October 2003 Commit Log

Number of Commits:
175
Number of Active Developers:
5
westram 2003-10-30 10:53 Rev.: 2141

added link to html-help in /usr/arb

5 lines of code changed in 1 file:

westram 2003-10-30 10:52 Rev.: 2140

- xml:space=preserve no longer allowed for xsl:template
- header changed

10 lines of code changed in 1 file:

westram 2003-10-30 10:52 Rev.: 2139

- xml:space=preserve no longer allowed for xsl:template

2 lines of code changed in 1 file:

westram 2003-10-30 10:52 Rev.: 2138

- detects file:// URLs

3 lines of code changed in 1 file:

westram 2003-10-30 10:52 Rev.: 2137

- date.xsl now is always generated

3 lines of code changed in 1 file:

westram 2003-10-29 13:29 Rev.: 2136

removed ghostview and xfig licences

0 lines of code changed in 1 file:

westram 2003-10-29 13:28 Rev.: 2135

- fails on help

3 lines of code changed in 1 file:

spanfeln 2003-10-22 17:50 Rev.: 2134

IDP changes

27 lines of code changed in 1 file:

westram 2003-10-22 15:53 Rev.: 2133

- hint for IDP

1 lines of code changed in 1 file:

spanfeln 2003-10-22 15:09 Rev.: 2132

IDP changes

15 lines of code changed in 2 files:

spanfeln 2003-10-22 13:15 Rev.: 2131

IDP changes

2 lines of code changed in 1 file:

huberj 2003-10-17 14:11 Rev.: 2130

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36 lines of code changed in 3 files:

westram 2003-10-17 12:41 Rev.: 2129

*** empty log message ***

1 lines of code changed in 1 file:

westram 2003-10-17 12:40 Rev.: 2128

- simplyfied temp name generation
- added a local awar (AWAR_PD_SELECTED_MATCH) for the selected probe_match
- added callback for AWAR_PD_SELECTED_MATCH which sets AWAR_SPECIES_NAME
- removed aliasing for AWAR_SPECIES_NAME

32 lines of code changed in 1 file:

yadhu 2003-10-16 14:32 Rev.: 2127

Updates for files related to read xml format tree!!!

89 lines of code changed in 5 files:

spanfeln 2003-10-15 16:28 Rev.: 2126

IDP changes

23 lines of code changed in 4 files:

spanfeln 2003-10-15 13:28 Rev.: 2125

IDP

92 lines of code changed in 4 files:

westram 2003-10-14 19:01 Rev.: 2124

- warning for juergen

6 lines of code changed in 1 file:

huberj 2003-10-14 15:52 Rev.: 2123

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55 lines of code changed in 4 files:

huberj 2003-10-13 16:10 Rev.: 2122

*** empty log message ***

67 lines of code changed in 3 files:

westram 2003-10-13 01:15 Rev.: 2121

- added arb_probe_server.config

1 lines of code changed in 1 file:

westram 2003-10-13 01:15 Rev.: 2120

- uses arb_probe_server.config to configure root-directory and running servers

42 lines of code changed in 1 file:

westram 2003-10-13 01:15 Rev.: 2119

- cosmetics

0 lines of code changed in 1 file:

westram 2003-10-13 01:14 Rev.: 2118

- converts 'plength' to int

2 lines of code changed in 1 file:

westram 2003-10-13 01:14 Rev.: 2117

- template for arb_probe_server.config

1 lines of code changed in 1 file:

westram 2003-10-13 00:49 Rev.: 2116

- template for arb_probe_server.config

7 lines of code changed in 1 file:

westram 2003-10-13 00:49 Rev.: 2115

error handling changed

16 lines of code changed in 2 files:

westram 2003-10-12 19:51 Rev.: 2114

warning if SKIP_PROBES_TO_TARGET_CONVERSION defined

8 lines of code changed in 1 file:

westram 2003-10-12 19:49 Rev.: 2113

- removed message

1 lines of code changed in 1 file:

westram 2003-10-11 14:44 Rev.: 2112

changes for non-zipped jar

6 lines of code changed in 2 files:

westram 2003-10-11 14:44 Rev.: 2111

does not zip client (jar is already zipped)

6 lines of code changed in 1 file:

westram 2003-10-11 12:42 Rev.: 2110

- added __attribute__
- rewrote put()

