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Ticket Summary Owner Type Priority Milestone Component
#265 Mussa annotation file didn't work if the last sequence wasn't terminated by a newline diane defect major release_1.1 core
#261 Mussa mupa comment character required a space diane defect minor release_1.1 core
#260 Mupa parser is cranky on windows files diane defect major release_1.1 core
#259 New Annotations hide the sequence when you zoom to sequence view diane defect critical release_1.1 Qt Gui
#257 Saving analysis saves at current threshold king defect major release_1.1 Qt Gui
#256 Assertion failed diane defect major release_1.1 Qt Gui
#255 Even telling cmake to use python2.3 mussa still builds against 2.5 diane defect major release_1.1 python interface
#254 Sub-analysis failing to draw paths on init king defect minor release_1.1 Qt Gui
#252 Make scroll wheel work king enhancement major release_1.1 Qt Gui
#251 Save to image crash king defect major release_1.1 Qt Gui
#250 Cmake build failure: /usr/bin/ld: cannot find -loptimized diane defect blocker release_1.1 Qt Gui
#247 Increase version number to 1.1.0 diane task blocker release_1.1 core
#246 Add "What's this?" documentation to as many elements of the GUI as possible. king enhancement major release_1.1 Qt Gui
#244 len(mussa.paths()) returns number of tracks, not the number of paths found diane defect major release_1.1 python interface
#243 Change mussa track to white boxes with Ns highlighted in black diane enhancement major release_1.2 Qt Gui
#240 When there are no matches, mussa doesn't seem to display anything king defect minor release_1.1 Qt Gui
#239 Report error when trying to load a directory as an annotation. diane defect major release_1.1 core
#237 Crashing with invalid file name diane defect major release_1.1 Qt Gui
#236 Error parsing annotation file should also include the filename in the exception. diane enhancement major release_1.1 core
#235 set version to 1.0 in version.h diane task major release_1.0 other
#233 when first displaying mussa the tracks aren't sized to the available viewport on os x diane defect major release_1.1 Qt Gui
#229 Package Everything for 1.0 diane task major release_1.0 other
#227 Document Python useage in Mussagl king task major document_1.0 Qt Gui
#226 QtTest is now a framework diane defect major release_1.1 other
#225 Document mussagl command line option king task minor document_1.0 Qt Gui
#223 Set the Window Icon to be the Mussa icon king enhancement trivial release_1.0 Qt Gui
#217 Use QtDesktopServices for openURL diane enhancement major release_1.1 Qt Gui
#216 subanalysis doesn't call setSoftThreshold to after finishing analysis diane defect major release_1.0 Qt Gui
#215 You should be able to paste into the motif editor diane enhancement critical release_1.1 Qt Gui
#214 Document why sub-analysis exists king enhancement minor document_1.0 other
#213 Document how to deselect tracks/paths king task minor document_1.0 Qt Gui
#212 ESC key should by bound to 'deselect' current selection. diane enhancement trivial release_1.2 Qt Gui
#211 Report how many basepairs are copied diane enhancement major release_1.1 Qt Gui
#208 the alg unittest executable needs to be broken up diane enhancement major unit tests core
#207 Reenable GUI tests diane defect major unit tests Qt Gui
#200 Pushing the threshold change button too fast will cause mussa to crash diane defect major release_1.0 Qt Gui
#199 After [451] I noticed that subanalyses didn't seem to have motif information diane defect major release_1.0 Qt Gui
#197 the subanalysis when using the original mck example draws lines off the sequence. diane defect major release_1.0 Qt Gui
#196 Motif editor: document how to delete a motif king enhancement major document_1.0 other
#195 Disable motif and closing motif editor causes loss of motifs. diane defect critical release_1.1 Qt Gui
#194 use window feedback to show that there are unsaved changes diane enhancement trivial release_1.1 Qt Gui
#192 Steven can't save with mussa diane defect major release_1.0 Qt Gui
#191 Update "Motif Dialog" section king enhancement major document_1.0 other
#190 Update 'save motifs' section after close of ticket #188. king task minor document_1.0 other
#189 Document "save on close" section after close of ticket:187 king task major document_1.0 other
#188 Save motifs action does not append .mtl or .txt by default diane enhancement minor release_1.0 Qt Gui
#187 Editing a motif does not set dirty flag. diane defect minor release_1.0 Qt Gui
#186 Motif dialog on load existing motifs behavior needs update. diane enhancement minor release_1.0 Qt Gui
#185 Update "Load an analysis" section (text/screenshots) king task major document_1.0 other
#184 Dont link against X11 on OS X diane defect major release_1.0 other
#183 Seqcomp is case sensitive diane defect major release_1.0 core
