__group__ ticket summary component status resolution version type priority owner modified _time _reporter unit tests 82 Unit test python API Qt Gui new enhancement critical diane 2006-10-20T13:10:30-07:00 00:40:43-07:00 diane unit tests 106 Figure out how to test copySelectedTracks core new enhancement major diane 2006-10-20T13:12:56-07:00 19:17:01-07:00 diane unit tests 203 Unit test the code that generates all the mussa filename core new enhancement major diane 2006-10-24T14:26:06-07:00 10:15:21-07:00 diane unit tests 208 the alg unittest executable needs to be broken up core closed fixed enhancement major diane 2007-01-04T16:18:59-08:00 13:17:17-07:00 diane unit tests 207 Reenable GUI tests Qt Gui closed fixed defect major diane 2006-10-24T14:25:27-07:00 13:15:58-07:00 diane release_1.2 30 "Allow ""leave one out"" nway transitive searches" core new enhancement blocker diane 2006-10-20T00:10:03-07:00 15:19:54-08:00 diane release_1.2 205 Add button for autofitting sequence to window Qt Gui new enhancement major diane 2006-10-20T11:40:00-07:00 11:40:00-07:00 diane release_1.2 218 Qt4.2 has a platform independent way to place Ok/Cancel buttons in dialog Qt Gui new enhancement major diane 2006-10-27T14:14:04-07:00 14:21:21-07:00 diane release_1.2 228 Allow more vertical collapse of description widgets Qt Gui new enhancement major diane 2006-11-22T11:44:46-08:00 14:22:21-07:00 diane release_1.2 241 One of the annotations needed is to show where the start of the gene is Qt Gui new enhancement major diane 2006-11-27T16:29:42-08:00 16:29:42-08:00 diane release_1.2 123 Allow hiding sidebars Qt Gui new enhancement minor diane 2006-10-20T00:25:26-07:00 15:33:14-07:00 diane release_1.2 124 report patch version core new enhancement minor diane 2006-10-20T15:50:23-07:00 15:35:27-07:00 diane release_1.2 230 shipit script should ship source distribution too. other new enhancement minor diane 2006-10-27T15:37:22-07:00 15:37:22-07:00 diane release_1.2 262 ThresholdWidget.reset() SIGNAL/SLOTS issue. Qt Gui new defect minor diane 2007-04-19T17:52:46-07:00 17:52:46-07:00 king release_1.2 193 Changing a species name doesn't set dirty flag. Qt Gui new 1.0 enhancement trivial diane 2006-10-20T00:06:54-07:00 10:50:07-07:00 king release_1.2 212 ESC key should by bound to 'deselect' current selection. Qt Gui closed fixed enhancement trivial diane 2007-04-16T16:57:51-07:00 16:43:53-07:00 king release_1.2 243 Change mussa track to white boxes with Ns highlighted in black Qt Gui closed fixed enhancement major diane 2007-04-11T16:56:45-07:00 17:37:19-08:00 diane release_1.1 249 darcs tag mussa_1.1.0 Qt Gui new defect critical diane 2007-02-22T15:58:43-08:00 15:58:43-08:00 king release_1.1 263 Compile warnings must die! Qt Gui new defect critical diane 2007-04-19T18:14:03-07:00 18:02:39-07:00 king release_1.1 248 Test latest build on all platforms Qt Gui new task major diane 2007-02-22T15:55:29-08:00 15:55:29-08:00 king release_1.1 266 Sub-analysis drawing bug (see attached screenshots) Qt Gui new defect major diane 2007-07-16T15:57:44-07:00 15:57:44-07:00 king release_1.1 267 Sequence View soft threshold control non-responsive Qt Gui new defect major diane 2007-07-17T11:21:56-07:00 11:21:56-07:00 king release_1.1 265 Mussa annotation file didn't work if the last sequence wasn't terminated by a newline core closed fixed defect major diane 2007-06-22T17:49:21-07:00 17:36:22-07:00 diane release_1.1 259 New Annotations hide the sequence when you zoom to sequence view Qt Gui closed fixed defect critical diane 2007-05-02T14:26:40-07:00 15:59:16-07:00 diane release_1.1 252 Make scroll wheel work Qt Gui closed fixed enhancement major king 2007-04-23T10:38:53-07:00 12:13:50-08:00 diane release_1.1 257 Saving analysis saves at current threshold Qt Gui closed fixed defect major king 2007-04-19T18:16:32-07:00 16:14:10-07:00 diane release_1.1 240 When there are no matches, mussa doesn't seem to display anything Qt Gui closed fixed defect minor king 2007-04-19T17:17:35-07:00 16:19:18-08:00 diane release_1.1 261 Mussa mupa comment character required a space core closed fixed defect minor diane 2007-04-19T16:15:55-07:00 16:14:15-07:00 diane release_1.1 260 Mupa parser is cranky on windows files core closed fixed defect major diane 2007-04-19T16:15:27-07:00 18:01:54-07:00 diane release_1.1 256 Assertion failed Qt Gui closed fixed defect major diane 2007-04-03T18:11:16-07:00 17:42:44-07:00 king release_1.1 255 Even telling cmake to use python2.3 mussa still builds against 2.5 python interface closed fixed defect major diane 2007-03-13T15:00:40-07:00 19:13:48-08:00 diane release_1.1 254 Sub-analysis failing to draw paths on init Qt Gui closed fixed defect minor king 2007-03-02T17:42:50-08:00 17:39:44-08:00 king release_1.1 251 Save to image crash Qt Gui closed fixed defect major king 2007-03-02T17:21:28-08:00 14:35:46-08:00 king release_1.1 250 Cmake build failure: /usr/bin/ld: cannot find -loptimized Qt Gui closed fixed defect blocker diane 2007-02-23T11:40:10-08:00 10:58:48-08:00 king release_1.1 247 Increase version number to 1.1.0 