ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/catch/trunk
Sticky Revision:
Sort logs by:
Revision 56 - Directory Listing
Modified Wed Jun 11 10:58:24 2008 UTC (8 years, 6 months ago) by glyn_dk
still debugging: alignment seems to work for clusters up to size five, but for clusters of clusters, something goes wrong in calculating the alignment shift. 
Revision 52 - Directory Listing
Modified Fri Jun 6 13:02:05 2008 UTC (8 years, 6 months ago) by glyn_dk
debugging alignmentshift: this version is tested (is working) for nomirror alignments with negative shifts. 
Revision 51 - Directory Listing
Modified Fri Jun 6 13:00:25 2008 UTC (8 years, 6 months ago) by glyn_dk
bug fixed: mirrored tracks were shortened by one because of incorrect rightoffset. 
Revision 49 - Directory Listing
Modified Wed Jun 4 14:42:56 2008 UTC (8 years, 6 months ago) by glyn_dk
working on implementing the Pearson correlation measures
Revision 48 - Directory Listing
Modified Tue Jun 3 12:10:32 2008 UTC (8 years, 6 months ago) by glyn_dk
FIXED pointercopy to deepcopy by populating initialScores simultaneously with scores. 
Revision 47 - Directory Listing
Modified Tue Jun 3 10:50:46 2008 UTC (8 years, 6 months ago) by glyn_dk
FIXED typecast: Optimised output of initialscores table. Thanks to Rune.
Revision 46 - Directory Listing
Modified Tue Jun 3 10:44:53 2008 UTC (8 years, 6 months ago) by glyn_dk
Optimised output of initialscores table. Thanks to Rune.
Revision 44 - Directory Listing
Modified Thu May 29 12:31:45 2008 UTC (8 years, 6 months ago) by glyn_dk
updated version number to 1.07
Revision 43 - Directory Listing
Modified Thu May 29 12:31:21 2008 UTC (8 years, 6 months ago) by glyn_dk
making compile work with AlignedDataSet.java
Revision 42 - Directory Listing
Modified Thu May 29 12:29:04 2008 UTC (8 years, 6 months ago) by glyn_dk
now it is possible to export csv of individual profiles (not only clusters).
Revision 41 - Directory Listing
Modified Tue May 27 09:32:54 2008 UTC (8 years, 6 months ago) by glyn_dk
Automatically export the initial pairwise scores to a temp file. The temp file is automatically deleted on program exit.
Revision 40 - Directory Listing
Modified Mon May 26 18:24:20 2008 UTC (8 years, 6 months ago) by glyn_dk
fixed bug: weight value drop mid sequence, caused by uninitalised(not copied) values when mirroring sequences.
Revision 39 - Directory Listing
Modified Mon May 26 13:00:33 2008 UTC (8 years, 6 months ago) by glyn_dk
SequenceDiagram: weights are drawn at the same shift as the rest of the profile plot
Revision 38 - Directory Listing
Modified Mon May 26 12:59:30 2008 UTC (8 years, 6 months ago) by glyn_dk
output weights with csv export
Revision 37 - Directory Listing
Modified Mon May 26 12:59:01 2008 UTC (8 years, 6 months ago) by glyn_dk
output weights with csv export
Revision 33 - Directory Listing
Modified Fri May 16 12:36:53 2008 UTC (8 years, 6 months ago) by blijklem
Fixed a small bug in some intermediate-code.
Revision 32 - Directory Listing
Modified Fri May 16 12:28:54 2008 UTC (8 years, 6 months ago) by blijklem
Fixed the typos...
Revision 30 - Directory Listing
Modified Fri May 16 11:01:41 2008 UTC (8 years, 6 months ago) by blijklem
Some changes to the data classes.
Revision 29 - Directory Listing
Modified Wed May 7 17:36:07 2008 UTC (8 years, 7 months ago) by blijklem
Testing permissions
Revision 28 - Directory Listing
Modified Tue May 6 13:35:56 2008 UTC (8 years, 7 months ago) by glyn_dk
still debugging correct visualisation of alignment. Calculating alignment shifts.
Revision 27 - Directory Listing
Modified Mon May 5 14:47:00 2008 UTC (8 years, 7 months ago) by glyn_dk
Selection tab shows the sequences shifted to their alignment positions. NOT debugged yet: only mirrored sequences are showed at their correct alignment.
Revision 26 - Directory Listing
Modified Mon May 5 11:15:26 2008 UTC (8 years, 7 months ago) by glyn_dk
Bug fixed: interpolation values started at zero for sequences where the first signal value was at the exact start position of the sequence.
