#76 |
Qt 4.1.1 crashes on barbara's computer
|
diane
|
defect
|
trivial
|
Few Small Repairs
|
Qt Gui
|
#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
|
#83 |
Mussa should complain about misformatted fasta files instead of crashing.
|
diane
|
defect
|
critical
|
Few Small Repairs
|
core
|
#84 |
The analysis title should report what file you loaded
|
diane
|
|
trivial
|
Standing on our heads
|
Qt Gui
|
#85 |
mussagl quits, just like i will AGAIN soon.
|
diane
|
defect
|
critical
|
Few Small Repairs
|
core
|
#86 |
Progresss bar
|
diane
|
defect
|
major
|
Few Small Repairs
|
Qt Gui
|
#90 |
the arrow keys aren't connected to the scrollbar
|
diane
|
defect
|
critical
|
|
python interface
|
#91 |
quits
|
diane
|
defect
|
major
|
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
|
#94 |
quits at viewing allignment
|
diane
|
defect
|
major
|
Few Small Repairs
|
Qt Gui
|
#95 |
Annotations masked out when motif defined and then undefined.
|
diane
|
defect
|
minor
|
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
|
#104 |
Loading a different analysis while a MussaAlignedWindow was open caused a crash
|
diane
|
defect
|
major
|
Few Small Repairs
|
Qt Gui
|
#105 |
Load Analysis should spawn a new window
|
diane
|
defect
|
minor
|
Standing on our heads
|
Qt Gui
|
#107 |
Motifs don't show up on the Mussa Aligned Sequence window anymore.
|
diane
|
defect
|
critical
|
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
|
#111 |
Set zero/alignment point for a sequence
|
diane
|
enhancement
|
critical
|
release_1.1
|
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
|
#115 |
The create an analysis screen create the sequences in the reverse order.
|
diane
|
defect
|
minor
|
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
|
#122 |
Motif editor needs to support more than 10 motifs
|
diane
|
enhancement
|
critical
|
Few Small Repairs
|
Qt Gui
|
#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
|
#128 |
the editable sequence name only shows the end of long names.
|
diane
|
defect
|
trivial
|
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
|
#133 |
Should be able to save motifs
|
diane
|
enhancement
|
critical
|
Few Small Repairs
|
core
|
#134 |
Width of seqcomp match line is wrong
|
diane
|
defect
|
blocker
|
Few Small Repairs
|
Qt Gui
|
#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
|
#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
|
#144 |
IUPAC codes are destroyed by the sequence normalization code
|
diane
|
defect
|
critical
|
Few Small Repairs
|
Qt Gui
|
#147 |
Sometimes the width of a quadrallateral is too small
|
diane
|
defect
|
trivial
|
Few Small Repairs
|
Qt Gui
|
#148 |
setup_analysis dialog should make sure that the threshold is not greater than the window size.
|
diane
|
defect
|
minor
|
Few Small Repairs
|
Qt Gui
|
#149 |
Handle " in motif names
|
diane
|
defect
|
trivial
|
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
|
#154 |
off by one error when drawing segments
|
diane
|
defect
|
blocker
|
Few Small Repairs
|
Qt Gui
|
#158 |
When unable to parse a fasta file report its name
|
diane
|
enhancement
|
critical
|
release_1.1
|
Qt Gui
|
#163 |
Motif loading doesn't work with release builds
|
diane
|
defect
|
major
|
release_1.0
|
Qt Gui
|
#174 |
Confirm file formats are documented and correct.
|
diane
|
task
|
major
|
document_1.0
|
other
|
#177 |
Confirm description of blue conservation tracks is correct.
|
diane
|
task
|
minor
|
document_1.0
|
other
|
#180 |
shipit script on os x needs to validate the archive
|
diane
|
defect
|
major
|
release_1.0
|
other
|
#182 |
Mussa views need vertical scrolls
|
diane
|
enhancement
|
critical
|
release_1.1
|
Qt Gui
|
#183 |
Seqcomp is case sensitive
|
diane
|
defect
|
major
|
release_1.0
|
core
|
#184 |
Dont link against X11 on OS X
|
diane
|
defect
|
major
|
release_1.0
|
other
|
#186 |
Motif dialog on load existing motifs behavior needs update.
|
diane
|
enhancement
|
minor
|
release_1.0
|
Qt Gui
|
#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
|
#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
|
#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
|
#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
|
#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
|
#235 |
set version to 1.0 in version.h
|
diane
|
task
|
major
|
release_1.0
|
other
|
#236 |
Error parsing annotation file should also include the filename in the exception.
|
diane
|
enhancement
|
major
|
release_1.1
|
core
|
#237 |
Crashing with invalid file name
|
diane
|
defect
|
major
|
release_1.1
|
Qt Gui
|
#239 |
Report error when trying to load a directory as an annotation.
|
diane
|
defect
|
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
|
#244 |
len(mussa.paths()) returns number of tracks, not the number of paths found
|
diane
|
defect
|
major
|
release_1.1
|
python interface
|
#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
|
#255 |
Even telling cmake to use python2.3 mussa still builds against 2.5
|
diane
|
defect
|
major
|
release_1.1
|
python interface
|
#256 |
Assertion failed
|
diane
|
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
|