14 lines of code changed in 1 file:

westram 2003-10-11 12:42 Rev.: 2109

- clears detail view during server access
- resets cursor to top after printing sth

13 lines of code changed in 1 file:

westram 2003-10-11 12:41 Rev.: 2108

- ignores missing 'probe_group_common' (prints warning on console)

5 lines of code changed in 1 file:

westram 2003-10-11 12:41 Rev.: 2107

- automatically matches complement probe

44 lines of code changed in 1 file:

westram 2003-10-11 12:39 Rev.: 2106

- added operator== for PG_Group

3 lines of code changed in 1 file:

westram 2003-10-11 12:39 Rev.: 2105

- checks different node types while traversing pos.tree
- when a leaf is reached in findLeftmostProbe() the probe is filled from sequence
- when a leaf/chain is reached in findNextProbe() false is returned (aka 'last probe reached')
- checks length of returned probe

32 lines of code changed in 1 file:

westram 2003-10-11 09:55 Rev.: 2104

- layout changed (removed IUPAC subwindow)
- added auto match toggle

61 lines of code changed in 1 file:

westram 2003-10-11 09:54 Rev.: 2103

- splitted off from probe match window

22 lines of code changed in 1 file:

westram 2003-10-11 09:54 Rev.: 2102

- added automatch toggle

20 lines of code changed in 1 file:

westram 2003-10-11 09:53 Rev.: 2101

- provides connection errors

6 lines of code changed in 1 file:

westram 2003-10-11 09:53 Rev.: 2100

- handles connection errors

50 lines of code changed in 1 file:

westram 2003-10-11 09:52 Rev.: 2099

- splitted match window into main and iupac-resolve parts
- added automatch toggle
- replaced hardcoded AWAR strings by defines
- added error for IDP + callback client parameters
- added target string modifiers
- fixed call to GBT_reverseComplementNucSequence

321 lines of code changed in 1 file:

westram 2003-10-11 09:52 Rev.: 2098

- mentioned automatch toggle

9 lines of code changed in 2 files:

westram 2003-10-11 02:08 Rev.: 2097

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1 lines of code changed in 1 file:

westram 2003-10-11 01:58 Rev.: 2096

- wrapper for probes->target conversion
- increased clip-result (40->1000)

8 lines of code changed in 1 file:

westram 2003-10-11 01:55 Rev.: 2095

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6 lines of code changed in 1 file:

westram 2003-10-11 01:54 Rev.: 2094

- checks different node types while traversing pos.tree
- when a leaf is reached probe is filled from sequence

71 lines of code changed in 1 file:

westram 2003-10-11 01:54 Rev.: 2093

- changed , -> /

1 lines of code changed in 1 file:

westram 2003-10-11 01:54 Rev.: 2092

- added number of hits

26 lines of code changed in 1 file:

huberj 2003-10-10 16:01 Rev.: 2091

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178 lines of code changed in 5 files:

huberj 2003-10-10 14:39 Rev.: 2090

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7 lines of code changed in 1 file:

westram 2003-10-10 12:49 Rev.: 2089

- downgraded server version

1 lines of code changed in 1 file:

westram 2003-10-10 12:48 Rev.: 2088

be quiet

27 lines of code changed in 9 files:

westram 2003-10-10 12:48 Rev.: 2087

- downgraded client version

2 lines of code changed in 1 file:

westram 2003-10-10 12:48 Rev.: 2086

- wraps test in ----

8 lines of code changed in 1 file:

westram 2003-10-10 12:47 Rev.: 2085

- converts probe-targets to probes
- uses output module

125 lines of code changed in 1 file:

westram 2003-10-10 12:47 Rev.: 2084

- changed types of some aisc parameters (for probe find)

9 lines of code changed in 1 file:

westram 2003-10-10 12:46 Rev.: 2083

- writes alignment_name and alignment_type into probe-group-database
- writes 'better coverage' and 'less mishit' counters

101 lines of code changed in 1 file:

westram 2003-10-10 12:45 Rev.: 2082

- uses GBT_determine_T_or_U

57 lines of code changed in 2 files:

westram 2003-10-10 12:44 Rev.: 2081

- fixed call to GBT_reverseComplementNucSequence

12 lines of code changed in 2 files:

westram 2003-10-10 12:44 Rev.: 2080

undated

3 lines of code changed in 1 file:

westram 2003-10-10 12:44 Rev.: 2079

- added GBT_determine_T_or_U
- GBT_reverseComplementNucSequence has similar interface as GBT_complementNucSequence

