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Ticket Summary Owner Type Priority Milestone Component
#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
#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
#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
#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
#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
#2 Connection view diane task major Bionic Mussa core
#3 View descriptions diane defect major Bionic Mussa Qt Gui
#5 Configure a mussa analysis from the Gui king defect major Bionic Mussa Qt Gui
#12 modify motifs attached to an analysis diane task major Bionic Mussa Qt Gui
#14 Motifs need to be creatable and editable from within the GUI diane defect major Bionic Mussa Qt Gui
#15 Unify build system diane defect major Few Small Repairs core
#16 figure out how to get selections to work with new segment based drawing diane defect major Bionic Mussa Qt Gui
#19 I broke the scrollbar too diane defect major Bionic Mussa Qt Gui
#23 The threshold widget was broken too diane defect major Bionic Mussa Qt Gui
#25 broke motif colors diane defect major Bionic Mussa Qt Gui
#31 Threshold Widget should use spinboxes diane major Few Small Repairs Qt Gui
#32 The trac pages should become the main mussa website king task major Bionic Mussa other
#33 changing threshold can cause the UI to freeze diane defect major Standing on our heads Qt Gui
#36 Make zoom widget make sense diane defect major Bionic Mussa Qt Gui
#38 Loading a new analysis while an alignment window was open causes segfault diane defect major Bionic Mussa Qt Gui
#39 sidebar rendering problems diane major Few Small Repairs Qt Gui
#45 recreate os x bless script diane task major Bionic Mussa Qt Gui
#51 Copying sequence might be useful diane enhancement major Few Small Repairs Qt Gui
#59 the washed out sequence should actually be partially transparent. diane defect major Few Small Repairs Qt Gui
#66 The annotation for myogenin needs to be checked. diane major Few Small Repairs Qt Gui
#68 The web site should have the Caltech and possibly BMNC logo king major Few Small Repairs Qt Gui
#70 Need to be able to save screenshots in View Alignment Page diane major Few Small Repairs Qt Gui
#86 Progresss bar diane defect major Few Small Repairs Qt Gui
#91 quits diane defect major Few Small Repairs Qt Gui
#94 quits at viewing allignment diane defect major Few Small Repairs Qt Gui
#101 On windows, the file browse button doesn't remember the previous path diane enhancement major Few Small Repairs Qt Gui
#104 Loading a different analysis while a MussaAlignedWindow was open caused a crash diane defect major Few Small Repairs Qt Gui
#109 Subanalysis sequence list wasn't being cleared diane defect major Few Small Repairs Qt Gui
#110 Running a subanalysis with nothing loaded causes the program to crash diane defect major Few Small Repairs Qt Gui
#114 Location analyses are saved to is ill-defined on OS X. diane defect major Few Small Repairs Qt Gui
#116 Perhaps the motif file should have a name field. diane enhancement major Few Small Repairs core
#117 Perhaps our fasta loading file loader could detect if we're being fed an html file. diane defect major Qt Gui
#118 Tracks need an edit properites option. diane enhancement major Few Small Repairs Qt Gui
#119 Add dependencies to MussaglBuild page diane task major Few Small Repairs other
#120 Windows doesn't have python installed by default diane enhancement major Few Small Repairs Qt Gui
#121 the load_mupa function choaks when given something other than a file diane defect major core
#125 autodetect if python needs -lutil 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
#127 The sidebar layout isn't right after loading a second analysis into the same window diane defect major Few Small Repairs Qt Gui
#129 Subseq doesn't support trees correctly diane defect major Few Small Repairs Qt Gui
#130 Save is relative to the current directory diane defect 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
#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
#20 Toggle Motif Button Implementation king defect minor Few Small Repairs Qt Gui
#24 Clean up the signals and slots diane defect minor Few Small Repairs Qt Gui
#27 Collect example sequences diane enhancement minor other
