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Ticket Summary Owner Type Priority Milestone Component
#1 Annotation color mapper diane critical Bionic Mussa core
#4 Aligned sequence view diane critical Bionic Mussa Qt Gui
#31 Threshold Widget should use spinboxes diane major Few Small Repairs Qt Gui
#35 Zoom Icon diane minor Few Small Repairs Qt Gui
#39 sidebar rendering problems diane major Few Small Repairs Qt Gui
#40 MussaAlignedWindow, left sequence position doesn't get initial value set diane minor Bionic Mussa Qt Gui
#44 Computation of reverse compliment colors is buggy diane critical Few Small Repairs Qt Gui
#53 Copy an example into the os x dmg diane trivial Few Small Repairs other
#57 Define analysis is annoying diane critical Few Small Repairs Qt Gui
#64 Occasionally ConservedPath crashes diane minor Few Small Repairs Qt Gui
#66 The annotation for myogenin needs to be checked. diane major Few Small Repairs Qt Gui
#67 You should be able to open multiple analyses diane major Standing on our heads Qt Gui
#68 The web site should have the Caltech and possibly BMNC logo king major Few Small Repairs Qt Gui
#69 motifs may not be rendering corectly diane critical Few Small Repairs Qt Gui
#70 Need to be able to save screenshots in View Alignment Page diane major Few Small Repairs Qt Gui
#72 Myogenin human mouse rat cow chicken files are odd diane critical Bionic Mussa core
#78 Reverse compliment alignment lines dont seem to match up diane critical Few Small Repairs core
#79 It'd be nice if you could annotate by providing fasta files diane blocker python interface
#84 The analysis title should report what file you loaded diane trivial Standing on our heads Qt Gui
#2 Connection view diane task major Bionic Mussa core
#12 modify motifs attached to an analysis diane task major Bionic Mussa Qt Gui
#32 The trac pages should become the main mussa website king task major Bionic Mussa other
#41 Selection box jumps slightly to the right of the rubber band diane task minor Bionic Mussa Qt Gui
#45 recreate os x bless script diane task major Bionic Mussa Qt Gui
#119 Add dependencies to MussaglBuild page diane task major Few Small Repairs other
#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
#150 Example data for 1.0 release diane task major Few Small Repairs Qt Gui
#152 Update mussa_manual.adp to latest tutorial version king task minor document_1.0 other
#153 Allow users to specify the file load file mask king task trivial document_1.0 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
#161 Add link to smn1 example data (since the UCSC tutorial is based on it) king task major document_1.0 other
#162 Mussa manual: Update major new features section king task minor document_1.0 other
#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
#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
#177 Confirm description of blue conservation tracks is correct. diane task minor 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
#181 Update 'Load a mussa parameter file' section king task major document_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
#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
#225 Document mussagl command line option king task minor document_1.0 Qt Gui
#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
#235 set version to 1.0 in version.h diane task major release_1.0 other
#247 Increase version number to 1.1.0 diane task blocker release_1.1 core
#26 SubAnalysis mode diane enhancement critical Few Small Repairs Qt Gui
#27 Collect example sequences diane enhancement minor other
#51 Copying sequence might be useful diane enhancement major Few Small Repairs Qt Gui
#99 Percent threshold shouldn't be editable. diane enhancement blocker 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
#102 Update "blocking the gui" comment in --no-gui mode. diane enhancement trivial Few Small Repairs core
#103 Motifs need a name field diane enhancement minor Few Small Repairs Qt Gui
#111 Set zero/alignment point for a sequence diane enhancement critical release_1.1 Qt Gui
#116 Perhaps the motif file should have a name field. diane enhancement major Few Small Repairs core
#118 Tracks need an edit properites option. diane enhancement major Few Small Repairs Qt Gui
#120 Windows doesn't have python installed by default diane enhancement major Few Small Repairs Qt Gui
#122 Motif editor needs to support more than 10 motifs diane enhancement critical Few Small Repairs Qt Gui
#132 Make open saved analysis open a new window diane enhancement major Few Small Repairs Qt Gui
#133 Should be able to save motifs diane enhancement critical Few Small Repairs core
#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
#158 When unable to parse a fasta file report its name diane enhancement critical release_1.1 Qt Gui
#172 Update "Dynamic Threshold" section as the widget has changed. king enhancement 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
#182 Mussa views need vertical scrolls diane enhancement critical release_1.1 Qt Gui
#186 Motif dialog on load existing motifs behavior needs update. diane enhancement 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
#191 Update "Motif Dialog" section king enhancement major document_1.0 other
#194 use window feedback to show that there are unsaved changes diane enhancement trivial release_1.1 Qt Gui
#196 Motif editor: document how to delete a motif king enhancement major document_1.0 other
#206 We need some way of indicating Ns diane enhancement critical release_1.1 Qt Gui
#208 the alg unittest executable needs to be broken up diane enhancement major unit tests core
#210 see about removing some of the wasted border width on the sidebars diane enhancement trivial release_1.1 Qt Gui
#211 Report how many basepairs are copied diane enhancement major release_1.1 Qt Gui
#212 ESC key should by bound to 'deselect' current selection. diane enhancement trivial release_1.2 Qt Gui
#214 Document why sub-analysis exists king enhancement minor document_1.0 other
#215 You should be able to paste into the motif editor diane enhancement critical release_1.1 Qt Gui
#217 Use QtDesktopServices for openURL diane enhancement major release_1.1 Qt Gui
#223 Set the Window Icon to be the Mussa icon king enhancement trivial release_1.0 Qt Gui
#236 Error parsing annotation file should also include the filename in the exception. diane enhancement 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
#246 Add "What's this?" documentation to as many elements of the GUI as possible. king enhancement major release_1.1 Qt Gui
#252 Make scroll wheel work king enhancement major release_1.1 Qt Gui
#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
#10 Integrate motifs with annotations diane defect major Standing on our heads core
#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
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