOrCreate_gene_data and GEN_expect_gene_data

4 lines of code changed in 1 file:

• ARBDB: adGene.h (+4 -2)

westram 2004-11-18 20:15 #55 Rev.: 3403

- splitted GEN_get_gene_data into GEN_find_gene_data, GEN_findOrCreate_gene_data and GEN_expect_gene_data
- uses new gene_data access functions
- GEN_find_gene returns 0 when no gene found
- GEN_..pseudo_species-functions assert argument is a pseudo_species

27 lines of code changed in 1 file:

• ARBDB: adGene.c (+27 -10)

westram 2004-11-18 15:17 #54 Rev.: 3402

- gcc 3.3.4 tested (reported by A.Tille)

1 lines of code changed in 1 file:

• Makefile (+1 -1)

westram 2004-11-18 15:17 #53 Rev.: 3401

- rsh -> ssh (untested!)

14 lines of code changed in 5 files:

• arb_install.sh (+4 -4)
• PROBE_DESIGN: probe_design.cxx (+7 -7)
• SERVERCNTRL: servercntrl.c (+1 -1)
• SH: arb_oneach (+1 -1)
• util: arb_update_copy (+1 -1)

westram 2004-11-18 14:07 #52 Rev.: 3400

- depends updated

41 lines of code changed in 8 files:

• ALIV3: Makefile (+15)
• ARBDB: Makefile (+2)
• ARBDB2: Makefile (+1)
• ARBDBS: Makefile (+1)
• AWTC: Makefile (+1)
• GENOM_IMPORT: Makefile (+13)
• NTREE: Makefile (+1)
• TOOLS: Makefile (+7)

westram 2004-11-18 14:06 #51 Rev.: 3399

- status display for sequence export (ARB method)

7 lines of code changed in 1 file:

• AWTI: AWTI_export.cxx (+7 -2)

westram 2004-11-18 14:05 #50 Rev.: 3398

- added TEMPLATES/perf_timer.h

1 lines of code changed in 1 file:

• SOURCE_TOOLS: generate_all_links.sh (+1)

westram 2004-11-18 14:04 #49 Rev.: 3397

- uses PerfTimer

16 lines of code changed in 1 file:

• GENOM_IMPORT: GAGenomEmbl.cpp (+16 -11)

westram 2004-11-18 14:04 #48 Rev.: 3396

- simple class for performance measuring

80 lines of code changed in 1 file:

• TEMPLATES: perf_timer.h (new 80)

artemov 2004-11-18 13:01 #47 Rev.: 3395

Reduced import duration to approx. 50%

14 lines of code changed in 1 file:

• GENOM_IMPORT: GAGenomUtilities.cpp (+14)

artemov 2004-11-18 12:58 #46 Rev.: 3394

Ralf: basic performance debug messages

16 lines of code changed in 1 file:

• GENOM_IMPORT: GAGenomEmbl.cpp (+16 -1)

artemov 2004-11-17 17:08 #45 Rev.: 3393

*** empty log message ***

6 lines of code changed in 1 file:

• ARBDB: adstring.c (+6)

westram 2004-11-12 20:49 #44 Rev.: 3392

- gcc 2.95.3 fix

1 lines of code changed in 1 file:

• TOOLS: arb_gene_probe.cxx (+1 -1)

westram 2004-11-12 20:46 #43 Rev.: 3391

- fixed a bug in name-map-generation (caused by looooooooong gene-names)
- intergenic regions are detected globally (ascending gene order was assumed before)

215 lines of code changed in 1 file:

• TOOLS: arb_gene_probe.cxx (+215 -51)

westram 2004-11-12 20:45 #42 Rev.: 3390

- 'intron' -> 'intergene'
- some words about results of gene-pt-server

6 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: probeadmin.hlp (+6 -1)

westram 2004-11-12 20:31 #41 Rev.: 3389

- raised wrong error

1 lines of code changed in 1 file:

• ARBDB: adlang1.c (+1 -2)

westram 2004-11-12 20:30 #40 Rev.: 3388

*** empty log message ***

32 lines of code changed in 1 file:

• SH: example_batch_probe_match.sh (new 32)

westram 2004-11-12 12:23 #39 Rev.: 3387

- forgot one 'gp'

1 lines of code changed in 1 file:

• Makefile (+1 -1)

westram 2004-11-12 12:12 #38 Rev.: 3386

- beautified
- fixed 2 asserts

79 lines of code changed in 1 file:

• TOOLS: arb_probe.cxx (+79 -79)

westram 2004-11-12 12:12 #37 Rev.: 3385

- moved GENE_PROBE/GP_main.cxx here

482 lines of code changed in 1 file:

• TOOLS: arb_gene_probe.cxx (new 482)

westram 2004-11-12 12:11 #36 Rev.: 3384

- added arb_gene_probe

1 lines of code changed in 1 file:

• TOOLS: Makefile (+1 -1)

westram 2004-11-12 12:11 #35 Rev.: 3383

- removed call to GENE_PROBE subdir

0 lines of code changed in 1 file:

• Makefile (-14)

westram 2004-11-11 13:01 #34 Rev.: 3382

- C fix

10 lines of code changed in 1 file:

• ARBDB: adGene.c (+10 -10)

westram 2004-11-11 12:52 #33 Rev.: 3381

- added AWTI_ImportType (differs between old and new flatfile importer)

7 lines of code changed in 1 file:

• AWTI: awti_import.hxx (+7)

westram 2004-11-11 12:52 #32 Rev.: 3380

- added AWAR_ALI_PROTECTION

6 lines of code changed in 1 file:

• AWTI: awti_imp_local.hxx (+6 -5)

westram 2004-11-11 12:52 #31 Rev.: 3379

- added ali protection selector -> sets default protection for new sequence data
- fixed 'flatfile/non-flatfile' toggle usage
- stores/restores ali name+type, when toggling between flatfile and normal seq.file

75 lines of code changed in 1 file:

• AWTI: AWTI_import.cxx (+75 -41)

westram 2004-11-11 12:51 #30 Rev.: 3378

- uses GENOM_ALIGNMENT instead of 'ali_genom'
- gbt_insert_character shows status
- fixed tree error message

14 lines of code changed in 1 file:

• ARBDB: adtools.c (+14 -9)

westram 2004-11-11 12:50 #29 Rev.: 3377

- added AWAR_GENE_COMPLEMENT

4 lines of code changed in 1 file:

• GENOM: GEN_local.hxx (+4 -3)

westram 2004-11-11 12:50 #28 Rev.: 3376

- uses GENOM_ALIGNMENT instead of 'ali_genom'
- fixed partly hidden text
- check genome length when creating genes manually
- init AWAR_GENE_COMPLEMENT, use it in gene_create_cb
- added a 'Complentary strand'-toggle to gene create window

51 lines of code changed in 1 file:

• GENOM: GEN_interface.cxx (+51 -18)

westram 2004-11-11 12:49 #27 Rev.: 3375

- moved GENOM_ALIGNMENT -> adGene.h

0 lines of code changed in 1 file:

• GENOM: GEN.hxx (-1)

westram 2004-11-11 12:48 #26 Rev.: 3374

- added GENOM_ALIGNMENT (has been in GEN.hxx)

4 lines of code changed in 1 file:

• ARBDB: adGene.h (+4 -2)

westram 2004-11-11 12:47 #25 Rev.: 3373

- GEN_create_gene_rel_gene_data() raises error if no name specified

6 lines of code changed in 1 file:

• ARBDB: adGene.c (+6 -1)

westram 2004-11-11 12:47 #24 Rev.: 3372

- senseless cast removed

1 lines of code changed in 1 file:

• AWT: AWT_tree.cxx (+1 -1)

westram 2004-11-11 12:47 #23 Rev.: 3371

- AWT_graphic_tree::load avoids error message when no tree is selected

30 lines of code changed in 1 file:

• AWT: AWT_dtree.cxx (+30 -26)

westram 2004-11-11 12:46 #22 Rev.: 3370

- fixed wildcard usage

4 lines of code changed in 1 file:

• AWT: AWT_file_selection.cxx (+4 -3)

westram 2004-11-11 12:45 #21 Rev.: 3369

- added protection selector

29 lines of code changed in 1 file:

• lib/pictures/awt: import_db.fig (+29 -29)

westram 2004-11-11 12:44 #20 Rev.: 3368

- added toggle (for complement)

11 lines of code changed in 1 file:

• lib/pictures: ad_al_si3.fig (+11 -12)

westram 2004-11-11 12:44 #19 Rev.: 3367

- fixed 'flatfile/non-flatfile' toggle usage
- uses GENOM_ALIGNMENT instead of 'ali_genom'

4 lines of code changed in 1 file:

• NTREE: NT_main.cxx (+4 -3)

westram 2004-11-11 12:43 #18 Rev.: 3366

- fixed 'flatfile/non-flatfile' toggle usage

6 lines of code changed in 1 file:

• NTREE: NT_import.cxx (+6 -4)

westram 2004-11-11 12:43 #17 Rev.: 3365

- uses GENOM_ALIGNMENT instead of 'ali_genom'

