Timeline



04/09/2006:

14:32 Ticket #83 (Mussa should complain about misformatted fasta files instead of crashing.) created by ghernand@…
i entered 3 sequences using the browser function. two sequences were …

04/07/2006:

00:40 Ticket #82 (Unit test python API) created by diane
With the new cmake system I should make sure that I also test my boost …

04/06/2006:

12:06 Ticket #81 (Storing and searching metadata) created by diane
It'd be really really nice if there was some way that a person could …

04/04/2006:

00:53 Ticket #74 (On OSX when maxmizing the sidebar stays on the GL canvas) closed by diane
fixed: [162] changed from using QSplitter to just a QHBoxLayout (with sizing …

03/30/2006:

15:50 Ticket #80 (Difference between analyses) created by diane
It would be useful if you could load an analysis and then load a …
14:59 Ticket #68 (The web site should have the Caltech and possibly BMNC logo) closed by king
fixed: Changed to Caltech Logo.
11:48 Ticket #79 (It'd be nice if you could annotate by providing fasta files) created by diane
Family relations does it... why cant mussa.

03/29/2006:

22:59 Ticket #78 (Reverse compliment alignment lines dont seem to match up) created by diane
As far as I can tell the lines connecting reverse compliments on the …
15:14 Ticket #77 (Font needs to be better...) created by diane
Its hard to read…
14:57 Ticket #76 (Qt 4.1.1 crashes on barbara's computer) created by diane
when going to the alignment view, when built on ali's computer it …
14:56 Ticket #75 (The scrollbar navigation when zoomed in jumps too far) created by diane
When you navigate by dragging the thumb around on the sequence view …
14:26 Ticket #74 (On OSX when maxmizing the sidebar stays on the GL canvas) created by diane
13:24 MussaglBuild edited by king
Comment about versions of Qt4.1 (diff)
13:23 MussaglBuild edited by king
(diff)
00:26 Ticket #69 (motifs may not be rendering corectly) closed by diane
fixed: [155] makes this bearable.
00:25 Ticket #71 (AnnotationColors don't always color motifs correctly) reopened by diane

03/28/2006:

23:18 Ticket #71 (AnnotationColors don't always color motifs correctly) closed by diane
duplicate: ticket:69 is very closely related.
22:55 Ticket #63 (with two sequences the align sequence view doesn't show any connections) closed by diane
fixed: Fixed by [154]
21:46 Ticket #66 (The annotation for myogenin needs to be checked.) closed by diane
fixed: I grabbed annotation for human and mouse from ucsc by clicking on the …
21:41 Ticket #60 (sequence alignment view needs zoom) closed by diane
fixed
18:03 WikiStart edited by king
(diff)

03/27/2006:

22:36 Ticket #34 (Unused variable 'max_range' in 'void ...) closed by diane
fixed: Fixed in [110] (Someone needs to check my OCD, why did I go hunt that …
22:14 Ticket #50 (Switch to using Qt4.1 resources (automatically compiles resources into ...) closed by diane
fixed: ticket:46 was a duplicate
22:14 Ticket #46 (link in icons) closed by diane
fixed: ticket:50 is duplicate idea specifying an implementation for this. …
21:59 Ticket #52 (Saved analysis needs to keep widow size and threshold for threshold widget) closed by diane
fixed: Dupe of ticket:55 this is effectively the same ticket as ticket:52, …
17:46 Ticket #55 (Somehow when reloading an analysis it needs to save threshold / window size) closed by diane
fixed
17:46 Ticket #31 (Threshold Widget should use spinboxes) closed by diane
fixed
13:05 Ticket #73 (Performance problems doing analysis) created by diane
Steven noticed that doing an analysis seemed far slower than with …
13:03 Ticket #72 (Myogenin human mouse rat cow chicken files are odd) created by diane
In no case was I able to see the feature I had highlighted shown in …
13:01 Ticket #71 (AnnotationColors don't always color motifs correctly) created by diane
I would show that on the sequence alignment view, some highlighted …
12:56 Ticket #70 (Need to be able to save screenshots in View Alignment Page) created by diane
1. when in view alignment screen, and you go to services to grab the …

03/24/2006:

18:27 Ticket #69 (motifs may not be rendering corectly) created by diane
Especially when moving around the sequence the motifs flash in and …
18:17 Ticket #68 (The web site should have the Caltech and possibly BMNC logo) created by diane
We should look more professional, and use boring logos
18:14 Ticket #67 (You should be able to open multiple analyses) created by diane
There should be a way to create multiple MussaAnalysis windows.
18:12 Ticket #57 (Define analysis is annoying) closed by diane
fixed
18:10 Ticket #53 (Copy an example into the os x dmg) closed by diane
fixed
18:09 Ticket #66 (The annotation for myogenin needs to be checked.) created by diane
Also the color could be brighter.
18:07 Ticket #65 (It'd be neat if you could select a region and go to ucsc) created by diane
This is also useful for fixing annotation problems
17:53 Ticket #64 (Occasionally ConservedPath crashes) created by diane
don't have good examples to trigger it but I've seen it happen twice
17:41 Ticket #63 (with two sequences the align sequence view doesn't show any connections) created by diane
I wonder if the alignment view needs at least 3 sequences to render?
17:32 Ticket #62 (Aligning sequence that has a reverse compliment doesn't fully align ...) created by diane
I suspect the because the reverse compliment is based from the right …
17:30 Ticket #61 (For mac users it'd be useful to make double clicking on a data file ...) created by diane
Of course somehow we'd need to make an analysis actually be …
17:29 Ticket #60 (sequence alignment view needs zoom) created by diane
It'd be useful to zoom out a bit from the sequence aligned view to …
17:27 Ticket #59 (the washed out sequence should actually be partially transparent.) created by diane
It's possible for the selected sequence to be completely hidden, so …
16:59 Ticket #58 (why does mussa take so long to recompute a large nway?) created by diane
you can load an nway and it'll show up correctly? but if you set back …

03/23/2006:

11:55 WikiStart edited by king
(diff)
11:53 WikiStart edited by king
(diff)
11:52 WikiStart edited by king
(diff)
11:03 Ticket #57 (Define analysis is annoying) created by diane
When something goes wrong with the define analysis, it catches the …
11:02 Ticket #56 (Define analysis should include scroll area when SequenceWidget count >= 3) created by king
Define analysis should include scroll area when SequenceWidget count …
10:54 Ticket #55 (Somehow when reloading an analysis it needs to save threshold / window size) created by diane
I need some way of knowing when what the threshold and window sizes …
10:24 Ticket #54 (Allow compressing repeat regions) created by diane
For MEME Ali compressed reprat regions and replaced them with a small …

03/22/2006:

18:13 Ticket #53 (Copy an example into the os x dmg) created by diane
It'd be useful to include one of the sequence examples when shipping …
16:52 Ticket #39 (sidebar rendering problems) closed by diane
fixed: [138] should fix this.
16:13 Ticket #41 (Selection box jumps slightly to the right of the rubber band) closed by diane
fixed: Fixed by [137] and this was caused by the same problem as ticket:43
16:11 Ticket #43 (After scrolling a sequence browser window, selection boxes break) closed by diane
fixed
15:28 Ticket #52 (Saved analysis needs to keep widow size and threshold for threshold widget) created by diane
The Mussa class when reloaded from an analysis needs to keep track of …
14:22 Ticket #51 (Copying sequence might be useful) created by diane
It'd be nice to be able to copy sequence from a sequence track.
14:19 Ticket #47 (OS X OpenGL rendering problems) closed by diane
fixed: Increasing the line thicknesses in [134] actually worked
13:51 Ticket #50 (Switch to using Qt4.1 resources (automatically compiles resources into ...) created by king
Switch to using Qt4.1 resources (automatically compiles resources into …
01:50 Ticket #49 (QAssistant Mussa Docs) created by king
A tutorial and/or user manual should be made and included within …
01:47 Ticket #48 (Automate win32 installer build) created by king
Wouldn't it be nice if a new build of the win32 installer could be me …