#182 Mussa views need vertical scrolls diane enhancement critical release_1.1 Qt Gui
#181 Update 'Load a mussa parameter file' section king task major document_1.0 other
#180 shipit script on os x needs to validate the archive diane defect major release_1.0 other
#179 Add a section on "File > New Mussa Window" feature. king task major document_1.0 other
#178 Update all screenshots to latest version of Mussa. king task major document_1.0 other
#177 Confirm description of blue conservation tracks is correct. diane task minor document_1.0 other
#176 Document 'Save Analysis' and 'Save Analysis As' features. king task major document_1.0 other
#175 Document new 'save motifs' feature. king task major document_1.0 other
#174 Confirm file formats are documented and correct. diane task major document_1.0 other
#173 Update "Sequence Information Bar" section, as it has changed in latest version. king enhancement minor document_1.0 other
#172 Update "Dynamic Threshold" section as the widget has changed. king enhancement major document_1.0 other
#171 Remove the "Motif Toggle" button from manual. king defect major document_1.0 other
#170 After implementing ticket:164, update 'Load Mupa' section to link to SMN1 example .mupa. king task major document_1.0 other
#169 Update "New Analysis" section as the Dialog box has changed. king task major document_1.0 other
#168 Mussa manual: Update Mac OS X install instructions king task major document_1.0 other
#167 Add an "Understanding Mussa" section to manual. king task major document_1.0 other
#166 Update Mussa summary screenshot to latest version king task major document_1.0 other
#164 Include a section on creating a .mupa file using the smn1 data. king task major document_1.0 other
#163 Motif loading doesn't work with release builds diane defect major release_1.0 Qt Gui
#162 Mussa manual: Update major new features section king task minor document_1.0 other
#161 Add link to smn1 example data (since the UCSC tutorial is based on it) king task major document_1.0 other
#160 error: default argument for parameter of type ‘MussaRef’ has type ‘int’ king defect major Few Small Repairs Qt Gui
#158 When unable to parse a fasta file report its name diane enhancement critical release_1.1 Qt Gui
#157 Mussa manual: document 'save to image' feature king task major document_1.0 other
#154 off by one error when drawing segments diane defect blocker Few Small Repairs Qt Gui
#153 Allow users to specify the file load file mask king task trivial document_1.0 Qt Gui
#152 Update mussa_manual.adp to latest tutorial version king task minor document_1.0 other
#151 Crash is possible when creating a subanalysis smaller than the window diane defect major Few Small Repairs Qt Gui
#150 Example data for 1.0 release diane task major Few Small Repairs Qt Gui
#149 Handle " in motif names diane defect trivial Few Small Repairs Qt Gui
#148 setup_analysis dialog should make sure that the threshold is not greater than the window size. diane defect minor Few Small Repairs Qt Gui
#147 Sometimes the width of a quadrallateral is too small diane defect trivial Few Small Repairs Qt Gui
#146 Win32: Create new analysis mystery crash king defect blocker Few Small Repairs Qt Gui
#144 IUPAC codes are destroyed by the sequence normalization code diane defect critical Few Small Repairs Qt Gui
#143 add command line option to annotate an analysis with a motif file. diane enhancement major Few Small Repairs Qt Gui
#142 It'd be really useful to trigger a subanalysis from an aligned sequence view. diane enhancement major Few Small Repairs Qt Gui
#140 Load Motifs doesn't do anything diane defect major Few Small Repairs Qt Gui
#139 Edit motif window looses motif information when closed diane defect major Few Small Repairs Qt Gui
#138 Sequence view window needs a title diane defect major Few Small Repairs Qt Gui
#137 Document why Base pair match lines on the sequence view don't always connect all the sequences diane task trivial document_1.0 other
#135 Win32: Save as not working... causes crash. king defect critical Few Small Repairs Qt Gui
#134 Width of seqcomp match line is wrong diane defect blocker Few Small Repairs Qt Gui
#133 Should be able to save motifs diane enhancement critical Few Small Repairs core
#130 Save is relative to the current directory diane defect major Few Small Repairs Qt Gui
#129 Subseq doesn't support trees correctly diane defect major Few Small Repairs Qt Gui
#128 the editable sequence name only shows the end of long names. diane defect trivial Few Small Repairs Qt Gui
#127 The sidebar layout isn't right after loading a second analysis into the same window diane defect major Few Small Repairs Qt Gui
#126 Figure out how to get the spirit parsers to report parse errors diane defect major Few Small Repairs core
#125 autodetect if python needs -lutil diane defect major Few Small Repairs Qt Gui
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