core closed fixed task blocker diane 2007-02-23T09:28:48-08:00 15:54:24-08:00 king release_1.1 246 "Add ""What's this?"" documentation to as many elements of the GUI as possible." Qt Gui closed fixed enhancement major king 2007-02-22T15:42:28-08:00 11:05:57-08:00 king release_1.1 195 Disable motif and closing motif editor causes loss of motifs. Qt Gui closed fixed 1.0 defect critical diane 2007-02-20T17:50:27-08:00 11:43:16-07:00 king release_1.1 239 Report error when trying to load a directory as an annotation. core closed fixed defect major diane 2007-02-20T15:41:03-08:00 16:17:52-08:00 diane release_1.1 244 len(mussa.paths()) returns number of tracks, not the number of paths found python interface closed fixed defect major diane 2006-12-14T13:30:02-08:00 12:33:37-08:00 diane release_1.1 206 We need some way of indicating Ns Qt Gui closed duplicate enhancement critical diane 2006-12-13T15:29:37-08:00 12:06:17-07:00 diane release_1.1 226 QtTest is now a framework other closed fixed defect major diane 2006-12-13T15:28:22-08:00 10:17:41-07:00 diane release_1.1 111 Set zero/alignment point for a sequence Qt Gui closed fixed enhancement critical diane 2006-11-22T12:31:33-08:00 15:33:01-07:00 diane release_1.1 237 Crashing with invalid file name Qt Gui closed fixed defect major diane 2006-11-17T15:42:36-08:00 16:57:19-08:00 diane release_1.1 236 Error parsing annotation file should also include the filename in the exception. core closed fixed enhancement major diane 2006-10-30T12:52:11-08:00 10:56:24-08:00 diane release_1.1 158 When unable to parse a fasta file report its name Qt Gui closed fixed enhancement critical diane 2006-10-30T12:22:00-08:00 16:53:55-07:00 diane release_1.1 210 see about removing some of the wasted border width on the sidebars Qt Gui closed wontfix enhancement trivial diane 2006-10-30T10:47:20-08:00 13:20:17-07:00 diane release_1.1 182 Mussa views need vertical scrolls Qt Gui closed fixed enhancement critical diane 2006-10-27T18:57:40-07:00 23:02:31-07:00 diane release_1.1 233 when first displaying mussa the tracks aren't sized to the available viewport on os x Qt Gui closed fixed defect major diane 2006-10-27T18:56:22-07:00 17:53:56-07:00 diane release_1.1 217 Use QtDesktopServices for openURL Qt Gui closed fixed enhancement major diane 2006-10-27T14:13:48-07:00 13:47:20-07:00 diane release_1.1 194 use window feedback to show that there are unsaved changes Qt Gui closed fixed 1.0 enhancement trivial diane 2006-10-27T11:00:13-07:00 10:51:38-07:00 king release_1.1 215 You should be able to paste into the motif editor Qt Gui closed fixed enhancement critical diane 2006-10-26T15:33:37-07:00 17:11:40-07:00 king release_1.1 211 Report how many basepairs are copied Qt Gui closed fixed enhancement major diane 2006-10-26T13:47:29-07:00 13:22:29-07:00 diane release_1.0 229 Package Everything for 1.0 other closed fixed task major diane 2006-11-22T11:43:55-08:00 15:36:25-07:00 diane release_1.0 235 set version to 1.0 in version.h other closed fixed task major diane 2006-11-01T10:10:11-08:00 18:22:49-07:00 diane release_1.0 223 Set the Window Icon to be the Mussa icon Qt Gui closed fixed 1.0 enhancement trivial king 2006-10-26T10:14:50-07:00 10:13:54-07:00 king release_1.0 216 subanalysis doesn't call setSoftThreshold to after finishing analysis Qt Gui closed fixed defect major diane 2006-10-23T17:46:36-07:00 17:51:40-07:00 diane release_1.0 199 After [451] I noticed that subanalyses didn't seem to have motif information Qt Gui closed fixed defect major diane 2006-10-19T18:38:59-07:00 16:35:11-07:00 diane release_1.0 200 Pushing the threshold change button too fast will cause mussa to crash Qt Gui closed fixed defect major diane 2006-10-19T18:37:00-07:00 17:20:12-07:00 diane release_1.0 163 Motif loading doesn't work with release builds Qt Gui closed fixed defect major diane 2006-10-19T17:20:42-07:00 18:26:01-07:00 diane release_1.0 197 the subanalysis when using the original mck example draws lines off the sequence. Qt Gui closed fixed defect major diane 2006-10-18T18:04:17-07:00 12:33:48-07:00 diane release_1.0 192 Steven can't save with mussa Qt Gui closed fixed defect major diane 2006-10-17T16:27:49-07:00 15:00:04-07:00 diane release_1.0 188 Save motifs action does not append .mtl or .txt by default Qt Gui closed fixed 1.0 enhancement minor diane 2006-10-17T13:42:52-07:00 11:06:16-07:00 king release_1.0 187 Editing a motif does not set dirty flag. Qt Gui closed fixed 1.0 defect minor diane 2006-10-17T12:07:29-07:00 10:43:49-07:00 king release_1.0 186 Motif dialog on load existing motifs behavior needs update. Qt Gui closed fixed 1.0 enhancement minor diane 2006-10-17T12:06:48-07:00 10:41:02-07:00 king release_1.0 180 shipit script on os x needs to validate the archive other closed fixed defect major diane 2006-10-16T23:57:30-07:00 13:50:53-07:00 diane release_1.0 184 Dont link against X11 on OS X other closed fixed defect major diane 2006-10-16T23:56:14-07:00 23:55:06-07:00 diane release_1.0 183 Seqcomp is case sensitive core closed fixed defect major diane 2006-10-16T23:54:42-07:00 