#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
|
#58 |
why does mussa take so long to recompute a large nway?
|
diane
|
defect
|
major
|
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
|
#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
|
#71 |
AnnotationColors don't always color motifs correctly
|
diane
|
defect
|
critical
|
Few Small Repairs
|
Qt Gui
|
#73 |
Performance problems doing analysis
|
diane
|
defect
|
major
|
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
|
#75 |
The scrollbar navigation when zoomed in jumps too far
|
diane
|
defect
|
critical
|
Few Small Repairs
|
Qt Gui
|
#76 |
Qt 4.1.1 crashes on barbara's computer
|
diane
|
defect
|
trivial
|
Few Small Repairs
|
Qt Gui
|
#84 |
The analysis title should report what file you loaded
|
diane
|
|
trivial
|
Standing on our heads
|
Qt Gui
|
#86 |
Progresss bar
|
diane
|
defect
|
major
|
Few Small Repairs
|
Qt Gui
|
#91 |
quits
|
diane
|
defect
|
major
|
Few Small Repairs
|
Qt Gui
|
#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
|
#96 |
Save to image broken
|
king
|
defect
|
minor
|
Few Small Repairs
|
Qt Gui
|
#97 |
Help > Mussa Manual... should have warning dialog upon error
|
king
|
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
|
#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
|
#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
|
#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
|
#125 |
autodetect if python needs -lutil
|
diane
|
defect
|
major
|
Few Small Repairs
|
Qt Gui
|
#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
|
#134 |
Width of seqcomp match line is wrong
|
diane
|
defect
|
blocker
|
Few Small Repairs
|
Qt Gui
|
#135 |
Win32: Save as not working... causes crash.
|
king
|
defect
|
critical
|
Few Small Repairs
|
Qt Gui
|
#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
|
#146 |
Win32: Create new analysis mystery crash
|
king
|
defect
|
blocker
|
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
|
#153 |
Allow users to specify the file load file mask
|
king
|
task
|
trivial
|
document_1.0
|
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
|
#160 |
error: default argument for parameter of type ‘MussaRef’ has type ‘int’
|
king
|
defect
|
major
|
Few Small Repairs
|
Qt Gui
|
#163 |
Motif loading doesn't work with release builds
|
diane
|
defect
|
major
|
release_1.0
|
Qt Gui
|
#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
|