#1 |
Annotation color mapper
|
diane
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|
critical
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Bionic Mussa
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core
|
#2 |
Connection view
|
diane
|
task
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major
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Bionic Mussa
|
core
|
#3 |
View descriptions
|
diane
|
defect
|
major
|
Bionic Mussa
|
Qt Gui
|
#4 |
Aligned sequence view
|
diane
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critical
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Bionic Mussa
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Qt Gui
|
#5 |
Configure a mussa analysis from the Gui
|
king
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defect
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major
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Bionic Mussa
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Qt Gui
|
#10 |
Integrate motifs with annotations
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diane
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defect
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major
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Standing on our heads
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core
|
#12 |
modify motifs attached to an analysis
|
diane
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task
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major
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Bionic Mussa
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Qt Gui
|
#14 |
Motifs need to be creatable and editable from within the GUI
|
diane
|
defect
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major
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Bionic Mussa
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Qt Gui
|
#15 |
Unify build system
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diane
|
defect
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major
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Few Small Repairs
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core
|
#16 |
figure out how to get selections to work with new segment based drawing
|
diane
|
defect
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major
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Bionic Mussa
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Qt Gui
|
#19 |
I broke the scrollbar too
|
diane
|
defect
|
major
|
Bionic Mussa
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Qt Gui
|
#20 |
Toggle Motif Button Implementation
|
king
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defect
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minor
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Few Small Repairs
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Qt Gui
|
#22 |
default size hint broken
|
diane
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defect
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trivial
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Few Small Repairs
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Qt Gui
|
#23 |
The threshold widget was broken too
|
diane
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defect
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major
|
Bionic Mussa
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Qt Gui
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#24 |
Clean up the signals and slots
|
diane
|
defect
|
minor
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Few Small Repairs
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Qt Gui
|
#25 |
broke motif colors
|
diane
|
defect
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major
|
Bionic Mussa
|
Qt Gui
|
#26 |
SubAnalysis mode
|
diane
|
enhancement
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critical
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Few Small Repairs
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Qt Gui
|
#27 |
Collect example sequences
|
diane
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enhancement
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minor
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|
other
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#31 |
Threshold Widget should use spinboxes
|
diane
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major
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Few Small Repairs
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Qt Gui
|
#32 |
The trac pages should become the main mussa website
|
king
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task
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major
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Bionic Mussa
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other
|
#33 |
changing threshold can cause the UI to freeze
|
diane
|
defect
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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
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Few Small Repairs
|
Qt Gui
|
#36 |
Make zoom widget make sense
|
diane
|
defect
|
major
|
Bionic Mussa
|
Qt Gui
|
#37 |
Skateboard Shoes
|
diane
|
defect
|
|
|
|
#38 |
Loading a new analysis while an alignment window was open causes segfault
|
diane
|
defect
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major
|
Bionic Mussa
|
Qt Gui
|
#39 |
sidebar rendering problems
|
diane
|
|
major
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Few Small Repairs
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Qt Gui
|
#40 |
MussaAlignedWindow, left sequence position doesn't get initial value set
|
diane
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|
minor
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Bionic Mussa
|
Qt Gui
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#41 |
Selection box jumps slightly to the right of the rubber band
|
diane
|
task
|
minor
|
Bionic Mussa
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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
|
#47 |
OS X OpenGL rendering problems
|
diane
|
defect
|
|
|
|
#49 |
QAssistant Mussa Docs
|
diane
|
defect
|
critical
|
Few Small Repairs
|
core
|
#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
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major
|
Few Small Repairs
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Qt Gui
|
#52 |
Saved analysis needs to keep widow size and threshold for threshold widget
|
diane
|
defect
|
minor
|
Few Small Repairs
|
Qt Gui
|
#53 |
Copy an example into the os x dmg
|
diane
|
|
trivial
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Few Small Repairs
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other
|
#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
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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
|
#60 |
sequence alignment view needs zoom
|
diane
|
defect
|
trivial
|
Few Small Repairs
|
core
|
#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
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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
|
#72 |
Myogenin human mouse rat cow chicken files are odd
|
diane
|
|
critical
|
Bionic Mussa
|
core
|
#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
|
#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
|
#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
|
#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
|