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Ticket Summary Owner Type Priority Milestone Component
#132 Make open saved analysis open a new window diane enhancement major Few Small Repairs Qt Gui
#138 Sequence view window needs a title 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
#140 Load Motifs doesn't do anything diane defect 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
#143 add command line option to annotate an analysis with a motif file. diane enhancement major Few Small Repairs Qt Gui
#150 Example data for 1.0 release diane task major Few Small Repairs Qt Gui
#151 Crash is possible when creating a subanalysis smaller than the window diane defect major Few Small Repairs Qt Gui
#156 Mussa manual - meta ticket king task major document_1.0 other
#157 Mussa manual: document 'save to image' feature 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
#161 Add link to smn1 example data (since the UCSC tutorial is based on it) king task major document_1.0 other
#163 Motif loading doesn't work with release builds diane defect major release_1.0 Qt Gui
#164 Include a section on creating a .mupa file using the smn1 data. king task major document_1.0 other
#166 Update Mussa summary screenshot to latest version king task major document_1.0 other
#167 Add an "Understanding Mussa" section to manual. king task major document_1.0 other
#168 Mussa manual: Update Mac OS X install instructions 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
#170 After implementing ticket:164, update 'Load Mupa' section to link to SMN1 example .mupa. king task major document_1.0 other
#171 Remove the "Motif Toggle" button from manual. king defect major document_1.0 other
#172 Update "Dynamic Threshold" section as the widget has changed. king enhancement major document_1.0 other
#174 Confirm file formats are documented and correct. diane task major document_1.0 other
#175 Document new 'save motifs' feature. king task major document_1.0 other
#176 Document 'Save Analysis' and 'Save Analysis As' features. king task major document_1.0 other
#178 Update all screenshots to latest version of Mussa. king task major document_1.0 other
#179 Add a section on "File > New Mussa Window" feature. 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
#181 Update 'Load a mussa parameter file' section king task major document_1.0 other
#183 Seqcomp is case sensitive diane defect major release_1.0 core
#184 Dont link against X11 on OS X diane defect major release_1.0 other
#185 Update "Load an analysis" section (text/screenshots) king task major document_1.0 other
#189 Document "save on close" section after close of ticket:187 king task major document_1.0 other
#191 Update "Motif Dialog" section king enhancement major document_1.0 other
#192 Steven can't save with mussa diane defect major release_1.0 Qt Gui
#196 Motif editor: document how to delete a motif king enhancement major document_1.0 other
#197 the subanalysis when using the original mck example draws lines off the sequence. 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
#200 Pushing the threshold change button too fast will cause mussa to crash diane defect major release_1.0 Qt Gui
#207 Reenable GUI tests diane defect major unit tests Qt Gui
#208 the alg unittest executable needs to be broken up diane enhancement major unit tests core
#211 Report how many basepairs are copied 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
#217 Use QtDesktopServices for openURL diane enhancement major release_1.1 Qt Gui
#226 QtTest is now a framework diane defect major release_1.1 other
#227 Document Python useage in Mussagl king task major document_1.0 Qt Gui
#229 Package Everything for 1.0 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
#235 set version to 1.0 in version.h diane task major release_1.0 other
#236 Error parsing annotation file should also include the filename in the exception. diane enhancement major release_1.1 core
#237 Crashing with invalid file name diane defect major release_1.1 Qt Gui
#239 Report error when trying to load a directory as an annotation. diane defect major release_1.1 core
#243 Change mussa track to white boxes with Ns highlighted in black diane enhancement major release_1.2 Qt Gui
#244 len(mussa.paths()) returns number of tracks, not the number of paths found diane defect major release_1.1 python interface