19 lines of code changed in 1 file:

westram 2003-10-10 11:24 Rev.: 2078

- cosmetics

4 lines of code changed in 1 file:

westram 2003-10-10 11:24 Rev.: 2077

- made GEN_select_gene global

2 lines of code changed in 1 file:

westram 2003-10-10 11:24 Rev.: 2076

- added GEN_select_gene

2 lines of code changed in 1 file:

richter 2003-10-09 16:25 Rev.: 2075

poster version;
probe sequence, melting temperatur, GC content and unordered hit list
displayed in bottom window
group names disabled, colors of scrollbars disabled
most stuff hacked in Client class

103 lines of code changed in 4 files:

westram 2003-10-09 11:40 Rev.: 2074

dependencies updated

7 lines of code changed in 3 files:

westram 2003-10-09 11:40 Rev.: 2073

- simple config parser

282 lines of code changed in 1 file:

westram 2003-10-09 11:39 Rev.: 2072

- If target does not exist, source is always moved to target

12 lines of code changed in 1 file:

westram 2003-10-09 11:39 Rev.: 2071

- added config_parser.h

1 lines of code changed in 1 file:

westram 2003-10-09 11:38 Rev.: 2070

- reads config and uses it instead of hardcoded parameters

76 lines of code changed in 1 file:

westram 2003-10-09 11:37 Rev.: 2069

- PG_probe_match_para -> probe_config_data

20 lines of code changed in 1 file:

westram 2003-10-09 11:37 Rev.: 2068

- does not use hardcoded parameters (uses config instead)
- PG_probe_match_para -> probe_config_data

33 lines of code changed in 1 file:

westram 2003-10-09 11:37 Rev.: 2067

- parses configfile
- does not use hardcoded parameters (uses config instead)
- restarts coverage search until all groups were searched

68 lines of code changed in 1 file:

westram 2003-10-09 11:33 Rev.: 2066

- config interpreter for probe_parameters.conf
- clears data before setting it

84 lines of code changed in 1 file:

westram 2003-10-09 11:32 Rev.: 2065

- configuration for probe design/match (for arb_probe_library)

14 lines of code changed in 1 file:

westram 2003-10-09 11:32 Rev.: 2064

- added probe_config_data

17 lines of code changed in 1 file:

westram 2003-10-09 11:30 Rev.: 2063

- added assertions (avoid index underflow)

11 lines of code changed in 1 file:

westram 2003-10-09 11:30 Rev.: 2062

- creates local .depends via AISC/Makefile
- depends on public server/client sources

21 lines of code changed in 3 files:

westram 2003-10-09 11:28 Rev.: 2061

added automatic dependencies to _COM objects

12 lines of code changed in 3 files:

westram 2003-10-09 11:27 Rev.: 2060

cosmetics

9 lines of code changed in 1 file:

westram 2003-10-09 11:18 Rev.: 2059

- changed error message
- some overflow checks

14 lines of code changed in 1 file:

westram 2003-10-09 11:17 Rev.: 2058

- makedepend couldn't handle #elseif
- LINUX sysent.h -> signal.h and define SIG_PF as __sighandler_t
- added aisc_assert

18 lines of code changed in 1 file:

westram 2003-10-09 11:17 Rev.: 2057

- rule to create depends (.depends is generated in various _COM directories)

5 lines of code changed in 1 file:

westram 2003-10-09 11:17 Rev.: 2056

- depends on public server/client sources
- creates local dummy .depends [hmm .. does not work]

8 lines of code changed in 1 file:

westram 2003-10-08 14:15 Rev.: 2055

updated

1 lines of code changed in 1 file:

westram 2003-10-08 14:13 Rev.: 2054

- calls Client.saveConfig

10 lines of code changed in 1 file:

westram 2003-10-08 14:12 Rev.: 2053

- calls Client.saveConfig on 'Quit'

