Timeline



04/18/2006:

19:38 Ticket #91 (quits) created by ghernand@…
greetings! mussagl quits when one red line is selected and you choose …

04/13/2006:

13:02 Ticket #83 (Mussa should complain about misformatted fasta files instead of crashing.) closed by diane
fixed: [180] fixes this

04/12/2006:

16:29 Ticket #64 (Occasionally ConservedPath crashes) closed by diane
fixed: I'm going to optimistcally assume that ticket:89 was a reliable way to …
16:28 Ticket #85 (mussagl quits, just like i will AGAIN soon.) closed by diane
fixed: [178] fixes this.
13:14 Ticket #90 (the arrow keys aren't connected to the scrollbar) created by ghernand@…
a small detail first. the arrows (left-right) on the bottom of the …

04/11/2006:

18:01 Ticket #15 (Unify build system) closed by diane
fixed
15:55 Ticket #89 (Blast to find mussa regions) created by diane
its unclear if this is a good idea or not, but it might be …
14:03 Ticket #88 (Find titus' paper on FR versus the bacterial genomes) created by diane
They had some conclusion about different models of evolution for the …
13:54 Ticket #87 (Autodetect threshold) created by diane
It might be useful to autodetect a reasonable threshold…
11:21 Ticket #86 (Progresss bar) created by diane
Some tasks take a long time to run, so we really should give some hint …
11:12 Ticket #85 (mussagl quits, just like i will AGAIN soon.) created by ghernand@…
once the three way screen shot is active, if i try to click on the up …
00:47 Ticket #84 (The analysis title should report what file you loaded) created by diane

04/10/2006:

15:56 MussaglBuild edited by diane
(diff)
15:53 MussaglBuild edited by diane
(diff)

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
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