23:49:19-07:00 diane from __future__ import magic 81 Storing and searching metadata Qt Gui new enhancement blocker diane 2006-10-13T13:47:49-07:00 12:06:32-07:00 diane from __future__ import magic 8 Per species thresholds core new enhancement major diane 2006-10-04T15:17:26-07:00 11:50:35-08:00 diane from __future__ import magic 28 Allow user to force a loaded sequence to be reverse complimented. Qt Gui new enhancement major diane 2006-10-04T15:14:50-07:00 11:14:00-08:00 diane from __future__ import magic 80 Difference between analyses Qt Gui new enhancement major diane 2006-10-13T13:48:02-07:00 15:50:04-08:00 diane from __future__ import magic 87 Autodetect threshold Qt Gui new enhancement major diane 2006-10-13T13:48:14-07:00 13:54:42-07:00 diane from __future__ import magic 219 Reordering sequences in an analysis would be really nice Qt Gui new enhancement major diane 2006-10-24T17:12:02-07:00 17:12:02-07:00 diane from __future__ import magic 222 Allow hyperlink annotations for CDS to PyMol rendering of protein structure Qt Gui new enhancement major diane 2006-10-25T17:12:57-07:00 17:12:57-07:00 diane from __future__ import magic 238 Set left offset graphically Qt Gui new enhancement major diane 2006-11-22T12:33:42-08:00 12:33:42-08:00 diane from __future__ import magic 245 Implement back_inserter for sequence type core new enhancement major diane 2007-01-04T13:15:11-08:00 13:15:11-08:00 diane from __future__ import magic 18 segments should indicate if they're both forward and reveresed core new enhancement minor diane 2006-10-13T13:48:33-07:00 02:37:08-08:00 diane from __future__ import magic 54 Allow compressing repeat regions Qt Gui new enhancement minor diane 2006-10-13T13:48:50-07:00 10:24:28-08:00 diane from __future__ import magic 112 Sequence logo Qt Gui new enhancement minor diane 2006-10-04T15:03:44-07:00 16:10:21-07:00 diane from __future__ import magic 155 Include a simple repeat filter core new enhancement minor diane 2006-10-13T13:49:57-07:00 13:49:49-07:00 diane from __future__ import docs 159 Create track macro to display changelog with build numbers other new 1.0 task minor king 2006-10-27T17:47:55-07:00 17:24:05-07:00 king from __future__ import docs 165 Include a section on creating a motif list file using the smn1 data. other new 1.0 task minor king 2006-10-27T17:48:32-07:00 10:01:52-07:00 king document_1.1 198 Document the multi add to sub-analysis feature. Qt Gui new 1.0 task major king 2006-10-27T17:56:44-07:00 18:00:05-07:00 king document_1.1 221 Discover/document effect of ordering species on analysis run times. core new 1.0 task major king 2006-10-27T17:57:00-07:00 15:30:30-07:00 king document_1.1 232 Document the report bp copied number. Qt Gui new task major king 2006-10-27T17:52:29-07:00 17:52:19-07:00 king document_1.1 234 Document * in title when there are unsaved changes Qt Gui new task major king 2006-10-27T17:54:20-07:00 17:54:20-07:00 king document_1.1 242 make really sure people understand how repeatmasking prevents motifs from being shown. Qt Gui new defect major diane 2006-11-27T17:10:19-08:00 17:10:19-08:00 diane document_1.1 258 document new escape to clear selection Qt Gui new task major king 2007-04-16T16:57:21-07:00 16:57:21-07:00 diane document_1.1 264 Document sequence properties other new task major king 2007-04-20T11:19:06-07:00 11:19:06-07:00 king document_1.1 231 Document copy and paste into motif editor now functional. Qt Gui new task minor king 2006-10-27T17:50:56-07:00 17:50:56-07:00 king document_1.0 177 Confirm description of blue conservation tracks is correct. other closed fixed 1.0 task minor diane 2007-02-14T13:47:56-08:00 11:21:00-07:00 king document_1.0 174 Confirm file formats are documented and correct. other closed fixed 1.0 task major diane 2007-02-14T13:46:42-08:00 10:40:42-07:00 king document_1.0 152 Update mussa_manual.adp to latest tutorial version other closed fixed task minor king 2006-11-01T09:49:49-08:00 15:18:17-07:00 king document_1.0 213 Document how to deselect tracks/paths Qt Gui closed fixed 1.0 task minor king 2006-10-27T18:08:49-07:00 16:44:39-07:00 king document_1.0 170 After implementing ticket:164, update 'Load Mupa' section to link to SMN1 example .mupa. other closed fixed 1.0 task major king 2006-10-27T18:08:45-07:00 10:35:35-07:00 king document_1.0 225 Document mussagl command line option Qt Gui closed fixed 1.0 task minor king 2006-10-27T17:58:47-07:00 16:13:59-07:00 king document_1.0 162 Mussa manual: Update major new features section other closed fixed 1.0 task minor king 2006-10-27T17:56:09-07:00 18:14:27-07:00 king document_1.0 168 Mussa manual: Update Mac OS X install instructions other closed fixed 1.0 task major king 2006-10-27T17:55:30-07:00 10:26:58-07:00 king document_1.0 214 Document why sub-analysis exists other closed fixed 1.0 enhancement minor king 2006-10-27T17:55:12-07:00 17:07:39-07:00 king document_1.0 137 Document why Base pair match lines on the sequence view don't always connect all the sequences other closed fixed task trivial diane 2006-10-27T17:31:43-07:00 