#246 Add "What's this?" documentation to as many elements of the GUI as possible. king enhancement major release_1.1 Qt Gui
#251 Save to image crash king defect major release_1.1 Qt Gui
#252 Make scroll wheel work king enhancement 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
#256 Assertion failed diane defect major release_1.1 Qt Gui
#257 Saving analysis saves at current threshold king defect major release_1.1 Qt Gui
#260 Mupa parser is cranky on windows files diane defect major release_1.1 core
#265 Mussa annotation file didn't work if the last sequence wasn't terminated by a newline diane defect major release_1.1 core
#1 Annotation color mapper diane critical Bionic Mussa core
#4 Aligned sequence view diane critical Bionic Mussa Qt Gui
#26 SubAnalysis mode diane enhancement critical Few Small Repairs Qt Gui
#44 Computation of reverse compliment colors is buggy diane critical Few Small Repairs Qt Gui
#49 QAssistant Mussa Docs diane defect critical Few Small Repairs core
#55 Somehow when reloading an analysis it needs to save threshold / window size diane defect critical Few Small Repairs Qt Gui
#57 Define analysis is annoying diane critical Few Small Repairs Qt Gui
#63 with two sequences the align sequence view doesn't show any connections diane defect critical Few Small Repairs Qt Gui
#69 motifs may not be rendering corectly diane critical Few Small Repairs Qt Gui
#71 AnnotationColors don't always color motifs correctly diane defect critical Few Small Repairs Qt Gui
#72 Myogenin human mouse rat cow chicken files are odd diane critical Bionic Mussa core
#75 The scrollbar navigation when zoomed in jumps too far diane defect critical Few Small Repairs Qt Gui
#78 Reverse compliment alignment lines dont seem to match up diane critical Few Small Repairs core
#83 Mussa should complain about misformatted fasta files instead of crashing. diane defect critical Few Small Repairs core
#85 mussagl quits, just like i will AGAIN soon. diane defect critical Few Small Repairs core
#90 the arrow keys aren't connected to the scrollbar diane defect critical python interface
#107 Motifs don't show up on the Mussa Aligned Sequence window anymore. diane defect critical Few Small Repairs Qt Gui
#111 Set zero/alignment point for a sequence diane enhancement critical release_1.1 Qt Gui
#122 Motif editor needs to support more than 10 motifs diane enhancement critical Few Small Repairs Qt Gui
#133 Should be able to save motifs diane enhancement critical Few Small Repairs core
#135 Win32: Save as not working... causes crash. king defect critical Few Small Repairs Qt Gui
#144 IUPAC codes are destroyed by the sequence normalization code diane defect critical Few Small Repairs Qt Gui
#158 When unable to parse a fasta file report its name diane enhancement critical release_1.1 Qt Gui
#182 Mussa views need vertical scrolls diane enhancement critical release_1.1 Qt Gui
#195 Disable motif and closing motif editor causes loss of motifs. diane defect critical release_1.1 Qt Gui
#206 We need some way of indicating Ns diane enhancement critical release_1.1 Qt Gui
#215 You should be able to paste into the motif editor diane enhancement critical release_1.1 Qt Gui
#259 New Annotations hide the sequence when you zoom to sequence view diane defect critical release_1.1 Qt Gui
#62 Aligning sequence that has a reverse compliment doesn't fully align correctly diane defect blocker Few Small Repairs Qt Gui
#79 It'd be nice if you could annotate by providing fasta files diane blocker python interface
#92 Allow one to temporarily disable a motif diane defect blocker Few Small Repairs core
#93 Allow opening two analyses at once. diane defect blocker Qt Gui
#99 Percent threshold shouldn't be editable. diane enhancement blocker Few Small Repairs Qt Gui
#134 Width of seqcomp match line is wrong diane defect blocker Few Small Repairs Qt Gui
#146 Win32: Create new analysis mystery crash king defect blocker Few Small Repairs Qt Gui
#154 off by one error when drawing segments diane defect blocker Few Small Repairs Qt Gui
#247 Increase version number to 1.1.0 diane task blocker release_1.1 core
#250 Cmake build failure: /usr/bin/ld: cannot find -loptimized diane defect blocker release_1.1 Qt Gui
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