1 lines of code changed in 1 file:

westram 2003-10-08 14:12 Rev.: 2052

- added getScrollPaneSize
- display modifications (size/pos) done here

43 lines of code changed in 1 file:

westram 2003-10-08 14:12 Rev.: 2051

- added saveConfig
- display modifications moved into ProbesGUI

14 lines of code changed in 1 file:

westram 2003-10-08 04:47 Rev.: 2050

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5 lines of code changed in 3 files:

westram 2003-10-08 04:20 Rev.: 2049

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2 lines of code changed in 42 files:

westram 2003-10-08 04:15 Rev.: 2048

help updated

1 lines of code changed in 1 file:

westram 2003-10-08 04:14 Rev.: 2047

updated

8 lines of code changed in 1 file:

westram 2003-10-08 04:13 Rev.: 2046

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3 lines of code changed in 1 file:

westram 2003-10-08 04:13 Rev.: 2045

- mark-functions return true when any mark changed

89 lines of code changed in 1 file:

westram 2003-10-08 04:12 Rev.: 2044

- cleanup

8 lines of code changed in 1 file:

westram 2003-10-08 04:11 Rev.: 2043

- uses getSelectedIndex+getProbeInfo instead of getSelectedItem
- changed from ActionListener to ItemListener

9 lines of code changed in 1 file:

westram 2003-10-08 04:11 Rev.: 2042

- only probe is displayed in list
- cleanup

16 lines of code changed in 1 file:

westram 2003-10-08 04:11 Rev.: 2041

- removed setLocation (seems to cause display problems with fvwm)
- selects first probe after retrieving probes

25 lines of code changed in 1 file:

westram 2003-10-08 04:09 Rev.: 2040

- configuration for probe design/match (for arb_probe_library) [not used yet]

32 lines of code changed in 1 file:

westram 2003-10-08 04:09 Rev.: 2039

- restarts coverage search until all groups were searched

30 lines of code changed in 1 file:

richter 2003-10-07 22:38 Rev.: 2038

ActinoListener for probeList added, act on doubleclick, no further selection
of listItem necessary
minor modifications in other classes;
matchProbes works in most cases; no parsion of anser yet

66 lines of code changed in 3 files:

westram 2003-10-07 16:33 Rev.: 2037

- returns coverage probes
- returns members of independent groups

96 lines of code changed in 1 file:

huberj 2003-10-07 15:46 Rev.: 2036

*** empty log message ***

12 lines of code changed in 2 files:

spanfeln 2003-10-07 15:28 Rev.: 2035

IDP changes

3 lines of code changed in 2 files:

spanfeln 2003-10-07 15:22 Rev.: 2034

IDP changes

55 lines of code changed in 4 files:

westram 2003-10-07 14:21 Rev.: 2033

- fixed call to PM_name2ID/PM_ID2name

3 lines of code changed in 1 file:

westram 2003-10-07 14:21 Rev.: 2032

- probe_design_event -> PGD_probe_design_event
- fixed memory leaks and buffer overflows
- handles subtree-independent groups
- fixed calls to PM_name2ID/PM_ID2name

59 lines of code changed in 1 file:

westram 2003-10-07 14:19 Rev.: 2031

prototypes

3 lines of code changed in 1 file:

westram 2003-10-07 14:13 Rev.: 2030

- fixed memory leak
- added PG_find_best_covering_probe_group_for_species

100 lines of code changed in 1 file:

westram 2003-10-07 14:11 Rev.: 2029

- searches better coverage for inner nodes
- coverage_id's pointing to groups prefixed by 'p'
- added species list for independent groups

197 lines of code changed in 1 file:

westram 2003-10-07 14:09 Rev.: 2028

- improved pt-server termination

24 lines of code changed in 1 file:

westram 2003-10-07 14:09 Rev.: 2027

- PM_name2ID/PM_ID2name return error if nothing found

21 lines of code changed in 1 file:

richter 2003-10-07 13:31 Rev.: 2026

cosmetics

1 lines of code changed in 1 file:

richter 2003-10-07 13:30 Rev.: 2025

width of probelist adjusted, constructor and invocation in ProbeList and ProbesGUI modified. Overloading of method getPreferredSize. see code comment.

