#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
|
#192 |
Steven can't save with mussa
|
diane
|
defect
|
major
|
release_1.0
|
Qt Gui
|
#194 |
use window feedback to show that there are unsaved changes
|
diane
|
enhancement
|
trivial
|
release_1.1
|
Qt Gui
|
#195 |
Disable motif and closing motif editor causes loss of motifs.
|
diane
|
defect
|
critical
|
release_1.1
|
Qt Gui
|
#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
|
#206 |
We need some way of indicating Ns
|
diane
|
enhancement
|
critical
|
release_1.1
|
Qt Gui
|
#207 |
Reenable GUI tests
|
diane
|
defect
|
major
|
unit tests
|
Qt Gui
|
#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
|
#213 |
Document how to deselect tracks/paths
|
king
|
task
|
minor
|
document_1.0
|
Qt Gui
|
#215 |
You should be able to paste into the motif editor
|
diane
|
enhancement
|
critical
|
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
|
#223 |
Set the Window Icon to be the Mussa icon
|
king
|
enhancement
|
trivial
|
release_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
|
#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
|
#237 |
Crashing with invalid file name
|
diane
|
defect
|
major
|
release_1.1
|
Qt Gui
|
#240 |
When there are no matches, mussa doesn't seem to display anything
|
king
|
defect
|
minor
|
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
|
#246 |
Add "What's this?" documentation to as many elements of the GUI as possible.
|
king
|
enhancement
|
major
|
release_1.1
|
Qt Gui
|
#250 |
Cmake build failure: /usr/bin/ld: cannot find -loptimized
|
diane
|
defect
|
blocker
|
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
|
#254 |
Sub-analysis failing to draw paths on init
|
king
|
defect
|
minor
|
release_1.1
|
Qt Gui
|
#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
|
#259 |
New Annotations hide the sequence when you zoom to sequence view
|
diane
|
defect
|
critical
|
release_1.1
|
Qt Gui
|
#1 |
Annotation color mapper
|
diane
|
|
critical
|
Bionic Mussa
|
core
|
#2 |
Connection view
|
diane
|
task
|
major
|
Bionic Mussa
|
core
|
#10 |
Integrate motifs with annotations
|
diane
|
defect
|
major
|
Standing on our heads
|
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
|
#102 |
Update "blocking the gui" comment in --no-gui mode.
|
diane
|
enhancement
|
trivial
|
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
|
#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
|
#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
|
#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
|
#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
|
#37 |
Skateboard Shoes
|
diane
|
defect
|
|
|
|
#47 |
OS X OpenGL rendering problems
|
diane
|
defect
|
|
|
|