November 2003 Commit Log

Number of Commits:
79
Number of Active Developers:
3
huberj 2003-11-30 15:53 Rev.: 2220

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233 lines of code changed in 3 files:

huberj 2003-11-26 12:07 Rev.: 2219

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42 lines of code changed in 1 file:

westram 2003-11-26 11:48 Rev.: 2218

- hotkeys fixed

10 lines of code changed in 5 files:

westram 2003-11-26 10:45 Rev.: 2217

- input string for PT_get_names made const
- avoiding copy of name map string

25 lines of code changed in 1 file:

spanfeln 2003-11-25 18:21 Rev.: 2216

IDP

49 lines of code changed in 2 files:

huberj 2003-11-25 14:09 Rev.: 2215

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210 lines of code changed in 6 files:

westram 2003-11-25 10:18 Rev.: 2214

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3 lines of code changed in 1 file:

westram 2003-11-25 10:18 Rev.: 2213

- added INTERACTIVE toggle to clustalw
- added NEGMATRIX for both protein alignment types

32 lines of code changed in 1 file:

westram 2003-11-25 10:16 Rev.: 2212

- added slider buttons for float awars

26 lines of code changed in 1 file:

westram 2003-11-25 09:40 Rev.: 2211

- always do newline for new arg in GDE menus

4 lines of code changed in 1 file:

westram 2003-11-25 09:40 Rev.: 2210

- separated fast and slow clustalw alignment
- added most clustalw parameter to interface

294 lines of code changed in 1 file:

spanfeln 2003-11-25 08:26 Rev.: 2209

Update

3 lines of code changed in 1 file:

huberj 2003-11-23 17:11 Rev.: 2208

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96 lines of code changed in 1 file:

westram 2003-11-23 14:48 Rev.: 2207

added clone()

8 lines of code changed in 1 file:

westram 2003-11-23 13:43 Rev.: 2206

dependency update

23 lines of code changed in 3 files:

westram 2003-11-23 13:42 Rev.: 2205

templated SQ_GroupData_Impl and derived 2 classes:
SQ_GroupData_RNA and SQ_GroupData_PRO

258 lines of code changed in 6 files:

westram 2003-11-23 13:41 Rev.: 2204

obsolete (directly handled by SQ_GroupData)

0 lines of code changed in 1 file:

westram 2003-11-23 13:41 Rev.: 2203

code moved back to SQ_GroupData.xx

0 lines of code changed in 2 files:

huberj 2003-11-22 17:29 Rev.: 2202

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249 lines of code changed in 12 files:

westram 2003-11-21 13:38 Rev.: 2201

- wrapper script for proml

54 lines of code changed in 1 file:

westram 2003-11-21 13:38 Rev.: 2200

- fixes for phylip 3.6
- works now with protpars, proml and dnapars

44 lines of code changed in 1 file:

westram 2003-11-21 13:22 Rev.: 2199

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3 lines of code changed in 1 file:

westram 2003-11-21 13:20 Rev.: 2198

- use std path to perl

1 lines of code changed in 1 file:

westram 2003-11-21 13:20 Rev.: 2197

- simply use 'perl' instead of path to deprecated integrated perl

1 lines of code changed in 1 file:

westram 2003-11-21 13:19 Rev.: 2196

- raise aw_message from external scripts

29 lines of code changed in 1 file:

westram 2003-11-21 13:19 Rev.: 2195

- added arb_message

1 lines of code changed in 1 file:

westram 2003-11-21 13:18 Rev.: 2194

- info how to profile ARB using 'calltree'

13 lines of code changed in 1 file:

westram 2003-11-21 13:18 Rev.: 2193

- wrapper for protpars

44 lines of code changed in 1 file:

westram 2003-11-21 13:18 Rev.: 2192

- fixed PROTML tree generation
- removed bootstrapping approches

42 lines of code changed in 1 file:

westram 2003-11-21 13:17 Rev.: 2191

- removed superfluous CR and y at end (should be handled by other scripts)

5 lines of code changed in 1 file:

westram 2003-11-21 13:16 Rev.: 2190

- wrapper for dnapars

56 lines of code changed in 1 file:

westram 2003-11-21 13:15 Rev.: 2189

cosmetics

2 lines of code changed in 1 file:

westram 2003-11-21 13:15 Rev.: 2188

- replaced all 'chooser' by 'choice_menu'
- replaced 'treefile' by 'outtree' for phylip programs

125 lines of code changed in 12 files:

westram 2003-11-21 13:14 Rev.: 2187

- menu for PROML (not equal to PROTML)

61 lines of code changed in 1 file:

westram 2003-11-21 13:14 Rev.: 2186

- removed bootstrapping

22 lines of code changed in 1 file:

westram 2003-11-21 13:14 Rev.: 2185

- fixed correction parameters for protdist and dnadist
- added new tree method UPGMA

32 lines of code changed in 1 file:

westram 2003-11-21 13:13 Rev.: 2184

- includes phylip_ml.genmenu
- treefile -> outtree

3 lines of code changed in 1 file:

westram 2003-11-21 13:12 Rev.: 2183

- distinguish between EOF and EOL
- show partly read name in case of error

92 lines of code changed in 1 file:

westram 2003-11-21 13:12 Rev.: 2182

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3 lines of code changed in 1 file:

westram 2003-11-21 13:10 Rev.: 2181

- forward XLIBS to submakefiles
- added 'gp' to 'arbapplications'