3 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+3 -3)

westram 2004-11-10 15:29 #16 Rev.: 3364

- added debugging code to file selection boxes
- if dir + previous_filename results in directory name -> clear previous_filename
- parent directory always shown (was hidden when 'Hide subdirs' was active)
- new browser command 'dot' to toggle display of files/directories starting with '.' (default: hide)

51 lines of code changed in 1 file:

• AWT: AWT_file_selection.cxx (+51 -21)

artemov 2004-11-10 14:34 #15 Rev.: 3363

*** empty log message ***

6 lines of code changed in 1 file:

• GENOM_IMPORT: GAGenomImport.cpp (+6)

westram 2004-11-10 13:45 #14 Rev.: 3362

- added gcc 3.4.3 to tested versions

1 lines of code changed in 1 file:

• Makefile (+1 -1)

westram 2004-11-09 15:00 #13 Rev.: 3361

- added *.java

1 lines of code changed in 1 file:

• util: arb_save (+1)

westram 2004-11-09 14:37 #12 Rev.: 3360

- like fasta_noalign.eft, but all data in one line

0 lines of code changed in 1 file:

• lib/export: fasta_wide_noalign.eft (new)

westram 2004-11-09 14:37 #11 Rev.: 3359

- like fasta.eft, but all data in one line

4 lines of code changed in 1 file:

• lib/export: fasta_wide.eft (new 4)

westram 2004-11-09 14:37 #10 Rev.: 3358

- fasta export filter (removes alignment from sequence)

0 lines of code changed in 1 file:

• lib/export: fasta_noalign.eft (new)

westram 2004-11-09 14:37 #9 Rev.: 3357

- renamed into fasta_noalign.eft

0 lines of code changed in 1 file:

• lib/export: fastacompressed.eft (del)

artemov 2004-11-09 12:20 #8 Rev.: 3356

*** empty log message ***

502 lines of code changed in 13 files:

• GENOM_IMPORT: GAGenom.cpp (+60), GAGenom.h (+12), GAGenomDDBJ.cpp (+55 -20), GAGenomDDBJ.h (+3), GAGenomFeatureTableSourceDDBJ.cpp (+76 -7), GAGenomFeatureTableSourceEmbl.cpp (+76 -8), GAGenomFeatureTableSourceGenBank.cpp (+76 -7), GAGenomGenBank.cpp (+45 -23), GAGenomGenBank.h (-3), GAGenomGeneDDBJ.cpp (+14 -1), GAGenomGeneEmbl.cpp (-3), GAGenomGeneGenBank.cpp (+14 -1), GAGenomImport.cpp (+71 -24)

westram 2004-11-08 21:06 #7 Rev.: 3355

Patch for Debian gcc

1 lines of code changed in 1 file:

• Makefile (+1 -1)

artemov 2004-11-08 17:26 #6 Rev.: 3354

*** empty log message ***

91 lines of code changed in 5 files:

• GENOM_IMPORT: GAGenomGenBank.cpp (+49 -10), GAGenomGenBank.h (+3), GAGenomGeneGenBank.cpp (+3), GAGenomImport.cpp (+10 -2), GAGenomReferenceGenBank.cpp (+26 -1)

artemov 2004-11-05 17:39 #5 Rev.: 3353

*** empty log message ***

204 lines of code changed in 8 files:

• GENOM_IMPORT: GAGenom.cpp (+12), GAGenom.h (+10), GAGenomDDBJ.cpp (+32 -33), GAGenomEmbl.cpp (+9 -2), GAGenomGenBank.cpp (+54 -38), GAGenomImport.cpp (+57 -6), GAGenomReferenceDDBJ.cpp (+14 -61), GAGenomReferenceGenBank.cpp (+16 -62)

meierh 2004-11-05 17:10 #4 Rev.: 3352

test

1 lines of code changed in 1 file:

• GENOM_IMPORT: GAGenomEmbl.cpp (+1)

artemov 2004-11-04 13:50 #3 Rev.: 3351

*** empty log message ***

5 lines of code changed in 1 file:

• GENOM_IMPORT: GAGenomImport.cpp (+5 -5)

artemov 2004-11-04 11:14 #2 Rev.: 3350

*** empty log message ***

12 lines of code changed in 1 file:

• GENOM_IMPORT: GAGenomEmbl.cpp (+12 -2)

artemov 2004-11-04 10:59 #1 Rev.: 3349

*** empty log message ***

91 lines of code changed in 5 files:

• ALIV3: Makefile (-15)
• ARBDB: Makefile (-1)
• GENOM_IMPORT: GAGenomEmbl.cpp (+4 -4), GAGenomGeneEmbl.cpp (+18 -3), GAGenomImport.cpp (+69)

October 2004 »