42 lines of code changed in 3 files:

spanfeln 2003-10-07 13:17 Rev.: 2024

IDP changes

89 lines of code changed in 4 files:

westram 2003-10-07 10:18 Rev.: 2023

- probe_design_event, probe_match_event -> AP_probe_design_event, AP_probe_match_event

4 lines of code changed in 1 file:

westram 2003-10-07 10:17 Rev.: 2022

- removed debug output

3 lines of code changed in 1 file:

westram 2003-10-07 10:17 Rev.: 2021

- recreates pt-server when db date differs (not only when older)

6 lines of code changed in 1 file:

westram 2003-10-07 10:16 Rev.: 2020

- fixed resource management in GBS_read_arb_tcp()

52 lines of code changed in 1 file:

westram 2003-10-06 18:59 Rev.: 2019

- added matchProbes
- call matchProbes with first found probe

38 lines of code changed in 1 file:

westram 2003-10-06 18:57 Rev.: 2018

- added markSpecies()

14 lines of code changed in 1 file:

westram 2003-10-06 18:57 Rev.: 2017

added getProbeList()
removed setProbeListContents

7 lines of code changed in 1 file:

westram 2003-10-06 18:56 Rev.: 2016

- getProbeInfo made public

1 lines of code changed in 1 file:

westram 2003-10-06 18:56 Rev.: 2015

- retrieves and caches group member information

12 lines of code changed in 1 file:

westram 2003-10-06 18:56 Rev.: 2014

- removed unneeded path encodings
- probe group caching based on id
- path coding moved to ../path_code.h
- fixed member extraction (currently for subtrees only)

109 lines of code changed in 1 file:

westram 2003-10-06 18:54 Rev.: 2013

- path cache uses encoded paths
- changed 'subtreepath' -> 'id' (prefixed by 'p')

83 lines of code changed in 1 file:

westram 2003-10-06 18:54 Rev.: 2012

- stores paths in encoded format (less big)
- changed 'subtreepath' -> 'id' (prefixed by 'p')

30 lines of code changed in 1 file:

westram 2003-10-06 18:53 Rev.: 2011

aborts more early in case of error

6 lines of code changed in 1 file:

westram 2003-10-06 18:52 Rev.: 2010

- moved path encoding here

153 lines of code changed in 1 file:

westram 2003-10-06 18:52 Rev.: 2009

test whether map initialized

14 lines of code changed in 1 file:

westram 2003-10-06 18:52 Rev.: 2008

avoid some warnings

3 lines of code changed in 1 file:

westram 2003-10-06 18:51 Rev.: 2007

*** empty log message ***

2 lines of code changed in 1 file:

huberj 2003-10-06 17:59 Rev.: 2006

*** empty log message ***

172 lines of code changed in 5 files:

spanfeln 2003-10-06 15:39 Rev.: 2005

IDP update

70 lines of code changed in 5 files:

spanfeln 2003-10-06 13:17 Rev.: 2004

IDP GENE changes

77 lines of code changed in 2 files:

westram 2003-10-06 12:03 Rev.: 2003

- fixed some memory leaks

39 lines of code changed in 1 file:

westram 2003-10-06 11:35 Rev.: 2002

- annotations for juergen

15 lines of code changed in 2 files:

westram 2003-10-06 11:35 Rev.: 2001

- improved error messages
- annotations for juergen

24 lines of code changed in 1 file:

westram 2003-10-06 11:16 Rev.: 2000

- getNodeInformation->getDisplayString

2 lines of code changed in 2 files:

westram 2003-10-06 11:16 Rev.: 1999

- getNodeInformation->getDisplayString
- calls updateNodeInformation instead of printing to console

14 lines of code changed in 1 file:

westram 2003-10-06 11:16 Rev.: 1998

- added setProbeListContents()
- tried to change size of probe_list [not working]

43 lines of code changed in 1 file:

westram 2003-10-06 11:16 Rev.: 1997

- holds probe info for last clicked node

40 lines of code changed in 1 file:

westram 2003-10-06 11:15 Rev.: 1996

- added retrieveGroupMembers()

9 lines of code changed in 1 file:

westram 2003-10-06 11:15 Rev.: 1995

- added updateNodeInformation()

