#37 |
Skateboard Shoes
|
diane
|
defect
|
|
|
|
#47 |
OS X OpenGL rendering problems
|
diane
|
defect
|
|
|
|
#79 |
It'd be nice if you could annotate by providing fasta files
|
diane
|
|
blocker
|
|
python interface
|
#90 |
the arrow keys aren't connected to the scrollbar
|
diane
|
defect
|
critical
|
|
python interface
|
#244 |
len(mussa.paths()) returns number of tracks, not the number of paths found
|
diane
|
defect
|
major
|
release_1.1
|
python interface
|
#255 |
Even telling cmake to use python2.3 mussa still builds against 2.5
|
diane
|
defect
|
major
|
release_1.1
|
python interface
|
#27 |
Collect example sequences
|
diane
|
enhancement
|
minor
|
|
other
|
#32 |
The trac pages should become the main mussa website
|
king
|
task
|
major
|
Bionic Mussa
|
other
|
#53 |
Copy an example into the os x dmg
|
diane
|
|
trivial
|
Few Small Repairs
|
other
|
#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
|
#152 |
Update mussa_manual.adp to latest tutorial version
|
king
|
task
|
minor
|
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
|
#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
|
#173 |
Update "Sequence Information Bar" section, as it has changed in latest version.
|
king
|
enhancement
|
minor
|
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
|
#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
|
#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
|
#190 |
Update 'save motifs' section after close of ticket #188.
|
king
|
task
|
minor
|
document_1.0
|
other
|
#191 |
Update "Motif Dialog" section
|
king
|
enhancement
|
major
|
document_1.0
|
other
|
#196 |
Motif editor: document how to delete a motif
|
king
|
enhancement
|
major
|
document_1.0
|
other
|
#214 |
Document why sub-analysis exists
|
king
|
enhancement
|
minor
|
document_1.0
|
other
|
#226 |
QtTest is now a framework
|
diane
|
defect
|
major
|
release_1.1
|
other
|
#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
|
#1 |
Annotation color mapper
|
diane
|
|
critical
|
Bionic Mussa
|
core
|
#2 |
Connection view
|
diane
|
task
|
major
|
Bionic Mussa
|
core
|
#15 |
Unify build system
|
diane
|
defect
|
major
|
Few Small Repairs
|
core
|
#49 |
QAssistant Mussa Docs
|
diane
|
defect
|
critical
|
Few Small Repairs
|
core
|
#60 |
sequence alignment view needs zoom
|
diane
|
defect
|
trivial
|
Few Small Repairs
|
core
|
#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
|
#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
|
#92 |
Allow one to temporarily disable a motif
|
diane
|
defect
|
blocker
|
Few Small Repairs
|
core
|
#116 |
Perhaps the motif file should have a name field.
|
diane
|
enhancement
|
major
|
Few Small Repairs
|
core
|
#121 |
the load_mupa function choaks when given something other than a file
|
diane
|
defect
|
major
|
|
core
|
#126 |
Figure out how to get the spirit parsers to report parse errors
|
diane
|
defect
|
major
|
Few Small Repairs
|
core
|
#133 |
Should be able to save motifs
|
diane
|
enhancement
|
critical
|
Few Small Repairs
|
core
|
#183 |
Seqcomp is case sensitive
|
diane
|
defect
|
major
|
release_1.0
|
core
|
#208 |
the alg unittest executable needs to be broken up
|
diane
|
enhancement
|
major
|
unit tests
|
core
|
#236 |
Error parsing annotation file should also include the filename in the exception.
|
diane
|
enhancement
|
major
|
release_1.1
|
core
|
#239 |
Report error when trying to load a directory as an annotation.
|
diane
|
defect
|
major
|
release_1.1
|
core
|
#247 |
Increase version number to 1.1.0
|
diane
|
task
|
blocker
|
release_1.1
|
core
|
#260 |
Mupa parser is cranky on windows files
|
diane
|
defect
|
major
|
release_1.1
|
core
|
#261 |
Mussa mupa comment character required a space
|
diane
|
defect
|
minor
|
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
|
#3 |
View descriptions
|
diane
|
defect
|
major
|
Bionic Mussa
|
Qt Gui
|
#4 |
Aligned sequence view
|
diane
|
|
critical
|
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
|
#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
|
#20 |
Toggle Motif Button Implementation
|
king
|
defect
|
minor
|
Few Small Repairs
|
Qt Gui
|
#22 |
default size hint broken
|
diane
|
defect
|
trivial
|
Few Small Repairs
|
Qt Gui
|
#23 |
The threshold widget was broken too
|
diane
|
defect
|
major
|
Bionic Mussa
|
Qt Gui
|
#24 |
Clean up the signals and slots
|
diane
|
defect
|
minor
|
Few Small Repairs
|
Qt Gui
|
#25 |
broke motif colors
|
diane
|
defect
|
major
|
Bionic Mussa
|
Qt Gui
|
#26 |
SubAnalysis mode
|
diane
|
enhancement
|
critical
|
Few Small Repairs
|
Qt Gui
|
#31 |
Threshold Widget should use spinboxes
|
diane
|
|
major
|
Few Small Repairs
|
Qt Gui
|
#33 |
changing threshold can cause the UI to freeze
|
diane
|
defect
|
major
|
Standing on our heads
|
Qt Gui
|
#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
|
#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
|
#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
|
#44 |
Computation of reverse compliment colors is buggy
|
diane
|
|
critical
|
Few Small Repairs
|
Qt Gui
|
#45 |
recreate os x bless script
|
diane
|
task
|
major
|
Bionic Mussa
|
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
|
#51 |
Copying sequence might be useful
|
diane
|
enhancement
|
major
|
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
|
#55 |
Somehow when reloading an analysis it needs to save threshold / window size
|
diane
|
defect
|
critical
|
Few Small Repairs
|
Qt Gui
|
#56 |
Define analysis should include scroll area when SequenceWidget count >= 3
|
king
|
defect
|
minor
|
Few Small Repairs
|
Qt Gui
|
#57 |
Define analysis is annoying
|
diane
|
|
critical
|
Few Small Repairs
|
Qt Gui
|
#59 |
the washed out sequence should actually be partially transparent.
|
diane
|
defect
|
major
|
Few Small Repairs
|
Qt Gui
|
#62 |
Aligning sequence that has a reverse compliment doesn't fully align correctly
|
diane
|
defect
|
blocker
|
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
|