December 2003 Commit Log

Number of Commits:

88

Number of Active Developers:

4

spanfeln 2003-12-30 17:21 #88 Rev.: 2308

Wiederherstellung verlorener Programmteile

73 lines of code changed in 3 files:

• ARBDB: ad_t_prot.h (+7), adtools.c (+38)
• PROBE_DESIGN: probe_design.cxx (+28 -34)

yadhu 2003-12-23 16:03 #87 Rev.: 2307

Feature to import xml format trees!!

325 lines of code changed in 4 files:

• XML_IMPORT/IMP_TREE: sax2Handler.cxx (new 165), sax2Handler.hxx (new 45), xmlParser.cxx (new 83), xmlParser.hxx (new 32)

yadhu 2003-12-23 16:01 #86 Rev.: 2306

visualization of SAIs in Probe Match Results !!

500 lines of code changed in 16 files:

• EDIT4: ED4_main.cxx (+1), ED4_text_terminals.cxx (+2), ED4_visualizeSAI.cxx (+1 -24), ed4_class.hxx (+1), ed4_visualizeSAI.hxx (+28 -2)
• NTREE: NT_extern.cxx (+2), ad_trees.cxx (+2 -6)
• PROBE_DESIGN: Makefile (+15 -1), SaiProbeVisualization.cxx (new 228), SaiProbeVisualization.hxx (new 36), probe_design.cxx (+120 -29), probe_design.hxx (-1)
• WINDOW: AW_button.cxx (+22), aw_awars.hxx (+2), aw_window.hxx (+2)
• lib/pictures: pd_match.fig (+38 -37)

westram 2003-12-18 14:11 #85 Rev.: 2305

- removed PERL directory
- GDEHELP is not included completely (only ARB_GDEmenus and DATA_FILES)
- excluded files/dirs starting with .
- excluded files starting with # and 'ChangeLog'

5 lines of code changed in 1 file:

• util: arb_compress (+5 -8)

westram 2003-12-18 14:06 #84 Rev.: 2304

- more messages

22 lines of code changed in 1 file:

• lib/macros/ARB/SEQ_DATA: dashes2dots_at_sequenceends_of_marked.amc (+22 -13)

westram 2003-12-18 14:03 #83 Rev.: 2303

- target for bin/Makefile depends on setting of DEBUG
- cosmetics

11 lines of code changed in 1 file:

• Makefile (+11 -3)

westram 2003-12-18 14:02 #82 Rev.: 2302

hide ARB.pm

1 lines of code changed in 1 file:

• lib: .cvsignore (+1)

westram 2003-12-18 14:01 #81 Rev.: 2301

- create links to SOURCE_TOOLS only in DEBUG mode
Otherwise they get into the release as broken links.

12 lines of code changed in 1 file:

• bin: Makefile (+12 -11)

westram 2003-12-18 14:00 #80 Rev.: 2300

- added XS interface for GB_find (because mode needs translation)

14 lines of code changed in 1 file:

• PERL2ARB: ARB.xs.default (+14)

westram 2003-12-18 13:59 #79 Rev.: 2299

added positions for two more buttons

24 lines of code changed in 1 file:

• lib/pictures: ad_kreo.fig (+24 -13)

westram 2003-12-18 13:58 #78 Rev.: 2298

- changed button text in 'reorder fields' window
- added 2 buttons for up/down movement
- added ad_list_reorder_cb2()
- cosmetics

94 lines of code changed in 1 file:

• NTREE: ad_spec.cxx (+94 -26)

westram 2003-12-18 13:58 #77 Rev.: 2297

updated deps

11 lines of code changed in 4 files:

• GENOM: Makefile (-11)
• NTREE: Makefile (+3 -2)
• PROBE_DESIGN: Makefile (+2)
• SEQ_QUALITY: Makefile (+6 -1)

westram 2003-12-18 13:55 #76 Rev.: 2296

- fixed bug introduced by Gene-PT-Server IDP
(selecting result from Gene-Search didn't select gene)

4 lines of code changed in 1 file:

• GENOM: GEN_interface.cxx (+4 -33)

westram 2003-12-18 13:54 #75 Rev.: 2295

all code moved to ARBDB

0 lines of code changed in 1 file:

• GENOM: GEN_db.cxx (del)

westram 2003-12-18 13:53 #74 Rev.: 2294

- cleanup

0 lines of code changed in 1 file:

• AWT: AWT_species_sel_box.cxx (-11)

westram 2003-12-18 13:52 #73 Rev.: 2293

- added GEN_find_organism

3 lines of code changed in 1 file:

• ARBDB: adGene.h (+3 -1)

westram 2003-12-18 13:49 #72 Rev.: 2292

- moved some functions here (used by IDP)

75 lines of code changed in 1 file:

• ARBDB: adGene.c (+75 -3)

westram 2003-12-18 13:48 #71 Rev.: 2291

removed unused file

0 lines of code changed in 1 file:

• GDEHELP: fastdnaml.help (del)

westram 2003-12-18 13:44 #70 Rev.: 2290

- perl script to import proteomdata

288 lines of code changed in 2 files:

• PERL_SCRIPTS/GENOME: GI.pm (new 192), import_proteomdata.pl (new 96)

westram 2003-12-18 13:44 #69 Rev.: 2289

removed old, broken useless scripts

0 lines of code changed in 4 files:

• PERL_SCRIPTS: arb_ptest_calc_gc_content.pl (del), arb_ptest_create_new_species.pl (del), arb_ptest_read_info_of_selected.pl (del), arb_ptest_read_sequence_of_marked.pl (del)

westram 2003-12-16 10:04 #68 Rev.: 2288

- uses SQ_reset_counters

2 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+2 -2)

westram 2003-12-16 10:03 #67 Rev.: 2287

- removed SQ_count_nr_of_groups()
- added SQ_reset_counters()

3 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.h (+3 -3)

westram 2003-12-16 10:02 #66 Rev.: 2286

- fixed SQ_count_nr_of_groups
- added SQ_reset_counters()

16 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+16 -16)

huberj 2003-12-13 14:26 #65 Rev.: 2285

*** empty log message ***

20 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_functions.cxx (+17 -21), SQ_functions.h (+1 -1), SQ_main.cxx (+2 -1)

spanfeln 2003-12-12 18:56 #64 Rev.: 2284

*** empty log message ***

4 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+4 -2)

westram 2003-12-12 14:22 #63 Rev.: 2283

perl script to convert '-' to '.' at sequence ends

102 lines of code changed in 1 file:

• lib/macros/ARB/SEQ_DATA: dashes2dots_at_sequenceends_of_marked.amc (new 102)

westram 2003-12-12 14:15 #62 Rev.: 2282

- NT_show_message displays mutltiple messages

15 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+15 -5)

westram 2003-12-12 14:14 #61 Rev.: 2281

- GBT_message stores multiple incoming messages by appending them
separated by \n

10 lines of code changed in 1 file:

• ARBDB: adtools.c (+10 -4)

westram 2003-12-11 15:37 #60 Rev.: 2280

- finally excluded names.dat

2 lines of code changed in 1 file:

• util: arb_compress (+2 -2)

westram 2003-12-11 15:04 #59 Rev.: 2279

- checks whether lynx dumps are non-empty

1 lines of code changed in 1 file:

• GDEHELP: Makefile.helpfiles (+1)

westram 2003-12-11 15:04 #58 Rev.: 2278

- mentioned lynx

1 lines of code changed in 1 file:

• arb_INSTALL.txt (+1)

westram 2003-12-11 12:57 #57 Rev.: 2277

- exclude names.dat

1 lines of code changed in 1 file:

• util: arb_compress (+1)

westram 2003-12-11 12:49 #56 Rev.: 2276

writes file.lst

1 lines of code changed in 1 file:

• util: arb_save (+1 -1)

westram 2003-12-11 11:02 #55 Rev.: 2275

- wraps GEN_* functions into P2AT_ "namespace"
- rewrote prototype parsing (depended too much on ad_prot layout)

99 lines of code changed in 1 file:

• TOOLS: arb_proto_2_xsub.cxx (+99 -26)

westram 2003-12-11 11:02 #54 Rev.: 2274

- minor fixes for changed function names

16 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+16 -5)

westram 2003-12-11 11:01 #53 Rev.: 2273

spelling fix

20 lines of code changed in 1 file:

• PERL2ARB: DOC.html (+20 -20)

westram 2003-12-11 11:01 #52 Rev.: 2272

- uses demo.arb if no ARB is running

58 lines of code changed in 1 file:

• PERL2ARB: test.pl (+58 -9)

westram 2003-12-11 11:01 #51 Rev.: 2271

- includes adGene.h

3 lines of code changed in 1 file:

• PERL2ARB: ARB.xs.default (+3 -1)

westram 2003-12-11 11:00 #50 Rev.: 2270

- edited stub doc

6 lines of code changed in 1 file:

• PERL2ARB: ARB.pm (+6 -9)

westram 2003-12-11 10:57 #49 Rev.: 2269

updated

0 lines of code changed in 1 file:

• ARBDB: ad_t_prot.h (-5)

westram 2003-12-11 10:57 #48 Rev.: 2268

- added GEN_first_marked_gene and GEN_next_marked_gene
- fixed file header
- C++ comments -> C comments
- removed some duplicated prototypes

28 lines of code changed in 1 file:

• ARBDB: adGene.h (+28 -31)

westram 2003-12-11 10:57 #47 Rev.: 2267

- moved some functions to adGene.c

0 lines of code changed in 1 file:

• ARBDB: adtools.c (-37)

westram 2003-12-11 10:57 #46 Rev.: 2266

- moved some functions here (used by IDP)

38 lines of code changed in 1 file:

• ARBDB: adGene.c (+38 -3)

westram 2003-12-11 10:55 #45 Rev.: 2265

- include adGene.h into perl interface
- removed deprecated include path to local perl

4 lines of code changed in 1 file:

• Makefile (+4 -2)

huberj 2003-12-09 13:56 #44 Rev.: 2264

*** empty log message ***

100 lines of code changed in 4 files:

• SEQ_QUALITY: SQ_GroupData.h (+1 -1), SQ_functions.cxx (+89 -11), SQ_functions.h (+4), SQ_main.cxx (+6)

westram 2003-12-03 18:37 #43 Rev.: 2263

- removed doc generation (doc is picked up by GDEHELP Makefile)

3 lines of code changed in 1 file:

• GDE/FASTDNAML: Makefile (+3 -14)

westram 2003-12-03 18:31 #42 Rev.: 2262

*** empty log message ***

15 lines of code changed in 1 file:

• GDE/AxML: AxML.doc (new 15)

westram 2003-12-03 18:31 #41 Rev.: 2261

- use ./

1 lines of code changed in 1 file:

• GDEHELP: genhelptree.sh (+1 -1)

westram 2003-12-03 18:30 #40 Rev.: 2260

- use ./ for scripts

5 lines of code changed in 1 file:

• GDEHELP: Makefile.helpfiles (+5 -5)

westram 2003-12-03 18:26 #39 Rev.: 2259

show tgz when done

2 lines of code changed in 1 file:

• util: arb_compress (+2)

westram 2003-12-03 18:26 #38 Rev.: 2258

unused

0 lines of code changed in 1 file:

• lib/pictures: gde_help.fig (del)

westram 2003-12-03 18:26 #37 Rev.: 2257

- added -w

1 lines of code changed in 1 file:

• lib: macro.head (+1 -1)

westram 2003-12-03 18:25 #36 Rev.: 2256

- text appended to generated agde.hlp

8 lines of code changed in 1 file:

• HELP_SOURCE/genhelp: agde.footer (new 8)

westram 2003-12-03 18:25 #35 Rev.: 2255

- converts doc files from external tools to fit into ARB help
(they have to be prepared inside $ARBHOME/GDEHELP)

22 lines of code changed in 1 file:

• HELP_SOURCE/genhelp: Makefile (+22 -7)

westram 2003-12-03 18:24 #34 Rev.: 2254

- many changes to run tasks in seperate directories
- removed deprecated stuff

52 lines of code changed in 9 files:

• GDEHELP/MENUS: align.menu (+24 -25), dnamlrates.menu (+2 -2), export.menu (+3 -2), fastdnaml.menu (+4 -4), import.menu (+4 -6), inc_fastdnaml.menu (+1 -1), phylip_dist.menu (+8 -7), phylip_dist_org.menu (+3 -2), puzzle.menu (+3 -3)

westram 2003-12-03 18:23 #33 Rev.: 2253

removed deprecated menus

0 lines of code changed in 5 files:

• GDEHELP/MENUS: blast.menu (del), blastp.menu (del), dna_rna.menu (del), protein.menu (del), seq_management.menu (del)

westram 2003-12-03 18:22 #32 Rev.: 2252

- added HELP_GEN, HELP_DOC_GEN and helpfiles.lst

3 lines of code changed in 1 file:

• GDEHELP: .cvsignore (+3)

westram 2003-12-03 18:22 #31 Rev.: 2251

- creates a list of all help files used in GDE menus
- calls Makefile.helpfiles to build these docs (or print an error)

21 lines of code changed in 1 file:

• GDEHELP: Makefile (+21 -1)

westram 2003-12-03 18:21 #30 Rev.: 2250

files and Makefile for generation of ARB help from docs of external tools

157 lines of code changed in 4 files:

• GDEHELP: Makefile.helpfiles (new 73), arb_help.head (new 11), genhelp.sh (new 30), genhelptree.sh (new 43)

westram 2003-12-03 18:20 #29 Rev.: 2249

- added GOTO_LOCAL_DIR and RM_LOCAL_DIR to run tasks in
seperate directories which allows running tree programms
parallel (used by GEN_INFILE and RM_LOCAL_FILES)
- removed deprecated blast menus, protein.menu, dna_rna.menu, seq_management.menu

9 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+9 -18)

westram 2003-12-03 18:18 #28 Rev.: 2248

cap help

161 lines of code changed in 1 file:

• GDEHELP/HELP_PLAIN: CAP2.help (new 161)

westram 2003-12-03 18:17 #27 Rev.: 2247

removed old help files

0 lines of code changed in 24 files:

• GDEHELP: CAP2.help (del), DotPlotTool.help (del), FASTA.help (del), LoopTool.help (del), MFOLD.help (del), MakeCons.help (del), PrintStrat.help (del), Restriction.help (del), arbgdemnus_13_01_97.tar.gz (del), blast.help (del), blast3.help (del), clustal_help (del), clustalw.help (del), dnapars.help (del), findall.help (del), heapsortHGL.help (del), lsadt.help (del), new_sequence.help (del), phylip.help (del), print_alignment.help (del), protml.help (del), readseq.help (del), save_selection.help (del), sho_helix.help (del)

westram 2003-12-03 17:48 #26 Rev.: 2246

fixed perl path
added -w

9 lines of code changed in 5 files:

• lib/macros: replamb.amc (+2 -2), test.amc (+2 -2), testwl.amc (+2 -2), toggle_color.amc (+1 -1), xopen.amc (+2 -2)

westram 2003-12-03 17:11 #25 Rev.: 2245

new filters from jack

284 lines of code changed in 3 files:

• lib/import: gcg-rsf_pir.ift (new 75), gcg-rsf_transl.ift (new 90), genbank_prot_from_translation_field.ift (new 119)

westram 2003-12-03 17:10 #24 Rev.: 2244

- changes from jack

131 lines of code changed in 3 files:

• lib/import: fasta.ift (+7 -1), genbank.ift (+62 -9), genbank_multi.ift (+62 -9)

westram 2003-12-03 17:10 #23 Rev.: 2243

removed generated file

0 lines of code changed in 1 file:

• lib: ARB.pm (del)

westram 2003-12-03 17:09 #22 Rev.: 2242

- added AWAR_TREE_REFRESH

1 lines of code changed in 1 file:

• WINDOW: aw_awars.hxx (+1)

westram 2003-12-03 17:08 #21 Rev.: 2241

- added "AWAR_REMOTE_TOUCH" to check_for_remote_command
- added printouts for debugging