#34 Unused variable 'max_range' in 'void ScrollableSequenceBrowser::updateScrollBar()' diane defect minor Few Small Repairs Qt Gui
#35 Zoom Icon diane minor Few Small Repairs Qt Gui
#40 MussaAlignedWindow, left sequence position doesn't get initial value set diane minor Bionic Mussa Qt Gui
#41 Selection box jumps slightly to the right of the rubber band diane task minor Bionic Mussa Qt Gui
#42 when resizing you should see more basepairs, not make them bigger. diane defect minor Bionic Mussa Qt Gui
#43 After scrolling a sequence browser window, selection boxes break diane defect minor Few Small Repairs Qt Gui
#46 link in icons diane defect minor Few Small Repairs Qt Gui
#50 Switch to using Qt4.1 resources (automatically compiles resources into binary). diane defect minor Few Small Repairs Qt Gui
#52 Saved analysis needs to keep widow size and threshold for threshold widget diane defect minor Few Small Repairs Qt Gui
#56 Define analysis should include scroll area when SequenceWidget count >= 3 king defect minor Few Small Repairs Qt Gui
#64 Occasionally ConservedPath crashes diane minor Few Small Repairs Qt Gui
#95 Annotations masked out when motif defined and then undefined. diane defect minor Few Small Repairs Qt Gui
#96 Save to image broken king defect minor Few Small Repairs Qt Gui
#97 Help > Mussa Manual... should have warning dialog upon error king defect minor Few Small Repairs Qt Gui
#103 Motifs need a name field diane enhancement minor Few Small Repairs Qt Gui
#105 Load Analysis should spawn a new window diane defect minor Standing on our heads Qt Gui
#115 The create an analysis screen create the sequences in the reverse order. diane defect minor 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
#152 Update mussa_manual.adp to latest tutorial version king task minor document_1.0 other
#162 Mussa manual: Update major new features section king task minor document_1.0 other
#173 Update "Sequence Information Bar" section, as it has changed in latest version. king enhancement minor document_1.0 other
#177 Confirm description of blue conservation tracks is correct. diane task minor document_1.0 other
#186 Motif dialog on load existing motifs behavior needs update. 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
#188 Save motifs action does not append .mtl or .txt by default diane enhancement minor release_1.0 Qt Gui
#190 Update 'save motifs' section after close of ticket #188. king task minor document_1.0 other
#213 Document how to deselect tracks/paths king task minor document_1.0 Qt Gui
#214 Document why sub-analysis exists king enhancement minor document_1.0 other
#225 Document mussagl command line option king task minor document_1.0 Qt Gui
#240 When there are no matches, mussa doesn't seem to display anything king defect minor release_1.1 Qt Gui
#254 Sub-analysis failing to draw paths on init king defect minor release_1.1 Qt Gui
#261 Mussa mupa comment character required a space diane defect minor release_1.1 core
#22 default size hint broken diane defect trivial Few Small Repairs Qt Gui
#53 Copy an example into the os x dmg diane trivial Few Small Repairs other
#60 sequence alignment view needs zoom diane defect trivial Few Small Repairs core
#74 On OSX when maxmizing the sidebar stays on the GL canvas diane defect trivial Few Small Repairs Qt Gui
#84 The analysis title should report what file you loaded diane trivial Standing on our heads Qt Gui
#128 the editable sequence name only shows the end of long names. diane defect trivial 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
#147 Sometimes the width of a quadrallateral is too small diane defect trivial Few Small Repairs Qt Gui
#149 Handle " in motif names diane defect trivial Few Small Repairs Qt Gui
#153 Allow users to specify the file load file mask king task trivial document_1.0 Qt Gui
#194 use window feedback to show that there are unsaved changes diane enhancement trivial release_1.1 Qt Gui
#212 ESC key should by bound to 'deselect' current selection. diane enhancement trivial release_1.2 Qt Gui
#223 Set the Window Icon to be the Mussa icon king enhancement trivial release_1.0 Qt Gui
#37 Skateboard Shoes diane defect
#47 OS X OpenGL rendering problems diane defect
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