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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
#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
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