17:38:52-07:00 diane document_1.0 227 Document Python useage in Mussagl Qt Gui closed fixed 1.0 task major king 2006-10-27T17:30:51-07:00 10:44:28-07:00 king document_1.0 167 "Add an ""Understanding Mussa"" section to manual." other closed fixed 1.0 task major king 2006-10-27T17:30:22-07:00 10:25:05-07:00 king document_1.0 164 Include a section on creating a .mupa file using the smn1 data. other closed fixed 1.0 task major king 2006-10-27T17:29:45-07:00 10:01:08-07:00 king document_1.0 178 Update all screenshots to latest version of Mussa. other closed fixed 1.0 task major king 2006-10-27T17:24:59-07:00 12:02:28-07:00 king document_1.0 196 Motif editor: document how to delete a motif other closed fixed 1.0 enhancement major king 2006-10-18T11:49:20-07:00 11:47:41-07:00 king document_1.0 179 "Add a section on ""File > New Mussa Window"" feature." other closed fixed 1.0 task major king 2006-10-18T11:34:13-07:00 12:04:01-07:00 king document_1.0 189 "Document ""save on close"" section after close of ticket:187" other closed fixed 1.0 task major king 2006-10-18T11:09:38-07:00 11:19:34-07:00 king document_1.0 190 Update 'save motifs' section after close of ticket #188. other closed fixed 1.0 task minor king 2006-10-18T11:09:13-07:00 11:21:27-07:00 king document_1.0 191 "Update ""Motif Dialog"" section" other closed fixed 1.0 enhancement major king 2006-10-17T12:03:18-07:00 11:32:12-07:00 king document_1.0 175 Document new 'save motifs' feature. other closed fixed 1.0 task major king 2006-10-17T11:23:48-07:00 10:42:24-07:00 king document_1.0 176 Document 'Save Analysis' and 'Save Analysis As' features. other closed fixed 1.0 task major king 2006-10-17T11:23:35-07:00 10:43:10-07:00 king document_1.0 181 Update 'Load a mussa parameter file' section other closed fixed task major king 2006-10-17T10:32:20-07:00 16:39:46-07:00 king document_1.0 185 "Update ""Load an analysis"" section (text/screenshots)" other closed fixed 1.0 task major king 2006-10-17T10:31:59-07:00 10:27:25-07:00 king document_1.0 169 "Update ""New Analysis"" section as the Dialog box has changed." other closed fixed 1.0 task major king 2006-10-17T10:31:50-07:00 10:33:47-07:00 king document_1.0 171 "Remove the ""Motif Toggle"" button from manual." other closed fixed 1.0 defect major king 2006-10-16T11:59:11-07:00 10:37:26-07:00 king document_1.0 173 "Update ""Sequence Information Bar"" section, as it has changed in latest version." other closed fixed 1.0 enhancement minor king 2006-10-16T11:58:58-07:00 10:39:43-07:00 king document_1.0 172 "Update ""Dynamic Threshold"" section as the widget has changed." other closed fixed 1.0 enhancement major king 2006-10-16T11:58:47-07:00 10:38:47-07:00 king document_1.0 166 Update Mussa summary screenshot to latest version other closed fixed task major king 2006-10-16T11:58:37-07:00 10:13:11-07:00 king document_1.0 161 Add link to smn1 example data (since the UCSC tutorial is based on it) other closed fixed 1.0 task major king 2006-10-16T10:09:17-07:00 18:13:25-07:00 king document_1.0 157 Mussa manual: document 'save to image' feature other closed fixed task major king 2006-10-16T10:03:26-07:00 16:13:36-07:00 king document_1.0 156 Mussa manual - meta ticket other closed invalid task major king 2006-10-13T18:15:39-07:00 16:08:52-07:00 king document_1.0 153 Allow users to specify the file load file mask Qt Gui closed fixed task trivial king 2006-10-13T17:27:54-07:00 15:48:16-07:00 diane Standing on our heads 77 Font needs to be better... Qt Gui new enhancement critical diane 2006-10-13T16:04:09-07:00 15:14:58-08:00 diane Standing on our heads 98 QtAssistant needs to be put in the right place on os x. Qt Gui new enhancement critical diane 2006-10-04T14:58:02-07:00 15:56:58-07:00 diane Standing on our heads 100 There should be some way to display the annotation name with the annotation track Qt Gui new enhancement critical diane 2006-10-04T15:13:35-07:00 18:48:36-07:00 diane Standing on our heads 108 Cancel on the progress bar should do something Qt Gui new enhancement critical diane 2006-10-13T13:44:06-07:00 17:34:23-07:00 diane Standing on our heads 6 Analysis saving is smelly core new task major diane 2006-10-13T13:45:45-07:00 11:47:46-08:00 diane Standing on our heads 7 Reuse seqcomps core new enhancement major diane 2006-10-20T13:12:32-07:00 11:49:14-08:00 diane Standing on our heads 9 Connect to cartwheel Qt Gui new enhancement major diane 2006-10-13T13:44:45-07:00 11:52:35-08:00 diane Standing on our heads 13 AnnotationColor mapper needs a user interface Qt Gui new enhancement major diane 2006-10-20T00:09:15-07:00 00:10:47-08:00 diane Standing on our heads 17 Allow user to specify an offset for base pair location label Qt Gui new enhancement major diane 2006-11-22T11:41:30-08:00 02:09:25-08:00 diane Standing on our heads 21 Implement a better way of handling the GL selection buffer core new task major diane 2006-10-13T13:54:01-07:00 17:50:59-08:00 diane Standing on our heads 61 For mac users it'd be useful to make double clicking on a data file actually load mussagl Qt Gui new enhancement major