added link to html-help in /usr/arb
5 lines of code changed in 1 file:
- xml:space=preserve no longer allowed for xsl:template
- header changed
10 lines of code changed in 1 file:
- xml:space=preserve no longer allowed for xsl:template
2 lines of code changed in 1 file:
- detects file:// URLs
3 lines of code changed in 1 file:
- date.xsl now is always generated
3 lines of code changed in 1 file:
removed ghostview and xfig licences
0 lines of code changed in 1 file:
- fails on help
3 lines of code changed in 1 file:
IDP changes
27 lines of code changed in 1 file:
- hint for IDP
1 lines of code changed in 1 file:
IDP changes
15 lines of code changed in 2 files:
IDP changes
2 lines of code changed in 1 file:
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36 lines of code changed in 3 files:
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1 lines of code changed in 1 file:
- 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:
Updates for files related to read xml format tree!!!
89 lines of code changed in 5 files:
IDP changes
23 lines of code changed in 4 files:
IDP
92 lines of code changed in 4 files:
- warning for juergen
6 lines of code changed in 1 file:
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55 lines of code changed in 4 files:
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67 lines of code changed in 3 files:
- added arb_probe_server.config
1 lines of code changed in 1 file:
- uses arb_probe_server.config to configure root-directory and running servers
42 lines of code changed in 1 file:
- cosmetics
0 lines of code changed in 1 file:
- converts 'plength' to int
2 lines of code changed in 1 file:
- template for arb_probe_server.config
1 lines of code changed in 1 file:
- template for arb_probe_server.config
7 lines of code changed in 1 file:
error handling changed
16 lines of code changed in 2 files:
warning if SKIP_PROBES_TO_TARGET_CONVERSION defined
8 lines of code changed in 1 file:
- removed message
1 lines of code changed in 1 file:
changes for non-zipped jar
6 lines of code changed in 2 files:
does not zip client (jar is already zipped)
6 lines of code changed in 1 file:
- added __attribute__
- rewrote put()
14 lines of code changed in 1 file:
- clears detail view during server access
- resets cursor to top after printing sth
13 lines of code changed in 1 file:
- ignores missing 'probe_group_common' (prints warning on console)
5 lines of code changed in 1 file:
- automatically matches complement probe
44 lines of code changed in 1 file:
- added operator== for PG_Group
3 lines of code changed in 1 file:
- 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:
- layout changed (removed IUPAC subwindow)
- added auto match toggle
61 lines of code changed in 1 file:
- splitted off from probe match window
22 lines of code changed in 1 file:
- added automatch toggle
20 lines of code changed in 1 file:
- provides connection errors
6 lines of code changed in 1 file:
- handles connection errors
50 lines of code changed in 1 file:
- 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:
- mentioned automatch toggle
9 lines of code changed in 2 files:
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1 lines of code changed in 1 file:
- wrapper for probes->target conversion
- increased clip-result (40->1000)
8 lines of code changed in 1 file:
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6 lines of code changed in 1 file:
- 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:
- changed , -> /
1 lines of code changed in 1 file:
- added number of hits
26 lines of code changed in 1 file:
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178 lines of code changed in 5 files:
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7 lines of code changed in 1 file:
- downgraded server version
1 lines of code changed in 1 file:
be quiet
27 lines of code changed in 9 files:
- downgraded client version
2 lines of code changed in 1 file:
- wraps test in ----
8 lines of code changed in 1 file:
- converts probe-targets to probes
- uses output module
125 lines of code changed in 1 file:
- changed types of some aisc parameters (for probe find)
9 lines of code changed in 1 file:
- 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:
- uses GBT_determine_T_or_U
57 lines of code changed in 2 files:
- fixed call to GBT_reverseComplementNucSequence
12 lines of code changed in 2 files:
undated
