id 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 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 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 10 Integrate motifs with annotations diane defect major Standing on our heads core 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 58 why does mussa take so long to recompute a large nway? diane defect 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 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 70 Need to be able to save screenshots in View Alignment Page diane major Few Small Repairs Qt Gui 73 Performance problems doing analysis diane defect 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 113 For some reason on Ali's machine cmake is linking in X11 diane defect major 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 131 When closing an analysis window, cancel doesn't prevent the close diane defect major Few Small Repairs Qt Gui 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 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 76 Qt 4.1.1 crashes on barbara's computer 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 102 "Update ""blocking the gui"" comment in --no-gui mode." diane enhancement trivial Few Small Repairs core 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 210 see about removing some of the wasted border width on the sidebars 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