#246 |
Add "What's this?" documentation to as many elements of the GUI as possible.
|
king
|
enhancement
|
major
|
release_1.1
|
Qt Gui
|
#179 |
Add a section on "File > New Mussa Window" feature.
|
king
|
task
|
major
|
document_1.0
|
other
|
#167 |
Add an "Understanding Mussa" section to manual.
|
king
|
task
|
major
|
document_1.0
|
other
|
#119 |
Add dependencies to MussaglBuild page
|
diane
|
task
|
major
|
Few Small Repairs
|
other
|
#161 |
Add link to smn1 example data (since the UCSC tutorial is based on it)
|
king
|
task
|
major
|
document_1.0
|
other
|
#199 |
After [451] I noticed that subanalyses didn't seem to have motif information
|
diane
|
defect
|
major
|
release_1.0
|
Qt Gui
|
#170 |
After implementing ticket:164, update 'Load Mupa' section to link to SMN1 example .mupa.
|
king
|
task
|
major
|
document_1.0
|
other
|
#43 |
After scrolling a sequence browser window, selection boxes break
|
diane
|
defect
|
minor
|
Few Small Repairs
|
Qt Gui
|
#4 |
Aligned sequence view
|
diane
|
|
critical
|
Bionic Mussa
|
Qt Gui
|
#62 |
Aligning sequence that has a reverse compliment doesn't fully align correctly
|
diane
|
defect
|
blocker
|
Few Small Repairs
|
Qt Gui
|
#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
|
#153 |
Allow users to specify the file load file mask
|
king
|
task
|
trivial
|
document_1.0
|
Qt Gui
|
#1 |
Annotation color mapper
|
diane
|
|
critical
|
Bionic Mussa
|
core
|
#71 |
AnnotationColors don't always color motifs correctly
|
diane
|
defect
|
critical
|
Few Small Repairs
|
Qt Gui
|
#95 |
Annotations masked out when motif defined and then undefined.
|
diane
|
defect
|
minor
|
Few Small Repairs
|
Qt Gui
|
#256 |
Assertion failed
|
diane
|
defect
|
major
|
release_1.1
|
Qt Gui
|
#243 |
Change mussa track to white boxes with Ns highlighted in black
|
diane
|
enhancement
|
major
|
release_1.2
|
Qt Gui
|
#24 |
Clean up the signals and slots
|
diane
|
defect
|
minor
|
Few Small Repairs
|
Qt Gui
|
#250 |
Cmake build failure: /usr/bin/ld: cannot find -loptimized
|
diane
|
defect
|
blocker
|
release_1.1
|
Qt Gui
|
#27 |
Collect example sequences
|
diane
|
enhancement
|
minor
|
|
other
|
#44 |
Computation of reverse compliment colors is buggy
|
diane
|
|
critical
|
Few Small Repairs
|
Qt Gui
|
#5 |
Configure a mussa analysis from the Gui
|
king
|
defect
|
major
|
Bionic Mussa
|
Qt Gui
|
#177 |
Confirm description of blue conservation tracks is correct.
|
diane
|
task
|
minor
|
document_1.0
|
other
|
#174 |
Confirm file formats are documented and correct.
|
diane
|
task
|
major
|
document_1.0
|
other
|
#2 |
Connection view
|
diane
|
task
|
major
|
Bionic Mussa
|
core
|
#53 |
Copy an example into the os x dmg
|
diane
|
|
trivial
|
Few Small Repairs
|
other
|
#51 |
Copying sequence might be useful
|
diane
|
enhancement
|
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
|
#237 |
Crashing with invalid file name
|
diane
|
defect
|
major
|
release_1.1
|
Qt Gui
|
#57 |
Define analysis is annoying
|
diane
|
|
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
|
#195 |
Disable motif and closing motif editor causes loss of motifs.
|
diane
|
defect
|
critical
|
release_1.1
|
Qt Gui
|
#189 |
Document "save on close" section after close of ticket:187
|
king
|
task
|
major
|
document_1.0
|
other
|
#176 |
Document 'Save Analysis' and 'Save Analysis As' features.
|
king
|
task
|
major
|
document_1.0
|
other
|
#227 |
Document Python useage in Mussagl
|
king
|
task
|
major
|
document_1.0
|
Qt Gui
|
#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
|
#175 |
Document new 'save motifs' feature.
|
king
|
task
|
major
|
document_1.0
|
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
|
#214 |
Document why sub-analysis exists
|
king
|
enhancement
|
minor
|
document_1.0
|
other
|
#184 |
Dont link against X11 on OS X
|
diane
|
defect
|
major
|
release_1.0
|
other
|
#212 |
ESC key should by bound to 'deselect' current selection.
|
diane
|
enhancement
|
trivial
|
release_1.2
|
Qt Gui
|
#139 |
Edit motif window looses motif information when closed
|
diane
|
defect
|
major
|
Few Small Repairs
|
Qt Gui
|
#187 |
Editing a motif does not set dirty flag.
|
diane
|
defect
|
minor
|
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
|
#255 |
Even telling cmake to use python2.3 mussa still builds against 2.5
|
diane
|
defect
|
major
|
release_1.1
|
python interface
|
#150 |
Example data for 1.0 release
|
diane
|
task
|
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
|
#113 |
For some reason on Ali's machine cmake is linking in X11
|
diane
|
defect
|
major
|
|
Qt Gui
|
#149 |
Handle " in motif names
|
diane
|
defect
|
trivial
|
Few Small Repairs
|
Qt Gui
|
#97 |
Help > Mussa Manual... should have warning dialog upon error
|
king
|
defect
|
minor
|
Few Small Repairs
|
Qt Gui
|
#19 |
I broke the scrollbar too
|
diane
|
defect
|
major
|
Bionic Mussa
|
Qt Gui
|
#144 |
IUPAC codes are destroyed by the sequence normalization code
|
diane
|
defect
|
critical
|
Few Small Repairs
|
Qt Gui
|
#164 |
Include a section on creating a .mupa file using the smn1 data.