diane 2006-10-13T13:45:26-07:00 17:30:37-08:00 diane Standing on our heads 65 It'd be neat if you could select a region and go to ucsc Qt Gui new enhancement major diane 2006-08-23T17:52:18-07:00 18:07:26-08:00 diane Standing on our heads 141 Vector output Qt Gui new enhancement major diane 2006-10-02T14:55:29-07:00 14:55:29-07:00 diane Standing on our heads 145 Use titus' paircomp and motility core new enhancement major diane 2006-10-04T15:11:50-07:00 15:11:50-07:00 diane Standing on our heads 201 Run analyses in worker thread core new enhancement major diane 2006-10-20T00:11:33-07:00 00:11:33-07:00 diane Standing on our heads 202 Investigate SIP instead of boost::python Qt Gui new task major king 2007-05-15T15:58:59-07:00 00:27:27-07:00 diane Standing on our heads 204 When you resize a mussa window, resize the drawing too. Qt Gui new enhancement major diane 2006-10-27T14:19:46-07:00 11:08:12-07:00 diane Standing on our heads 209 Extend the command line parsing to allow fully specifying an analysis Qt Gui new enhancement major diane 2006-10-20T13:19:03-07:00 13:19:03-07:00 diane Standing on our heads 224 Define a common base class between MussaWindow and MussAlignedWindow Qt Gui new enhancement major diane 2006-10-26T15:05:48-07:00 15:05:48-07:00 diane Standing on our heads 11 create unifed sequence type core new enhancement minor diane 2006-10-20T00:09:46-07:00 17:54:41-08:00 diane Standing on our heads 29 Connect to Core Match core new enhancement minor diane 2006-10-13T13:47:21-07:00 15:18:12-08:00 diane Standing on our heads 136 allow absolute positioning Qt Gui new enhancement minor diane 2006-10-04T15:16:46-07:00 00:22:41-07:00 diane Standing on our heads 253 Show conserved window on local alignment display Qt Gui new enhancement minor diane 2007-03-02T15:25:23-08:00 15:25:23-08:00 diane Standing on our heads 89 Blast to find mussa regions core new enhancement trivial diane 2006-10-13T13:47:08-07:00 15:55:59-07:00 diane Standing on our heads 10 Integrate motifs with annotations core closed duplicate defect major diane 2006-10-04T15:20:41-07:00 00:17:47-08:00 diane Standing on our heads 105 Load Analysis should spawn a new window Qt Gui closed fixed defect minor diane 2006-09-15T17:14:58-07:00 15:15:57-07:00 diane Standing on our heads 33 changing threshold can cause the UI to freeze Qt Gui closed fixed defect major diane 2006-06-28T17:40:29-07:00 20:58:35-08:00 diane Standing on our heads 84 The analysis title should report what file you loaded Qt Gui closed fixed trivial diane 2006-06-25T12:52:30-07:00 00:47:52-07:00 diane Standing on our heads 67 You should be able to open multiple analyses Qt Gui closed duplicate major diane 2006-06-25T08:36:51-07:00 18:14:32-08:00 diane Few Small Repairs 150 Example data for 1.0 release Qt Gui closed fixed task major diane 2006-10-13T18:51:27-07:00 16:15:11-07:00 diane Few Small Repairs 151 Crash is possible when creating a subanalysis smaller than the window Qt Gui closed fixed defect major diane 2006-10-13T18:09:30-07:00 02:04:41-07:00 diane Few Small Repairs 160 error: default argument for parameter of type ‘MussaRef’ has type ‘int’ Qt Gui closed fixed defect major king 2006-10-13T17:34:41-07:00 17:30:39-07:00 king Few Small Repairs 131 When closing an analysis window, cancel doesn't prevent the close Qt Gui closed worksforme defect major diane 2006-10-13T17:14:36-07:00 15:55:51-07:00 diane Few Small Repairs 96 Save to image broken Qt Gui closed fixed defect minor king 2006-10-13T15:17:02-07:00 12:12:11-07:00 king Few Small Repairs 49 QAssistant Mussa Docs core closed fixed defect critical diane 2006-10-13T13:52:28-07:00 01:50:44-08:00 king Few Small Repairs 133 Should be able to save motifs core closed fixed enhancement critical diane 2006-10-12T22:54:39-07:00 16:49:21-07:00 diane Few Small Repairs 154 off by one error when drawing segments Qt Gui closed fixed defect blocker diane 2006-10-12T22:23:23-07:00 22:22:38-07:00 diane Few Small Repairs 120 Windows doesn't have python installed by default Qt Gui closed fixed enhancement major diane 2006-10-12T16:00:33-07:00 14:57:40-07:00 diane Few Small Repairs 149 "Handle "" in motif names" Qt Gui closed fixed defect trivial diane 2006-10-11T15:57:37-07:00 14:41:57-07:00 diane Few Small Repairs 126 Figure out how to get the spirit parsers to report parse errors core closed fixed defect major diane 2006-10-11T15:56:59-07:00 18:38:06-07:00 diane Few Small Repairs 148 setup_analysis dialog should make sure that the threshold is not greater than the window size. Qt Gui closed fixed defect minor diane 2006-10-10T17:55:09-07:00 16:29:15-07:00 diane Few Small Repairs 146 Win32: Create new analysis mystery crash Qt Gui closed fixed defect blocker king 2006-10-10T17:17:47-07:00 15:27:49-07:00 king Few Small Repairs 147 Sometimes the width of a quadrallateral is too small Qt Gui closed fixed defect trivial diane 2006-10-10T17:09:06-07:00 15:46:44-07:00 diane Few Small Repairs 139 Edit motif window looses motif information when closed Qt Gui closed fixed defect major diane 2006-10-10T16:25:49-07:00 