26 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+26)

westram 2003-12-03 16:41 #20 Rev.: 2240

- minor changes to template code

9 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_GroupData.h (+9 -6)

westram 2003-12-03 16:40 #19 Rev.: 2239

- fixed mostly cosmetic diffs to latest READSEQ release

52 lines of code changed in 1 file:

• READSEQ: ureadseq.c (+52 -45)

westram 2003-12-03 16:39 #18 Rev.: 2238

- fixed NEXUS format export (missing,gap,interleave)
- fixed mostly cosmetic diffs to latest READSEQ release

7 lines of code changed in 1 file:

• READSEQ: readseq.c (+7 -6)

westram 2003-12-03 16:37 #17 Rev.: 2237

- warning fix

1 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+1 -1)

westram 2003-12-03 16:28 #16 Rev.: 2236

- added NT_recompute_cb to AWAR_COLOR_GROUPS_USE

2 lines of code changed in 1 file:

• PARSIMONY: PARS_main.cxx (+2)

westram 2003-12-03 16:27 #15 Rev.: 2235

- cosmetics

13 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: macro.hlp (+13 -13)

westram 2003-12-03 16:26 #14 Rev.: 2234

- added version info to command line help output
- better handling of illegal cmd line arguments

64 lines of code changed in 1 file:

• NTREE: NT_main.cxx (+64 -43)

westram 2003-12-03 16:26 #13 Rev.: 2233

- tree refresh bound to AWAR_COLOR_GROUPS_USE and AWAR_DTREE_REFRESH
(if some function should refresh the tree, simply touch AWAR_DTREE_REFRESH)
- changed order in export menu

3 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+3 -2)

westram 2003-12-03 16:26 #12 Rev.: 2232

- fixed generation of nt_date.h
- nt_date.h got new define DATE_YEAR

11 lines of code changed in 1 file:

• NTREE: Makefile (+11 -5)

westram 2003-12-03 16:22 #11 Rev.: 2231

- removed deprecated sources HGL_SRC and LOOPTOOL from build

4 lines of code changed in 1 file:

• GDE: Makefile (+4 -2)

westram 2003-12-03 16:21 #10 Rev.: 2230

- added AWAR_DTREE_REFRESH

7 lines of code changed in 1 file:

• AWT: awt_dtree.hxx (+7 -5)

westram 2003-12-03 16:21 #9 Rev.: 2229

- creates AWAR_DTREE_REFRESH

2 lines of code changed in 1 file:

• AWT: AWT_dtree.cxx (+2)

westram 2003-12-03 16:20 #8 Rev.: 2228

- added NT_recompute_cb

8 lines of code changed in 2 files:

• AWT: AWT_tree_cb.cxx (+7), awt_tree_cb.hxx (+1)

westram 2003-12-03 16:18 #7 Rev.: 2227

- added AWT_is_file

7 lines of code changed in 2 files:

• AWT: AWT_file_selection.cxx (+6), awt.hxx (+1)

westram 2003-12-03 16:17 #6 Rev.: 2226

- uses normal ARB help system

9 lines of code changed in 1 file:

• ARB_GDE: GDE.cxx (+9 -40)

westram 2003-12-03 16:15 #5 Rev.: 2225

updated

1 lines of code changed in 1 file:

• ARBDB: ad_t_prot.h (+1)

westram 2003-12-03 16:15 #4 Rev.: 2224

- rewrote remote command functions
to remove duplicated code and oversized stack arrays
- added GBT_remote_touch_awar()

103 lines of code changed in 1 file:

• ARBDB: adtools.c (+103 -107)

westram 2003-12-03 16:01 #3 Rev.: 2223

- inserted many dependencies (multiple targets build straight after 'realclean')

39 lines of code changed in 1 file:

• Makefile (+39 -12)

huberj 2003-12-03 13:46 #2 Rev.: 2222

*** empty log message ***

5 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.cxx (+4 -2), SQ_main.cxx (+1 -1)

huberj 2003-12-02 14:35 #1 Rev.: 2221

*** empty log message ***

27 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_functions.cxx (+23 -76), SQ_functions.h (+2 -2), SQ_main.cxx (+2)

November 2003 »