03/21/2006:

22:11 WikiStart edited by king
Got Win32 Installer? (diff)
21:12 Milestone Bionic Mussa completed
Duplicate the core functionality of Tristan's FLTK mussa.
20:55 Ticket #5 (Configure a mussa analysis from the Gui) closed by diane
fixed: Implementation finished in [135] however it revealed a bug on os x …
16:46 Ticket #47 (OS X OpenGL rendering problems) created by diane
The line widths in the opengl canvas on os x are badly pixelated on …
16:44 Ticket #45 (recreate os x bless script) closed by diane
fixed: Added in [131]
15:03 MussaglBuild edited by diane
(diff)
12:22 Ticket #46 (link in icons) created by diane
OS X can't find the menu icons. It would be best if they were linked …
01:28 Ticket #45 (recreate os x bless script) created by diane
Need to recreate the qt-mac bless script so I can actually …
01:23 darcs edited by diane
(diff)
00:49 Ticket #14 (Motifs need to be creatable and editable from within the GUI) closed by diane
fixed

03/20/2006:

17:35 Ticket #44 (Computation of reverse compliment colors is buggy) created by diane
For both types of links (mussa windows and base pair alignments) the …
17:23 Ticket #37 (Skateboard Shoes) closed by diane
fixed: Computations involving ceil hurt my head... I had ceil(left) - seq_x …
16:08 Ticket #42 (when resizing you should see more basepairs, not make them bigger.) closed by diane
fixed
16:07 Ticket #40 (MussaAlignedWindow, left sequence position doesn't get initial value set) closed by anonymous
fixed
16:02 Ticket #37 (Skateboard Shoes) reopened by diane
15:19 Ticket #37 (Skateboard Shoes) closed by diane
fixed: it magically went away.
14:13 Ticket #43 (After scrolling a sequence browser window, selection boxes break) created by diane
The selection box doesn't work correctly when you've scrolled the …
13:55 Ticket #42 (when resizing you should see more basepairs, not make them bigger.) created by diane
When resizing the window instead of "zooming" you should see more base …
13:48 Ticket #41 (Selection box jumps slightly to the right of the rubber band) created by diane
11:59 Ticket #40 (MussaAlignedWindow, left sequence position doesn't get initial value set) created by diane
The left sequence position indicator shows zero, when it should show …
00:55 Ticket #39 (sidebar rendering problems) created by diane
When there were more than 3 sequences the SequenceBrowserWidget's …
00:50 Ticket #4 (Aligned sequence view) closed by diane
fixed: [119] seems to at least basically work. I think the reverse …

03/19/2006:

16:13 Ticket #38 (Loading a new analysis while an alignment window was open causes segfault) closed by diane
fixed
16:13 Ticket #38 (Loading a new analysis while an alignment window was open causes segfault) created by diane
01:53 Ticket #37 (Skateboard Shoes) created by diane
Somewhere there's an off by one error that only affects the leftbase …
01:04 Ticket #36 (Make zoom widget make sense) closed by diane
fixed

03/18/2006:

01:02 Ticket #36 (Make zoom widget make sense) created by diane
The current calculation for the zoom widget is rather odd. It'd be …

03/17/2006:

17:11 Ticket #35 (Zoom Icon) closed by king
fixed: See changeset:111
16:49 Ticket #35 (Zoom Icon) created by king
Zoom icon for zoom spin box.
16:38 Ticket #34 (Unused variable 'max_range' in 'void ...) created by king
qui/seqbrowser/ScrollableSequenceBrowser.cpp: In member function ‘void …
16:34 Ticket #32 (The trac pages should become the main mussa website) closed by king
fixed: That should be good enough for now... closing ticket.
16:32 WikiStart edited by king
(diff)
16:31 WikiStart edited by king
(diff)
16:30 WikiStart edited by king
(diff)
16:28 WikiStart edited by king
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16:26 WikiStart edited by king
(diff)
16:26 WikiStart edited by king
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16:26 WikiStart edited by king
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16:25 WikiStart edited by king
(diff)
16:11 MussaFltk edited by king
(diff)
16:06 WikiStart edited by king
links to tickets. (diff)
16:03 WikiStart edited by king
(diff)
16:01 WikiStart edited by king
(diff)
15:56 WikiStart edited by king
(diff)
15:49 WikiStart edited by king
Adding documentation links. (diff)
15:46 MussaglBuild edited by king
(diff)
15:45 MussaglBuild created by king
Basic build information (needs work)
15:31 darcs edited by king
(diff)
15:29 darcs edited by king
directions for checking out a copy of mussagl from darcs repository. (diff)
15:11 darcs edited by king
creating darcs instructions (in progress) (diff)
15:07 darcs edited by king
(diff)
15:07 darcs created by king
15:02 WikiStart edited by king
(diff)
15:00 WikiStart edited by king
Adding download information (slowly) (diff)
14:54 WikiStart edited by king
(diff)
14:52 WikiStart edited by king
(diff)
14:48 WikiStart edited by king
(diff)
14:43 MussaFltk edited by king
Mussa C++/FLTK (diff)
14:39 MussaFltk created by king
14:36 WikiStart edited by king
(diff)
14:35 WikiStart edited by king
(diff)
14:34 WikiStart edited by king
(diff)
14:33 WikiStart edited by king
(diff)
14:29 MussaProtoype edited by king
(diff)
14:28 MussaProtoype edited by king
(diff)
14:26 MussaPrototypeCommandline edited by king
(diff)
14:26 MussaPrototypeCommandline created by king
14:24 MussaProtoype created by king
14:21 WikiStart edited by king
(diff)
14:19 WikiStart edited by king
(diff)
14:19 WikiStart edited by king
Info on mussa versions (diff)
13:49 WikiStart edited by king
cartwheel link (diff)
13:42 WikiStart edited by king
(diff)
13:41 transitivity edited by king
(diff)
13:41 4way_trans.png attached to transitivity by king
13:40 transitivity created by king
13:39 WikiStart edited by king
Porting useful information from old mussa website to trac wiki (easier … (diff)

03/16/2006:

23:26 Ticket #24 (Clean up the signals and slots) closed by diane
fixed: It could've been more refactored, but the API is fairly …
20:58 Ticket #33 (changing threshold can cause the UI to freeze) created by diane
For larger datasets, the length of time it takes to recompute the nway …
19:10 Ticket #32 (The trac pages should become the main mussa website) created by diane
The trac pages should become the main mussa page. Preferably with …
18:02 WikiStart edited by king
(diff)
18:01 OriginalTracStartPage created by king
Moving the trac start page out of the way.
18:01 WikiStart edited by king
(diff)
17:20 Ticket #31 (Threshold Widget should use spinboxes) created by diane
There are some weaknesses with the slider bar approach for the mussa …
15:19 Ticket #30 (Allow "leave one out" nway transitive searches) created by diane
It would be really useful if a path could still be drawn even if it …
15:18 Ticket #29 (Connect to Core Match) created by diane
Integrate tony's core match algorithm. (Hmm... might also want to …
11:14 Ticket #28 (Allow user to force a loaded sequence to be reverse complimented.) created by diane
When loading a sequence, it'd be nice to be able indicate that it …
11:02 Ticket #27 (Collect example sequences) created by diane
mck5 myogenin (stevens worm region) myf4/myf5 big region test case …
10:57 Ticket #26 (SubAnalysis mode) created by diane
Implement some form of subanalysis mode (last original mussa feature).
01:03 Ticket #25 (broke motif colors) closed by diane
fixed
00:46 Ticket #25 (broke motif colors) created by diane
00:39 Ticket #24 (Clean up the signals and slots) created by diane
I don't think I've set up the signals & slots for updating the various …
00:37 Ticket #3 (View descriptions) closed by diane
fixed: It works though the formatting isn't good, and the class hierarchy …
00:16 Ticket #23 (The threshold widget was broken too) closed by diane
fixed
00:16 Ticket #23 (The threshold widget was broken too) created by diane
The change to segment based drawing broke the threshold widget, as …
00:12 Ticket #22 (default size hint broken) closed by diane
fixed