14:46:05-07:00 diane Few Small Repairs 134 Width of seqcomp match line is wrong Qt Gui closed fixed defect blocker diane 2006-10-10T15:45:02-07:00 14:26:05-07:00 diane Few Small Repairs 144 IUPAC codes are destroyed by the sequence normalization code Qt Gui closed fixed defect critical diane 2006-10-10T15:43:03-07:00 10:09:32-07:00 diane Few Small Repairs 103 Motifs need a name field Qt Gui closed fixed enhancement minor diane 2006-10-05T00:50:28-07:00 18:51:03-07:00 king Few Small Repairs 143 add command line option to annotate an analysis with a motif file. Qt Gui closed fixed enhancement major diane 2006-10-04T15:02:32-07:00 15:19:12-07:00 diane Few Small Repairs 142 It'd be really useful to trigger a subanalysis from an aligned sequence view. Qt Gui closed fixed enhancement major diane 2006-10-03T18:17:55-07:00 14:56:12-07:00 diane Few Small Repairs 140 Load Motifs doesn't do anything Qt Gui closed fixed defect major diane 2006-10-03T18:17:18-07:00 14:54:13-07:00 diane Few Small Repairs 138 Sequence view window needs a title Qt Gui closed fixed defect major diane 2006-10-03T18:16:19-07:00 13:46:12-07:00 diane Few Small Repairs 122 Motif editor needs to support more than 10 motifs Qt Gui closed fixed enhancement critical diane 2006-09-28T18:05:25-07:00 17:31:00-07:00 diane Few Small Repairs 135 Win32: Save as not working... causes crash. Qt Gui closed fixed defect critical king 2006-09-25T10:14:21-07:00 16:30:20-07:00 king Few Small Repairs 125 autodetect if python needs -lutil Qt Gui closed fixed defect major diane 2006-09-18T16:24:34-07:00 15:36:21-07:00 diane Few Small Repairs 132 Make open saved analysis open a new window Qt Gui closed duplicate enhancement major diane 2006-09-15T17:09:06-07:00 17:02:49-07:00 diane Few Small Repairs 130 Save is relative to the current directory Qt Gui closed fixed defect major diane 2006-09-15T15:34:23-07:00 11:52:23-07:00 diane Few Small Repairs 129 Subseq doesn't support trees correctly Qt Gui closed fixed defect major diane 2006-09-15T11:11:39-07:00 17:47:08-07:00 diane Few Small Repairs 127 The sidebar layout isn't right after loading a second analysis into the same window Qt Gui closed fixed defect major diane 2006-09-14T14:12:07-07:00 13:05:08-07:00 diane Few Small Repairs 128 the editable sequence name only shows the end of long names. Qt Gui closed fixed defect trivial diane 2006-09-14T13:12:31-07:00 13:06:00-07:00 diane Few Small Repairs 116 Perhaps the motif file should have a name field. core closed fixed enhancement major diane 2006-09-13T18:36:58-07:00 15:37:19-07:00 diane Few Small Repairs 73 Performance problems doing analysis Qt Gui closed invalid defect major diane 2006-09-13T15:52:38-07:00 13:05:46-08:00 diane Few Small Repairs 101 On windows, the file browse button doesn't remember the previous path Qt Gui closed fixed enhancement major diane 2006-09-12T18:21:24-07:00 16:09:50-07:00 diane Few Small Repairs 107 Motifs don't show up on the Mussa Aligned Sequence window anymore. Qt Gui closed worksforme defect critical diane 2006-09-12T17:13:04-07:00 21:15:50-07:00 diane Few Small Repairs 114 Location analyses are saved to is ill-defined on OS X. Qt Gui closed fixed defect major diane 2006-09-12T17:10:04-07:00 14:36:24-07:00 diane Few Small Repairs 119 Add dependencies to MussaglBuild page other closed fixed task major diane 2006-09-12T16:57:57-07:00 16:30:25-07:00 king Few Small Repairs 118 Tracks need an edit properites option. Qt Gui closed fixed enhancement major diane 2006-08-23T17:51:33-07:00 11:38:53-07:00 diane Few Small Repairs 86 Progresss bar Qt Gui closed fixed defect major diane 2006-08-23T14:49:33-07:00 11:21:28-07:00 diane Few Small Repairs 75 The scrollbar navigation when zoomed in jumps too far Qt Gui closed fixed defect critical diane 2006-08-10T16:38:43-07:00 14:56:25-08:00 diane Few Small Repairs 59 the washed out sequence should actually be partially transparent. Qt Gui closed fixed defect major diane 2006-08-10T16:24:15-07:00 17:27:40-08:00 diane Few Small Repairs 115 The create an analysis screen create the sequences in the reverse order. Qt Gui closed fixed defect minor diane 2006-08-10T16:04:43-07:00 11:43:53-07:00 diane Few Small Repairs 56 Define analysis should include scroll area when SequenceWidget count >= 3 Qt Gui closed fixed defect minor king 2006-08-02T11:40:55-07:00 11:02:27-08:00 king Few Small Repairs 110 Running a subanalysis with nothing loaded causes the program to crash Qt Gui closed fixed defect major diane 2006-07-06T12:32:56-07:00 11:58:08-07:00 diane Few Small Repairs 109 Subanalysis sequence list wasn't being cleared Qt Gui closed fixed defect major diane 2006-07-06T11:57:28-07:00 11:56:41-07:00 diane Few Small Repairs 20 Toggle Motif Button Implementation Qt Gui closed fixed defect minor king 2006-07-01T00:00:04-07:00 12:02:37-08:00 king Few Small Repairs 26 SubAnalysis mode Qt Gui closed fixed enhancement critical diane 2006-06-30T23:57:03-07:00 10:57:32-08:00 diane Few Small Repairs 71 AnnotationColors don't always color motifs correctly Qt Gui closed worksforme defect critical diane 2006-06-29T17:35:21-07:00 13:01:57-08:00 diane Few Small Repairs 92 Allow one to temporarily disable a motif core closed fixed defect blocker diane 2006-06-29T17:32:52-07:00 15:25:28-07:00 diane Few Small Repairs 95 Annotations masked out when motif defined and then undefined. Qt Gui closed fixed defect minor diane 2006-06-29T14:41:48-07:00 15:09:09-07:00 king Few Small Repairs 51 Copying sequence might be useful Qt Gui closed fixed enhancement major diane 2006-06-28T17:13:55-07:00 14:22:02-08:00 diane Few Small Repairs 102 "Update ""blocking the gui"" comment in --no-gui mode." core closed wontfix enhancement trivial diane 2006-06-28T12:40:24-07:00 17:29:16-07:00 king Few Small Repairs 52 Saved analysis needs to keep widow size and threshold for threshold widget Qt Gui closed fixed defect minor diane 2006-06-28T12:18:34-07:00 15:28:25-08:00 diane Few Small Repairs 24 Clean up the signals and slots Qt Gui closed fixed defect minor diane 2006-06-28T12:01:31-07:00 00:39:22-08:00 diane Few Small Repairs 22 default size hint broken Qt Gui closed fixed defect trivial diane 2006-06-28T12:00:40-07:00 19:25:22-08:00 diane Few Small Repairs 15 Unify build system core closed fixed defect major diane 2006-06-28T11:57:49-07:00 14:26:26-08:00 diane Few Small Repairs 35 Zoom Icon Qt Gui closed fixed minor diane 2006-06-25T15:47:38-07:00 16:49:16-08:00 king Few Small Repairs 68 The web site should have the Caltech and possibly BMNC logo Qt Gui closed fixed major king 2006-06-25T15:27:34-07:00 18:17:28-08:00 diane Few Small Repairs 58 why does mussa take so long to recompute a large nway? Qt Gui closed duplicate defect major diane 2006-06-25T14:23:52-07:00 16:59:20-08:00 diane Few Small Repairs 43 After scrolling a sequence browser window, selection boxes break Qt Gui closed fixed defect minor diane 2006-06-25T14:18:37-07:00 14:13:25-08:00 diane Few Small Repairs 50 Switch to using Qt4.1 resources (automatically compiles resources into binary). Qt Gui closed fixed defect minor diane 2006-06-25T14:01:29-07:00 13:51:13-08:00 king Few Small Repairs 39 sidebar rendering problems Qt Gui closed fixed major diane 2006-06-25T13:48:39-07:00 00:55:36-08:00 diane Few Small Repairs 44 Computation of reverse compliment colors is buggy Qt Gui closed fixed critical diane 2006-06-25T13:26:16-07:00 17:35:47-08:00 diane Few Small Repairs 76 Qt 4.1.1 crashes on barbara's computer Qt Gui closed invalid defect trivial diane 2006-06-25T12:55:00-07:00 14:57:29-08:00 diane Few Small Repairs 83 Mussa should complain about misformatted fasta files instead of crashing. core closed fixed defect critical diane 2006-06-25T12:35:43-07:00 14:32:35-07:00 ghernand@… Few Small Repairs 94 quits at viewing allignment Qt Gui closed fixed defect major diane 2006-06-25T11:58:44-07:00 19:41:21-07:00 ghernand@… Few Small Repairs 62 Aligning sequence that has a reverse compliment doesn't fully align correctly Qt Gui closed fixed defect blocker diane 2006-06-25T11:49:21-07:00 17:32:58-08:00 diane Few Small Repairs 91 quits Qt Gui closed fixed defect major diane 2006-06-25T11:34:41-07:00 19:38:37-07:00 ghernand@… Few Small Repairs 34 Unused variable 'max_range' in 'void ScrollableSequenceBrowser::updateScrollBar()' Qt Gui closed fixed defect minor diane 2006-06-25T10:42:25-07:00 16:38:41-08:00 king Few Small Repairs 57 Define analysis is annoying Qt Gui closed fixed critical diane 2006-06-25T10:33:45-07:00 11:03:16-08:00 diane Few Small Repairs 53 Copy an example into the os x dmg other closed fixed trivial diane 2006-06-25T09:59:15-07:00 18:13:43-08:00 diane Few Small Repairs 46 link in icons Qt Gui closed fixed defect minor diane 2006-06-25T09:07:57-07:00 12:22:09-08:00 diane Few Small Repairs 31 Threshold Widget should use spinboxes Qt Gui closed fixed major diane 2006-06-25T06:17:45-07:00 17:20:03-08:00 diane Few Small Repairs 78 Reverse compliment alignment lines dont seem to match up core closed fixed critical diane 2006-06-25T05:42:32-07:00 22:59:03-08:00 diane Few Small Repairs 66 The annotation for myogenin needs to be checked. Qt Gui closed fixed major diane 2006-06-25T05:19:44-07:00 18:09:53-08:00 diane Few Small Repairs 74 On OSX when maxmizing the sidebar stays on the GL canvas Qt Gui closed fixed defect trivial diane 2006-06-25T04:50:45-07:00 14:26:55-08:00 diane Few Small Repairs 70 Need to be able to save screenshots in View Alignment Page Qt Gui closed fixed major diane 2006-06-25T03:01:14-07:00 12:56:59-08:00 diane Few Small Repairs 64 Occasionally ConservedPath crashes Qt Gui closed fixed minor diane 2006-06-25T02:37:02-07:00 17:53:55-08:00 diane Few Small Repairs 85 mussagl quits, just like i will AGAIN soon. core closed fixed defect critical diane 2006-06-25T02:35:35-07:00 11:12:00-07:00 ghernand@… Few Small Repairs 63 with two sequences the align sequence view doesn't show any connections Qt Gui closed fixed defect critical diane 2006-06-25T02:10:54-07:00 17:41:52-08:00 diane Few Small Repairs 60 sequence alignment view needs zoom core closed fixed defect trivial diane 2006-06-25T01:41:47-07:00 17:29:10-08:00 diane Few Small Repairs 69 motifs may not be rendering corectly Qt Gui closed fixed critical diane 2006-06-25T01:23:16-07:00 18:27:59-08:00 diane Few Small Repairs 55 Somehow when reloading an analysis it needs to save threshold / window size Qt Gui closed fixed defect critical diane 2006-06-25T00:38:43-07:00 10:54:39-08:00 diane Few Small Repairs 104 Loading a different analysis while a MussaAlignedWindow was open caused a crash Qt Gui closed fixed defect major diane 2006-06-15T17:33:38-07:00 17:28:20-07:00 diane Few Small Repairs 99 Percent threshold shouldn't be editable. Qt Gui closed fixed enhancement blocker diane 2006-06-12T15:08:29-07:00 16:42:39-07:00 diane Few Small Repairs 97 Help > Mussa Manual... should have warning dialog upon error Qt Gui closed fixed defect minor king 2006-06-12T03:27:57-07:00 11:17:50-07:00 king Bionic Mussa 25 broke motif colors Qt Gui closed fixed defect major diane 2006-06-28T12:01:56-07:00 00:46:15-08:00 diane Bionic Mussa 23 The threshold widget was broken too Qt Gui closed fixed defect major diane 2006-06-28T12:00:55-07:00 00:16:10-08:00 diane Bionic Mussa 19 I broke the scrollbar too Qt Gui closed fixed defect major diane 2006-06-28T11:59:41-07:00 11:23:50-08:00 diane Bionic Mussa 16 figure out how to get selections to work with new segment based drawing Qt Gui closed fixed defect major diane 2006-06-28T11:59:04-07:00 02:00:33-08:00 diane Bionic Mussa 14 Motifs need to be creatable and editable from within the GUI Qt Gui closed fixed defect major diane 2006-06-28T11:57:14-07:00 00:16:52-08:00 diane Bionic Mussa 12 modify motifs attached to an analysis Qt Gui closed fixed task major diane 2006-06-28T11:56:17-07:00 18:03:39-08:00 diane Bionic Mussa 42 when resizing you should see more basepairs, not make them bigger. Qt Gui closed fixed defect minor diane 2006-06-25T13:49:55-07:00 13:55:10-08:00 diane Bionic Mussa 1 Annotation color mapper core closed fixed critical diane 2006-06-25T10:53:53-07:00 23:40:52-08:00 diane Bionic Mussa 40 MussaAlignedWindow, left sequence position doesn't get initial value set Qt Gui closed fixed minor diane 2006-06-25T10:53:36-07:00 11:59:27-08:00 diane Bionic Mussa 3 View descriptions Qt Gui closed fixed defect major diane 2006-06-25T10:45:50-07:00 23:44:43-08:00 diane Bionic Mussa 41 Selection box jumps slightly to the right of the rubber band Qt Gui closed fixed task minor diane 2006-06-25T09:34:13-07:00 13:48:03-08:00 diane Bionic Mussa 5 Configure a mussa analysis from the Gui Qt Gui closed fixed defect major king 2006-06-25T03:22:31-07:00 23:47:39-08:00 diane Bionic Mussa 72 Myogenin human mouse rat cow chicken files are odd core closed fixed critical diane 2006-06-25T00:32:47-07:00 13:03:59-08:00 diane Bionic Mussa 4 Aligned sequence view Qt Gui closed fixed critical diane 2006-06-12T04:12:14-07:00 23:46:09-08:00 diane Bionic Mussa 45 recreate os x bless script Qt Gui closed fixed task major diane 2006-05-30T03:27:01-07:00 01:28:15-08:00 diane Bionic Mussa 36 Make zoom widget make sense Qt Gui closed fixed defect major diane 2006-05-28T11:28:11-07:00 01:02:30-08:00 diane Bionic Mussa 38 Loading a new analysis while an alignment window was open causes segfault Qt Gui closed fixed defect major diane 2006-03-19T16:13:49-08:00 16:13:40-08:00 diane Bionic Mussa 32 The trac pages should become the main mussa website other closed fixed task major king 2006-03-17T16:34:38-08:00 19:10:32-08:00 diane Bionic Mussa 2 Connection view core closed fixed task major diane 2006-03-15T01:58:33-08:00 23:43:18-08:00 diane 220 mussa command line seems to be broken... core new 1.0 defect critical diane 2006-10-25T15:05:04-07:00 14:00:01-07:00 king 88 Find titus' paper on FR versus the bacterial genomes other assigned task major diane 2006-10-13T16:02:36-07:00 14:03:09-07:00 diane 268 files that lack a new line would make the mupa parser choke Qt Gui new defect major diane 2007-08-02T18:41:48-07:00 18:41:48-07:00 diane 48 Automate win32 installer build other new enhancement minor diane 2006-10-13T16:03:03-07:00 01:47:49-08:00 king 27 Collect example sequences other closed fixed enhancement minor diane 2006-09-12T17:11:53-07:00 11:02:27-08:00 diane 121 the load_mupa function choaks when given something other than a file core closed fixed defect major diane 2006-09-08T22:13:57-07:00 17:01:46-07:00 diane 117 Perhaps our fasta loading file loader could detect if we're being fed an html file. Qt Gui closed fixed defect major diane 2006-08-10T15:58:54-07:00 10:51:13-07:00 diane 113 For some reason on Ali's machine cmake is linking in X11 Qt Gui closed worksforme defect major diane 2006-07-28T14:59:09-07:00 12:45:53-07:00 diane 93 Allow opening two analyses at once. Qt Gui closed fixed defect blocker diane 2006-06-27T12:19:01-07:00 15:36:38-07:00 diane 79 It'd be nice if you could annotate by providing fasta files python interface closed fixed blocker diane 2006-06-25T07:52:27-07:00 11:48:12-08:00 diane 90 the arrow keys aren't connected to the scrollbar python interface closed fixed defect critical diane 2006-06-25T02:44:57-07:00 13:14:10-07:00 ghernand@…