|
king
|
task
|
major
|
document_1.0
|
other
|
#247 |
Increase version number to 1.1.0
|
diane
|
task
|
blocker
|
release_1.1
|
core
|
#10 |
Integrate motifs with annotations
|
diane
|
defect
|
major
|
Standing on our heads
|
core
|
#79 |
It'd be nice if you could annotate by providing fasta files
|
diane
|
|
blocker
|
|
python interface
|
#142 |
It'd be really useful to trigger a subanalysis from an aligned sequence view.
|
diane
|
enhancement
|
major
|
Few Small Repairs
|
Qt Gui
|
#105 |
Load Analysis should spawn a new window
|
diane
|
defect
|
minor
|
Standing on our heads
|
Qt Gui
|
#140 |
Load Motifs doesn't do anything
|
diane
|
defect
|
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
|
#38 |
Loading a new analysis while an alignment window was open causes segfault
|
diane
|
defect
|
major
|
Bionic Mussa
|
Qt Gui
|
#114 |
Location analyses are saved to is ill-defined on OS X.
|
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
|
#252 |
Make scroll wheel work
|
king
|
enhancement
|
major
|
release_1.1
|
Qt Gui
|
#36 |
Make zoom widget make sense
|
diane
|
defect
|
major
|
Bionic Mussa
|
Qt Gui
|
#186 |
Motif dialog on load existing motifs behavior needs update.
|
diane
|
enhancement
|
minor
|
release_1.0
|
Qt Gui
|
#122 |
Motif editor needs to support more than 10 motifs
|
diane
|
enhancement
|
critical
|
Few Small Repairs
|
Qt Gui
|
#196 |
Motif editor: document how to delete a motif
|
king
|
enhancement
|
major
|
document_1.0
|
other
|
#163 |
Motif loading doesn't work with release builds
|
diane
|
defect
|
major
|
release_1.0
|
Qt Gui
|
#107 |
Motifs don't show up on the Mussa Aligned Sequence window anymore.
|
diane
|
defect
|
critical
|
Few Small Repairs
|
Qt Gui
|
#103 |
Motifs need a name field
|
diane
|
enhancement
|
minor
|
Few Small Repairs
|
Qt Gui
|
#14 |
Motifs need to be creatable and editable from within the GUI
|
diane
|
defect
|
major
|
Bionic Mussa
|
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
|
#156 |
Mussa manual - meta ticket
|
king
|
task
|
major
|
document_1.0
|
other
|
#168 |
Mussa manual: Update Mac OS X install instructions
|
king
|
task
|
major
|
document_1.0
|
other
|
#162 |
Mussa manual: Update major new features section
|
king
|
task
|
minor
|
document_1.0
|
other
|
#157 |
Mussa manual: document 'save to image' feature
|
king
|
task
|
major
|
document_1.0
|
other
|
#261 |
Mussa mupa comment character required a space
|
diane
|
defect
|
minor
|
release_1.1
|
core
|
#83 |
Mussa should complain about misformatted fasta files instead of crashing.
|
diane
|
defect
|
critical
|
Few Small Repairs
|
core
|
#182 |
Mussa views need vertical scrolls
|
diane
|
enhancement
|
critical
|
release_1.1
|
Qt Gui
|
#40 |
MussaAlignedWindow, left sequence position doesn't get initial value set
|
diane
|
|
minor
|
Bionic Mussa
|
Qt Gui
|
#72 |
Myogenin human mouse rat cow chicken files are odd
|
diane
|
|
critical
|
Bionic Mussa
|
core
|
#70 |
Need to be able to save screenshots in View Alignment Page
|
diane
|
|
major
|
Few Small Repairs
|
Qt Gui
|
#259 |
New Annotations hide the sequence when you zoom to sequence view
|
diane
|
defect
|
critical
|
release_1.1
|
Qt Gui
|
#47 |
OS X OpenGL rendering problems
|
diane
|
defect
|
|
|
|
#64 |
Occasionally ConservedPath crashes
|
diane
|
|
minor
|
Few Small Repairs
|
Qt Gui
|
#74 |
On OSX when maxmizing the sidebar stays on the GL canvas
|
diane
|
defect
|
trivial
|
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
|
#229 |
Package Everything for 1.0
|
diane
|
task
|
major
|
release_1.0
|
other
|
#99 |
Percent threshold shouldn't be editable.
|
diane
|
enhancement
|
blocker
|
Few Small Repairs
|
Qt Gui
|
#73 |
Performance problems doing analysis
|
diane
|
defect
|
major
|
Few Small Repairs
|
Qt Gui
|
#117 |
Perhaps our fasta loading file loader could detect if we're being fed an html file.
|
diane
|
defect
|
major
|
|
Qt Gui
|
#116 |
Perhaps the motif file should have a name field.
|
diane
|
enhancement
|
major
|
Few Small Repairs
|
core
|
#86 |
Progresss bar
|
diane
|
defect
|
major
|
Few Small Repairs
|
Qt Gui
|
#200 |
Pushing the threshold change button too fast will cause mussa to crash
|
diane
|
defect
|
major
|
release_1.0
|
Qt Gui
|
#49 |
QAssistant Mussa Docs
|
diane
|
defect
|
critical
|
Few Small Repairs
|
core
|
#76 |
Qt 4.1.1 crashes on barbara's computer
|
diane
|
defect
|
trivial
|
Few Small Repairs
|
Qt Gui
|