3 lines of code changed in 1 file:

westram 2003-11-21 13:10 Rev.: 2180

- forward XLIBS to submakefiles

1 lines of code changed in 1 file:

westram 2003-11-21 13:09 Rev.: 2179

- does not print space at EO-headline (new protdist does not like this)

6 lines of code changed in 1 file:

westram 2003-11-21 13:08 Rev.: 2178

- changed feedback request

21 lines of code changed in 1 file:

westram 2003-11-21 13:08 Rev.: 2177

- added a warning when sequences where skipped during export

8 lines of code changed in 1 file:

westram 2003-11-20 12:37 Rev.: 2176

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21478 lines of code changed in 42 files:

westram 2003-11-20 12:36 Rev.: 2175

upgrade to PHYLIP 3.6

54568 lines of code changed in 123 files:

westram 2003-11-19 15:54 Rev.: 2174

- changed label

1 lines of code changed in 1 file:

westram 2003-11-19 15:53 Rev.: 2173

- changed label and button text

2 lines of code changed in 1 file:

westram 2003-11-19 15:53 Rev.: 2172

- Basic note about GENE PT Servers

8 lines of code changed in 1 file:

westram 2003-11-19 12:24 Rev.: 2171


clean removes NTREE/nt_date.h to ensure version information
in ARB_NT is up-to-date.

1 lines of code changed in 1 file:

spanfeln 2003-11-19 11:57 Rev.: 2170

IDP: With comment where error occures

1 lines of code changed in 1 file:

huberj 2003-11-16 17:26 Rev.: 2169

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78 lines of code changed in 7 files:

westram 2003-11-14 15:49 Rev.: 2168

optimized

56 lines of code changed in 4 files:

huberj 2003-11-14 14:34 Rev.: 2167

changes by Juergen and Ralf

25 lines of code changed in 5 files:

westram 2003-11-14 14:32 Rev.: 2166

- converted old-formatted strings

3 lines of code changed in 1 file:

westram 2003-11-14 14:31 Rev.: 2165

- forwards some parameters to arb_2_bin

5 lines of code changed in 1 file:

westram 2003-11-14 14:31 Rev.: 2164

- added ssh option -f

1 lines of code changed in 1 file:

westram 2003-11-14 14:30 Rev.: 2163

- '\n' -> '|'

1 lines of code changed in 1 file:

westram 2003-11-14 14:30 Rev.: 2162

- bugfix: check_update crashed w/o tree

22 lines of code changed in 1 file:

westram 2003-11-14 14:29 Rev.: 2161

- increased cache size to 25M (was 2M)
(this fixes problems with alignments length of 400.000 and hopefully more)

1 lines of code changed in 1 file:

westram 2003-11-13 10:02 Rev.: 2160

- database repair script

10 lines of code changed in 1 file:

westram 2003-11-13 10:02 Rev.: 2159

- can read ascii db from stdin
- error handling improved

82 lines of code changed in 1 file:

westram 2003-11-13 10:01 Rev.: 2158

- may dump database to stdout
- info printed to stderr (so filtering is possible)

33 lines of code changed in 1 file:

westram 2003-11-13 10:01 Rev.: 2157

warning text changed

1 lines of code changed in 1 file:

westram 2003-11-13 10:00 Rev.: 2156

prototypes updated

3 lines of code changed in 2 files:

westram 2003-11-13 10:00 Rev.: 2155

- gb_uncompress_by_dictionary prints meaningful errors
- fake content if illegal key quark is found during decompression

10 lines of code changed in 1 file:

westram 2003-11-13 09:59 Rev.: 2154

cosmetics

1 lines of code changed in 1 file:

westram 2003-11-13 09:59 Rev.: 2153

- dont change GB_MAIN(gb)->path if dumping to stdout

5 lines of code changed in 1 file:

westram 2003-11-13 09:58 Rev.: 2152

- complete redesign of ASCII database loading (now able to read from stdin)
- added helper code to read ascii file in portions
- gb_read_ascii returns GB_ERROR
- GB_login does not abort early in recovery mode (need dictionaries!!)
- better error messages on quicksave-loading

539 lines of code changed in 1 file:

spanfeln 2003-11-11 16:27 Rev.: 2151

IDP Changes

27 lines of code changed in 2 files:

huberj 2003-11-09 17:49 Rev.: 2150

Code cleanup with my newly acquired c++ skills :)
instantiation changed completely to deep copies (->heap)
declared everything below four simple lines as inline
added SQ_functions.backup

765 lines of code changed in 9 files:

westram 2003-11-06 19:07 Rev.: 2149

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6 lines of code changed in 1 file:

westram 2003-11-03 11:51 Rev.: 2148

minor changes

2 lines of code changed in 2 files:

westram 2003-11-03 11:49 Rev.: 2147

- upgraded copyright and license information
- removed statements about future versions
- fixed indentation for help generator
- added disclaimer

155 lines of code changed in 1 file:

westram 2003-11-03 11:49 Rev.: 2146

- sablotron version 1.0 'needed'

1 lines of code changed in 1 file:

westram 2003-11-03 11:17 Rev.: 2145

- includes debug.h

1 lines of code changed in 1 file:

westram 2003-11-03 11:17 Rev.: 2144

- added debug.h

1 lines of code changed in 1 file:

westram 2003-11-03 11:17 Rev.: 2143

- changed DEBUG/NDEBUG check warnings

4 lines of code changed in 1 file:

westram 2003-11-03 11:16 Rev.: 2142

- finetuned perl dependencies
- wrapped perl make code
- generates debug.h (defines either DEBUG or NDEBUG)

30 lines of code changed in 1 file:

October 2003 »

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