3 lines of code changed in 1 file:
- added GBT_determine_T_or_U
- GBT_reverseComplementNucSequence has similar interface as GBT_complementNucSequence
19 lines of code changed in 1 file:
- cosmetics
4 lines of code changed in 1 file:
- made GEN_select_gene global
2 lines of code changed in 1 file:
- added GEN_select_gene
2 lines of code changed in 1 file:
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:
dependencies updated
7 lines of code changed in 3 files:
- simple config parser
282 lines of code changed in 1 file:
- If target does not exist, source is always moved to target
12 lines of code changed in 1 file:
- added config_parser.h
1 lines of code changed in 1 file:
- reads config and uses it instead of hardcoded parameters
76 lines of code changed in 1 file:
- PG_probe_match_para -> probe_config_data
20 lines of code changed in 1 file:
- does not use hardcoded parameters (uses config instead)
- PG_probe_match_para -> probe_config_data
33 lines of code changed in 1 file:
- 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:
- config interpreter for probe_parameters.conf
- clears data before setting it
84 lines of code changed in 1 file:
- configuration for probe design/match (for arb_probe_library)
14 lines of code changed in 1 file:
- added probe_config_data
17 lines of code changed in 1 file:
- added assertions (avoid index underflow)
11 lines of code changed in 1 file:
- creates local .depends via AISC/Makefile
- depends on public server/client sources
21 lines of code changed in 3 files:
added automatic dependencies to _COM objects
12 lines of code changed in 3 files:
cosmetics
9 lines of code changed in 1 file:
- changed error message
- some overflow checks
14 lines of code changed in 1 file:
- 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:
- rule to create depends (.depends is generated in various _COM directories)
5 lines of code changed in 1 file:
- depends on public server/client sources
- creates local dummy .depends [hmm .. does not work]
8 lines of code changed in 1 file:
updated
1 lines of code changed in 1 file:
- calls Client.saveConfig
10 lines of code changed in 1 file:
- calls Client.saveConfig on 'Quit'
1 lines of code changed in 1 file:
- added getScrollPaneSize
- display modifications (size/pos) done here
43 lines of code changed in 1 file:
- added saveConfig
- display modifications moved into ProbesGUI
14 lines of code changed in 1 file:
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5 lines of code changed in 3 files:
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2 lines of code changed in 42 files:
help updated
1 lines of code changed in 1 file:
updated
8 lines of code changed in 1 file:
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3 lines of code changed in 1 file:
- mark-functions return true when any mark changed
89 lines of code changed in 1 file:
- cleanup
8 lines of code changed in 1 file:
- uses getSelectedIndex+getProbeInfo instead of getSelectedItem
- changed from ActionListener to ItemListener
9 lines of code changed in 1 file:
- only probe is displayed in list
- cleanup
16 lines of code changed in 1 file:
- removed setLocation (seems to cause display problems with fvwm)
- selects first probe after retrieving probes
25 lines of code changed in 1 file:
- configuration for probe design/match (for arb_probe_library) [not used yet]
32 lines of code changed in 1 file:
- restarts coverage search until all groups were searched
30 lines of code changed in 1 file:
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:
- returns coverage probes
- returns members of independent groups
96 lines of code changed in 1 file:
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12 lines of code changed in 2 files:
IDP changes
3 lines of code changed in 2 files:
IDP changes
55 lines of code changed in 4 files:
- fixed call to PM_name2ID/PM_ID2name
3 lines of code changed in 1 file:
- 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:
prototypes
3 lines of code changed in 1 file:
- fixed memory leak
- added PG_find_best_covering_probe_group_for_species
100 lines of code changed in 1 file:
- 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:
- improved pt-server termination
24 lines of code changed in 1 file:
- PM_name2ID/PM_ID2name return error if nothing found
21 lines of code changed in 1 file:
cosmetics
1 lines of code changed in 1 file:
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:
IDP changes
89 lines of code changed in 4 files:
- probe_design_event, probe_match_event -> AP_probe_design_event, AP_probe_match_event
4 lines of code changed in 1 file:
- removed debug output
3 lines of code changed in 1 file:
- recreates pt-server when db date differs (not only when older)
6 lines of code changed in 1 file:
- fixed resource management in GBS_read_arb_tcp()
52 lines of code changed in 1 file:
- added matchProbes
- call matchProbes with first found probe
38 lines of code changed in 1 file:
- added markSpecies()
14 lines of code changed in 1 file:
added getProbeList()
removed setProbeListContents
7 lines of code changed in 1 file:
- getProbeInfo made public
1 lines of code changed in 1 file:
- retrieves and caches group member information
12 lines of code changed in 1 file:
- 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:
- path cache uses encoded paths
- changed 'subtreepath' -> 'id' (prefixed by 'p')
83 lines of code changed in 1 file:
- stores paths in encoded format (less big)
- changed 'subtreepath' -> 'id' (prefixed by 'p')
30 lines of code changed in 1 file:
aborts more early in case of error
6 lines of code changed in 1 file:
- moved path encoding here
153 lines of code changed in 1 file:
test whether map initialized
14 lines of code changed in 1 file:
avoid some warnings
3 lines of code changed in 1 file:
*** empty log message ***
2 lines of code changed in 1 file:
*** empty log message ***
172 lines of code changed in 5 files:
IDP update
70 lines of code changed in 5 files:
IDP GENE changes
77 lines of code changed in 2 files:
- fixed some memory leaks
39 lines of code changed in 1 file:
- annotations for juergen
15 lines of code changed in 2 files:
- improved error messages
- annotations for juergen
24 lines of code changed in 1 file:
- getNodeInformation->getDisplayString
2 lines of code changed in 2 files:
- getNodeInformation->getDisplayString
- calls updateNodeInformation instead of printing to console
14 lines of code changed in 1 file:
- added setProbeListContents()
- tried to change size of probe_list [not working]
43 lines of code changed in 1 file:
- holds probe info for last clicked node
40 lines of code changed in 1 file:
- added retrieveGroupMembers()
9 lines of code changed in 1 file:
- added updateNodeInformation()
12 lines of code changed in 1 file:
Headerstring edited for IDP
10 lines of code changed in 1 file:
*** empty log message ***
45 lines of code changed in 4 files:
*** empty log message ***
25 lines of code changed in 2 files:
fix
55 lines of code changed in 3 files:
*** empty log message ***
1 lines of code changed in 1 file:
made resizeable
35 lines of code changed in 1 file:
- 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:
- 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:
- warns if filelist seems out-of-date
- added full filename to index
13 lines of code changed in 1 file:
- added available_servers
- added get_std_result
42 lines of code changed in 1 file:
- returns the probe lengths that are currently available
9 lines of code changed in 1 file:
- if plength==all -> write multiple requests to different workers and merge them
74 lines of code changed in 1 file:
- draws inner node info in different colors (exact match or not)
- displays group names
25 lines of code changed in 1 file:
- output format slightly changed
2 lines of code changed in 1 file:
- 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:
- saves empty node-info for inner-nodes
8 lines of code changed in 1 file:
- added PG_find_probe_group_for_species, removed PG_find_probe_for_subtree + PG_get_id
7 lines of code changed in 1 file:
- 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:
- 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:
- element 'num' is GB_INT now
8 lines of code changed in 1 file:
depends
9 lines of code changed in 2 files:
- configuration section on top
28 lines of code changed in 1 file:
- added 'ngi' and 'mci'
3 lines of code changed in 1 file:
- cosmetics
20 lines of code changed in 1 file:
- 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:
- overlapping strcpy replaced by memmove
- cosmetics
33 lines of code changed in 1 file:
- GB_find_sub_by_quark is able to search values of other types than GB_STRING
41 lines of code changed in 1 file:
*** empty log message ***
62 lines of code changed in 3 files: