id Summary Status Owner Type Priority Milestone 30 "Allow ""leave one out"" nway transitive searches" new diane enhancement blocker release_1.2 81 Storing and searching metadata new diane enhancement blocker from __future__ import magic 77 Font needs to be better... new diane enhancement critical Standing on our heads 82 Unit test python API new diane enhancement critical unit tests 98 QtAssistant needs to be put in the right place on os x. new diane enhancement critical Standing on our heads 100 There should be some way to display the annotation name with the annotation track new diane enhancement critical Standing on our heads 108 Cancel on the progress bar should do something new diane enhancement critical Standing on our heads 220 mussa command line seems to be broken... new diane defect critical 249 darcs tag mussa_1.1.0 new diane defect critical release_1.1 263 Compile warnings must die! new diane defect critical release_1.1 6 Analysis saving is smelly new diane task major Standing on our heads 7 Reuse seqcomps new diane enhancement major Standing on our heads 8 Per species thresholds new diane enhancement major from __future__ import magic 9 Connect to cartwheel new diane enhancement major Standing on our heads 13 AnnotationColor mapper needs a user interface new diane enhancement major Standing on our heads 17 Allow user to specify an offset for base pair location label new diane enhancement major Standing on our heads 21 Implement a better way of handling the GL selection buffer new diane task major Standing on our heads 28 Allow user to force a loaded sequence to be reverse complimented. new diane enhancement major from __future__ import magic 61 For mac users it'd be useful to make double clicking on a data file actually load mussagl new diane enhancement major Standing on our heads 65 It'd be neat if you could select a region and go to ucsc new diane enhancement major Standing on our heads 80 Difference between analyses new diane enhancement major from __future__ import magic 87 Autodetect threshold new diane enhancement major from __future__ import magic 88 Find titus' paper on FR versus the bacterial genomes assigned diane task major 106 Figure out how to test copySelectedTracks new diane enhancement major unit tests 141 Vector output new diane enhancement major Standing on our heads 145 Use titus' paircomp and motility new diane enhancement major Standing on our heads 198 Document the multi add to sub-analysis feature. new king task major document_1.1 201 Run analyses in worker thread new diane enhancement major Standing on our heads 202 Investigate SIP instead of boost::python new king task major Standing on our heads 203 Unit test the code that generates all the mussa filename new diane enhancement major unit tests 204 When you resize a mussa window, resize the drawing too. new diane enhancement major Standing on our heads 205 Add button for autofitting sequence to window new diane enhancement major release_1.2 209 Extend the command line parsing to allow fully specifying an analysis new diane enhancement major Standing on our heads 218 Qt4.2 has a platform independent way to place Ok/Cancel buttons in dialog new diane enhancement major release_1.2 219 Reordering sequences in an analysis would be really nice new diane enhancement major from __future__ import magic 221 Discover/document effect of ordering species on analysis run times. new king task major document_1.1 222 Allow hyperlink annotations for CDS to PyMol rendering of protein structure new diane enhancement major from __future__ import magic 224 Define a common base class between MussaWindow and MussAlignedWindow new diane enhancement major Standing on our heads 228 Allow more vertical collapse of description widgets new diane enhancement major release_1.2 232 Document the report bp copied number. new king task major document_1.1 234 Document * in title when there are unsaved changes new king task major document_1.1 238 Set left offset graphically new diane enhancement major from __future__ import magic 241 One of the annotations needed is to show where the start of the gene is new diane enhancement major release_1.2 242 make really sure people understand how repeatmasking prevents motifs from being shown. new diane defect major document_1.1 245 Implement back_inserter for sequence type new diane enhancement major from __future__ import magic 248 Test latest build on all platforms new diane task major release_1.1 258 document new escape to clear selection new king task major document_1.1 264 Document sequence properties new king task major document_1.1 266 Sub-analysis drawing bug (see attached screenshots) new diane defect major release_1.1 267 Sequence View soft threshold control non-responsive new diane defect major release_1.1 268 files that lack a new line would make the mupa parser choke new diane defect major 11 create unifed sequence type new diane enhancement minor Standing on our heads 18 segments should indicate if they're both forward and reveresed new diane enhancement minor from __future__ import magic 29 Connect to Core Match new diane enhancement minor Standing on our heads 48 Automate win32 installer build new diane enhancement minor 54 Allow compressing repeat regions new diane enhancement minor from __future__ import magic 112 Sequence logo new diane enhancement minor from __future__ import magic 123 Allow hiding sidebars new diane enhancement minor release_1.2 124 report patch version new diane enhancement minor release_1.2 136 allow absolute positioning new diane enhancement minor Standing on our heads 155 Include a simple repeat filter new diane enhancement minor from __future__ import magic 159 Create track macro to display changelog with build numbers new king task minor from __future__ import docs 165 Include a section on creating a motif list file using the smn1 data. new king task minor from __future__ import docs 230 shipit script should ship source distribution too. new diane enhancement minor release_1.2 231 Document copy and paste into motif editor now functional. new king task minor document_1.1 253 Show conserved window on local alignment display new diane enhancement minor Standing on our heads 262 ThresholdWidget.reset() SIGNAL/SLOTS issue. new diane defect minor release_1.2 89 Blast to find mussa regions new diane enhancement trivial Standing on our heads 193 Changing a species name doesn't set dirty flag. new diane enhancement trivial release_1.2