| #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
|
| #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
|
| #26 |
SubAnalysis mode
|
diane
|
enhancement
|
critical
|
Few Small Repairs
|
Qt Gui
|
| #27 |
Collect example sequences
|
diane
|
enhancement
|
minor
|
|
other
|
| #51 |
Copying sequence might be useful
|
diane
|
enhancement
|
major
|
Few Small Repairs
|
Qt Gui
|
| #99 |
Percent threshold shouldn't be editable.
|
diane
|
enhancement
|
blocker
|
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
|
| #102 |
Update "blocking the gui" comment in --no-gui mode.
|
diane
|
enhancement
|
trivial
|
Few Small Repairs
|
core
|
| #103 |
Motifs need a name field
|
diane
|
enhancement
|
minor
|
Few Small Repairs
|
Qt Gui
|
| #111 |
Set zero/alignment point for a sequence
|
diane
|
enhancement
|
critical
|
release_1.1
|
Qt Gui
|
| #116 |
Perhaps the motif file should have a name field.
|
diane
|
enhancement
|
major
|
Few Small Repairs
|
core
|
| #118 |
Tracks need an edit properites option.
|
diane
|
enhancement
|
major
|
Few Small Repairs
|
Qt Gui
|
| #120 |
Windows doesn't have python installed by default
|
diane
|
enhancement
|
major
|
Few Small Repairs
|
Qt Gui
|
| #122 |
Motif editor needs to support more than 10 motifs
|
diane
|
enhancement
|
critical
|
Few Small Repairs
|
Qt Gui
|
| #132 |
Make open saved analysis open a new window
|
diane
|
enhancement
|
major
|
Few Small Repairs
|
Qt Gui
|
| #133 |
Should be able to save motifs
|
diane
|
enhancement
|
critical
|
Few Small Repairs
|
core
|
| #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
|
| #158 |
When unable to parse a fasta file report its name
|
diane
|
enhancement
|
critical
|
release_1.1
|
Qt Gui
|
| #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
|
| #182 |
Mussa views need vertical scrolls
|
diane
|
enhancement
|
critical
|
release_1.1
|
Qt Gui
|
| #186 |
Motif dialog on load existing motifs behavior needs update.
|
diane
|
enhancement
|
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
|
| #191 |
Update "Motif Dialog" section
|
king
|
enhancement
|
major
|
document_1.0
|
other
|
| #194 |
use window feedback to show that there are unsaved changes
|
diane
|
enhancement
|
trivial
|
release_1.1
|
Qt Gui
|
| #196 |
Motif editor: document how to delete a motif
|
king
|
enhancement
|
major
|
document_1.0
|
other
|
| #206 |
We need some way of indicating Ns
|
diane
|
enhancement
|
critical
|
release_1.1
|
Qt Gui
|
| #208 |
the alg unittest executable needs to be broken up
|
diane
|
enhancement
|
major
|
unit tests
|
core
|
| #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
|
| #214 |
Document why sub-analysis exists
|
king
|
enhancement
|
minor
|
document_1.0
|
other
|
| #215 |
You should be able to paste into the motif editor
|
diane
|
enhancement
|
critical
|
release_1.1
|
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
|
| #236 |
Error parsing annotation file should also include the filename in the exception.
|
diane
|
enhancement
|
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
|
| #246 |
Add "What's this?" documentation to as many elements of the GUI as possible.
|
king
|
enhancement
|
major
|
release_1.1
|
Qt Gui
|
| #252 |
Make scroll wheel work
|
king
|
enhancement
|
major
|
release_1.1
|
Qt Gui
|
| #2 |
Connection view
|
diane
|
task
|
major
|
Bionic Mussa
|
core
|
| #12 |
modify motifs attached to an analysis
|
diane
|
task
|
major
|
Bionic Mussa
|
Qt Gui
|
| #32 |
The trac pages should become the main mussa website
|
king
|
task
|
major
|
Bionic Mussa
|
other
|
| #41 |
Selection box jumps slightly to the right of the rubber band
|
diane
|
task
|
minor
|
Bionic Mussa
|
Qt Gui
|
| #45 |
recreate os x bless script
|
diane
|
task
|
major
|
Bionic Mussa
|
Qt Gui
|
| #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
|
| #150 |
Example data for 1.0 release
|
diane
|
task
|
major
|
Few Small Repairs
|
Qt Gui
|
| #152 |
Update mussa_manual.adp to latest tutorial version
|
king
|
task
|
minor
|
document_1.0
|
other
|
| #153 |
Allow users to specify the file load file mask
|
king
|
task
|
trivial
|
document_1.0
|
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
|
| #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
|
| #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
|
| #181 |
Update 'Load a mussa parameter file' section
|
king
|
task
|
major
|
document_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
|
| #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
|
| #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
|
| #235 |
set version to 1.0 in version.h
|
diane
|
task
|
major
|
release_1.0
|
other
|
| #247 |
Increase version number to 1.1.0
|
diane
|
task
|
blocker
|
release_1.1
|
core
|
| #1 |
Annotation color mapper
|
diane
|
|
critical
|
Bionic Mussa
|
core
|
| #4 |
Aligned sequence view
|
diane
|
|
critical
|
Bionic Mussa
|
Qt Gui
|
| #31 |
Threshold Widget should use spinboxes
|
diane
|
|
major
|
Few Small Repairs
|
Qt Gui
|
| #35 |
Zoom Icon
|
diane
|
|
minor
|
Few Small Repairs
|
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
|
| #44 |
Computation of reverse compliment colors is buggy
|
diane
|
|
critical
|
Few Small Repairs
|
Qt Gui
|
| #53 |
Copy an example into the os x dmg
|
diane
|
|
trivial
|
Few Small Repairs
|
other
|
| #57 |
Define analysis is annoying
|
diane
|
|
critical
|
Few Small Repairs
|
Qt Gui
|
| #64 |
Occasionally ConservedPath crashes
|
diane
|
|
minor
|
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
|
| #69 |
motifs may not be rendering corectly
|
diane
|
|
critical
|
Few Small Repairs
|
Qt Gui
|
| #70 |
Need to be able to save screenshots in View Alignment Page
|
diane
|
|
major
|
Few Small Repairs
|
Qt Gui
|
| #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
|
| #79 |
It'd be nice if you could annotate by providing fasta files
|
diane
|
|
blocker
|
|
python interface
|
| #84 |
The analysis title should report what file you loaded
|
diane
|
|
trivial
|
Standing on our heads
|
Qt Gui
|