03/15/2006:

19:25 Ticket #22 (default size hint broken) created by diane
When launching mussagl without any analysis, it doesn't pick a …
17:57 Ticket #16 (figure out how to get selections to work with new segment based drawing) closed by diane
fixed: Whenever I close a ticket I seem to immediately open a new one, …
17:50 Ticket #21 (Implement a better way of handling the GL selection buffer) created by diane
The current opengl selection code uses a hard coded buffer size, which …
14:08 Ticket #19 (I broke the scrollbar too) closed by diane
fixed: Calls to setLayout from within the QGLWidget derived class' …
12:02 Ticket #20 (Toggle Motif Button Implementation) created by king
Make motifs go away... we don't like them... well some times we do.
11:23 Ticket #19 (I broke the scrollbar too) created by diane
The new draw code also broke the scroll bar. And is there a chance to …
02:37 Ticket #18 (segments should indicate if they're both forward and reveresed) created by diane
a segment should track forward and reverse compliment separately, as …
02:09 Ticket #17 (Allow user to specify an offset for base pair location label) created by diane
In order to make it easer to map some random fasta file back to the …
02:00 Ticket #16 (figure out how to get selections to work with new segment based drawing) created by diane
Though the new segment based drawing is faster it does make selection …
01:58 Ticket #2 (Connection view) closed by diane
fixed

03/14/2006:

14:26 Ticket #15 (Unify build system) created by diane
It'd be nice if I didn't have to deal with both the qmake-qt4 derived …
00:16 Ticket #14 (Motifs need to be creatable and editable from within the GUI) created by diane
I hacked in loading motifs from a file, but there really should be …
00:11 Ticket #12 (modify motifs attached to an analysis) closed by diane
fixed: Splattering done. User interface missing.
00:10 Ticket #13 (AnnotationColor mapper needs a user interface) created by diane
One might imagine that users would actually like to edit colors by …
00:05 Ticket #1 (Annotation color mapper) closed by diane
fixed: The colors are tracked, but there's no UI. I'm going to close this …

03/13/2006:

18:03 Ticket #12 (modify motifs attached to an analysis) created by diane
There are many ways of going about this, ticket:10 for instance. …
17:54 Ticket #11 (create unifed sequence type) created by diane
There are many different types of things that we attach to a sequence, …
00:17 Ticket #10 (Integrate motifs with annotations) created by diane
The old code treated motifis and annotations differently. I think …

03/12/2006:

11:52 Ticket #9 (Connect to cartwheel) created by diane
Can we connect to cartwheel and be both a front end for cartwheel and …
11:50 Ticket #8 (Per species thresholds) created by diane
One requested feature was that one could set the threshold of …
11:49 Ticket #7 (Reuse seqcomps) created by diane
When running a batch of analysis mussa doesn't understand that its …
11:47 Ticket #6 (Analysis saving is smelly) created by diane
Analysis saving uses system calls to make a directory and splatter a …

03/11/2006:

23:47 Ticket #5 (Configure a mussa analysis from the Gui) created by diane
Need to be able to provide the sequence and parameters needed to run a …
23:46 Ticket #4 (Aligned sequence view) created by diane
In addition to the view showing the connections between different …
23:44 Ticket #3 (View descriptions) created by diane
Users should be able to see things describing a sequence track, like …
23:43 Ticket #2 (Connection view) created by diane
Provide a GL widget like thing that handles the linking of base pair …
23:40 Ticket #1 (Annotation color mapper) created by diane
We need some way of tracking the colors an annotation (and motifs) …
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