12 lines of code changed in 1 file:

spanfeln 2003-10-06 09:31 Rev.: 1994

Headerstring edited for IDP

10 lines of code changed in 1 file:

huberj 2003-10-05 17:57 Rev.: 1993

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45 lines of code changed in 4 files:

huberj 2003-10-03 18:08 Rev.: 1992

*** empty log message ***

25 lines of code changed in 2 files:

westram 2003-10-02 18:13 Rev.: 1991

fix

55 lines of code changed in 3 files:

westram 2003-10-02 17:08 Rev.: 1990

*** empty log message ***

1 lines of code changed in 1 file:

westram 2003-10-02 17:06 Rev.: 1989

made resizeable

35 lines of code changed in 1 file:

westram 2003-10-02 17:05 Rev.: 1988

- reduced AW_GAUGE_GRANULARITY to 1000
- ARB_LOGGING undefined by default
- added debug output
- added some (maybe unneeded) failure tests

54 lines of code changed in 1 file:

westram 2003-10-02 17:04 Rev.: 1987

- if DUMP_SMART_PTRS is defined -> shows creation/destruction/reference counting
- now there are 3 flavors of SmartPtrs (for new, new[] and malloc)

130 lines of code changed in 1 file:

westram 2003-10-02 17:02 Rev.: 1986

- warns if filelist seems out-of-date
- added full filename to index

13 lines of code changed in 1 file:

westram 2003-10-02 17:00 Rev.: 1985

- added available_servers
- added get_std_result

42 lines of code changed in 1 file:

westram 2003-10-02 17:00 Rev.: 1984

- returns the probe lengths that are currently available

9 lines of code changed in 1 file:

westram 2003-10-02 16:59 Rev.: 1983

- if plength==all -> write multiple requests to different workers and merge them

74 lines of code changed in 1 file:

westram 2003-10-02 16:58 Rev.: 1982

- draws inner node info in different colors (exact match or not)
- displays group names

25 lines of code changed in 1 file:

westram 2003-10-02 16:56 Rev.: 1981

- output format slightly changed

2 lines of code changed in 1 file:

westram 2003-10-02 16:56 Rev.: 1980

- can handle empty node-info in input trees
- does NOT write empty merged node-info to output tree
- able to "merge" a single tree (it only removes empty node-infos in that case)

37 lines of code changed in 1 file:

westram 2003-10-02 16:56 Rev.: 1979

- saves empty node-info for inner-nodes

8 lines of code changed in 1 file:

westram 2003-10-02 16:55 Rev.: 1978

- added PG_find_probe_group_for_species, removed PG_find_probe_for_subtree + PG_get_id

7 lines of code changed in 1 file:

westram 2003-10-02 16:55 Rev.: 1977

- element 'num' is GB_INT now
- added PG_find_probe_group_for_species, removed PG_find_probe_for_subtree

43 lines of code changed in 1 file:

westram 2003-10-02 16:54 Rev.: 1976

- fixed calculation of max. possible groups
- calculates number of possible species-combinations that need to
be tested to find better coverages
- uses new malloc-flavor of SmartPtr for SpeciesBags, because
deque seems to be allocated by malloc
- valgrinded (stays angry about deallocation of deque)
- only the first probe subtree was searched -> most probes were not found!
- TreeTraversal able to use both tree-linkage-types

245 lines of code changed in 1 file:

westram 2003-10-02 16:54 Rev.: 1975

- element 'num' is GB_INT now

8 lines of code changed in 1 file:

westram 2003-10-02 16:53 Rev.: 1974

depends

9 lines of code changed in 2 files:

westram 2003-10-02 16:53 Rev.: 1973

- configuration section on top

28 lines of code changed in 1 file:

westram 2003-10-02 16:53 Rev.: 1972

- added 'ngi' and 'mci'

3 lines of code changed in 1 file:

westram 2003-10-02 16:51 Rev.: 1971

- cosmetics

20 lines of code changed in 1 file:

westram 2003-10-02 16:51 Rev.: 1970

- rewrote error/resource-handling of AP_calc_pos_var_pars
- crashed when poison characters were in sequence

59 lines of code changed in 1 file:

westram 2003-10-02 16:49 Rev.: 1969

- overlapping strcpy replaced by memmove
- cosmetics

33 lines of code changed in 1 file:

westram 2003-10-02 16:49 Rev.: 1968

- GB_find_sub_by_quark is able to search values of other types than GB_STRING

41 lines of code changed in 1 file:

huberj 2003-10-02 16:25 Rev.: 1967

*** empty log message ***

62 lines of code changed in 3 files:

September 2003 »

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