Revision 25 - Directory Listing
Modified Mon May 5 10:04:47 2008 UTC (8 years, 7 months ago) by glyn_dk
Updated to CATCH version 1.0.6.  Sequence now stores the absolute alignment shift. SequenceDiagram writes the absolute alignment shift to the plot. 
Revision 24 - Directory Listing
Modified Fri May 2 14:33:47 2008 UTC (8 years, 7 months ago) by glyn_dk
fixed plotting bug: plots no longer start. automatically at 0 on left side
Revision 23 - Directory Listing
Modified Fri May 2 12:41:05 2008 UTC (8 years, 7 months ago) by glyn_dk
progressScoring and progressClustering return percentage completed of scoring and clustering, respectively.
Revision 22 - Directory Listing
Modified Fri May 2 12:37:07 2008 UTC (8 years, 7 months ago) by glyn_dk
progressScoring and progressClustering return percentage completed of scoring and clustering, respectively.
Revision 21 - Directory Listing
Modified Fri May 2 12:36:16 2008 UTC (8 years, 7 months ago) by glyn_dk
saving results to temp file
Revision 20 - Directory Listing
Modified Wed Apr 23 08:44:38 2008 UTC (8 years, 7 months ago) by glyn_dk
added the GPL header to all .java files
Revision 18 - Directory Listing
Modified Fri Apr 11 09:20:21 2008 UTC (8 years, 8 months ago) by glyn_dk
set allow mirroring as default option. Updated version number to v.1.05
Revision 17 - Directory Listing
Modified Thu Apr 10 15:30:53 2008 UTC (8 years, 8 months ago) by glyn_dk
moved merge option from ActionsPanel to OptionsPanel. \nAligner saves CATCH options to Profile objects as String. \nProfile writes CATCH options to BED format output. \nSequence writes isMirrored to BED output as extra column
Revision 16 - Directory Listing
Modified Thu Apr 10 12:48:17 2008 UTC (8 years, 8 months ago) by glyn_dk
write mirroring status and profile information on SequenceDiagram
Revision 15 - Directory Listing
Modified Thu Apr 10 08:26:57 2008 UTC (8 years, 8 months ago) by glyn_dk
updated version number to 1.04
Revision 13 - Directory Listing
Modified Tue Apr 8 15:56:44 2008 UTC (8 years, 8 months ago) by glyn_dk
removed class files from repository. \n Export functions fixed: export csv, export BED, save dataset. Removed function: saveDatasetIDs
Revision 12 - Directory Listing
Modified Tue Apr 8 11:42:07 2008 UTC (8 years, 8 months ago) by glyn_dk
save and load CATCH file format implemented
Revision 10 - Directory Listing
Modified Fri Apr 4 11:43:28 2008 UTC (8 years, 8 months ago) by glyn_dk
updated version number to 1.02, changed default options to SSD and max
Revision 9 - Directory Listing
Modified Fri Apr 4 10:28:31 2008 UTC (8 years, 8 months ago) by glyn_dk
Mirroring implemented
Revision 8 - Directory Listing
Modified Fri Apr 4 08:41:44 2008 UTC (8 years, 8 months ago) by glyn_dk
prepared for mirrored alignment: mirrorTrack, scoreMirror
Revision 6 - Directory Listing
Modified Sat Mar 29 00:43:42 2008 UTC (8 years, 8 months ago) by glyn_dk
changed version number to 1.01
Revision 5 - Directory Listing
Modified Sun Mar 23 10:09:40 2008 UTC (8 years, 8 months ago) by glyn_dk
added mirrored flag in Sequence in preparation for mirrored alignment
Revision 4 - Directory Listing
Modified Fri Mar 21 19:01:32 2008 UTC (8 years, 8 months ago) by glyn_dk
Save Current tree (Newick) - added feature: internal node names correspond to cluster names
Revision 3 - Directory Listing
Modified Fri Mar 21 18:36:25 2008 UTC (8 years, 8 months ago) by glyn_dk
Save Current tree (Newick) - debugged: branch lengths positive
Revision 2 - Directory Listing
Modified Fri Mar 21 11:32:09 2008 UTC (8 years, 8 months ago) by glyn_dk
Save Current tree (Newick) - implemented 
Revision 1 - Directory Listing
Added Thu Mar 6 07:16:30 2008 UTC (8 years, 9 months ago) by glyn_dk
initial import\nCATCH v.1.00\nWednesday March 5, 2008