Timeline



10/27/2006:

18:57 Ticket #182 (Mussa views need vertical scrolls) closed by diane
fixed: [470] changes SequenceBrowserWidget to inherit from QScrollArea. the …
18:56 Ticket #233 (when first displaying mussa the tracks aren't sized to the available ...) closed by diane
fixed: [469] brute forces a sizeHint to make this work.
18:22 Ticket #235 (set version to 1.0 in version.h) created by diane
when releasing lets set the version number.
18:08 Ticket #213 (Document how to deselect tracks/paths) closed by king
fixed: Done in change set [467].
18:08 Ticket #170 (After implementing ticket:164, update 'Load Mupa' section to link to ...) closed by king
fixed: Done in change set [467].
17:58 Ticket #225 (Document mussagl command line option) closed by king
fixed: Done in change set [465].
17:56 Ticket #162 (Mussa manual: Update major new features section) closed by king
fixed
17:55 Ticket #168 (Mussa manual: Update Mac OS X install instructions) closed by king
fixed: Done in change set [466].
17:55 Ticket #214 (Document why sub-analysis exists) closed by king
fixed: Done in change set [466].
17:54 Ticket #234 (Document * in title when there are unsaved changes) created by king
See ticket:194.
17:53 Ticket #233 (when first displaying mussa the tracks aren't sized to the available ...) created by diane
little bits of the sequence is hidden by the sidebars for some unknown …
17:52 Ticket #232 (Document the report bp copied number.) created by king
See ticket #211 for more information.
17:50 Ticket #231 (Document copy and paste into motif editor now functional.) created by king
17:31 Ticket #137 (Document why Base pair match lines on the sequence view don't always ...) closed by king
fixed: Done in change set [465].
17:30 Ticket #227 (Document Python useage in Mussagl) closed by king
fixed: Done in change set [465].
17:30 Ticket #167 (Add an "Understanding Mussa" section to manual.) closed by king
fixed: Done in change set [465].
17:29 Ticket #164 (Include a section on creating a .mupa file using the smn1 data.) closed by king
fixed: Done in change set [465].
17:24 Ticket #178 (Update all screenshots to latest version of Mussa.) closed by king
fixed: Done
16:37 MussaglAnimated edited by king
(diff)
16:37 mussagl_animation_large.gif attached to MussaglAnimated by king
Mussagl threshold in action.
16:33 MussaglAnimated created by king
16:26 WikiStart edited by king
testing (diff)
16:24 mussagl_animation.gif attached to WikiStart by king
Mussagl in action.
15:37 Ticket #230 (shipit script should ship source distribution too.) created by diane
15:36 Ticket #229 (Package Everything for 1.0) created by diane
Include documentation and a source distribution.
14:22 Ticket #228 (Allow more vertical collapse of description widgets) created by diane
In order to cram more tracks on a screen, we might want to be allowed …
14:13 Ticket #217 (Use QtDesktopServices for openURL) closed by diane
fixed: Implemented in [464]. Also this means we dependon Qt 4.2, but loose …
11:00 Ticket #194 (use window feedback to show that there are unsaved changes) closed by diane
fixed: [463] implemented
10:48 WikiStart edited by king
Added some contact information. (diff)
10:44 Ticket #227 (Document Python useage in Mussagl) created by king
It might be useful to let people know there is some features for …
10:33 WikiStart edited by king
Try to include some contact information... js test. (diff)
10:17 Ticket #226 (QtTest is now a framework) created by diane
Need to update cmakes scripts to handle qt 4.2

10/26/2006:

16:13 Ticket #225 (Document mussagl command line option) created by king
It would be useful to document the Mussa command line options.
15:33 Ticket #215 (You should be able to paste into the motif editor) closed by diane
fixed: Resolved [461] (it was actually a problem with the copy always being a …
15:05 Ticket #224 (Define a common base class between MussaWindow and MussAlignedWindow) created by diane
I'm starting to duplicate code between the two classes like copying …
13:47 Ticket #211 (Report how many basepairs are copied) closed by diane
fixed: The basic version that reports the sum of base pairs copied was …
10:14 Ticket #223 (Set the Window Icon to be the Mussa icon) closed by king
fixed: Done in change set [459].
10:13 Ticket #223 (Set the Window Icon to be the Mussa icon) created by king
Mussa Window + Icon = Finding minimized Mussa easier.

10/25/2006:

17:12 Ticket #222 (Allow hyperlink annotations for CDS to PyMol rendering of protein structure) created by diane
Especially with highlighting where the chunk of dna shows up on protein.
15:30 Ticket #221 (Discover/document effect of ordering species on analysis run times.) created by king
Discover/document effect of ordering species on analysis run times.
14:00 Ticket #220 (mussa command line seems to be broken...) created by king
I have been trying to run mupa files from the command line, but it …

10/24/2006:

17:12 Ticket #219 (Reordering sequences in an analysis would be really nice) created by diane
Gee I wish I could click on a sequence track and drag it into a …
14:25 Ticket #207 (Reenable GUI tests) closed by diane
fixed
14:21 Ticket #218 (Qt4.2 has a platform independent way to place Ok/Cancel buttons in dialog) created by diane
One fo the neat new features of 4.2 was it had a way of putting …
13:47 Ticket #217 (Use QtDesktopServices for openURL) created by diane
Qt 4.2 has an openURL command

10/23/2006:

17:46 Ticket #216 (subanalysis doesn't call setSoftThreshold to after finishing analysis) closed by diane
fixed: fixed in [456]

10/20/2006:

17:51 Ticket #216 (subanalysis doesn't call setSoftThreshold to after finishing analysis) created by diane
So when you first look at a display it's not showing the lowest level …
17:11 Ticket #215 (You should be able to paste into the motif editor) created by king
17:07 Ticket #214 (Document why sub-analysis exists) created by king
Document the reason for sub-analysis. Meaning mention that you can run …
16:44 Ticket #213 (Document how to deselect tracks/paths) created by king
16:43 Ticket #212 (ESC key should by bound to 'deselect' current selection.) created by king
13:22 Ticket #211 (Report how many basepairs are copied) created by diane
The question is how to handle it when sequences on multiple tracks are …
13:20 Ticket #210 (see about removing some of the wasted border width on the sidebars) created by diane
13:19 Ticket #209 (Extend the command line parsing to allow fully specifying an analysis) created by diane
This would be useful so I could use make to more easily run/update …
13:17 Ticket #208 (the alg unittest executable needs to be broken up) created by diane
./alg/test/unittest is taking too long to run, I should probably split …
13:15 Ticket #207 (Reenable GUI tests) created by diane
For some reason some the Qt specific tests wouldn't build correctly on …
12:06 Ticket #206 (We need some way of indicating Ns) created by diane
perhaps narrowing the sequence track to show where Ns are would help?
11:40 Ticket #205 (Add button for autofitting sequence to window) created by diane
Brandon even reminded me that there's even code for it, we just need …
11:08 Ticket #204 (When you resize a mussa window, resize the drawing too.) created by diane
10:15 Ticket #203 (Unit test the code that generates all the mussa filename) created by diane
This will require pulling the naming code out into seperate functions …
00:27 Ticket #202 (Investigate SIP instead of boost::python) created by diane
The hope is that perhapis it'd be easier to export mussa classes to pyqt?
00:11 Ticket #201 (Run analyses in worker thread) created by diane
[108] depends on this. Allow at leas some actions to run in seperate …

10/19/2006:

18:38 Ticket #199 (After [451] I noticed that subanalyses didn't seem to have motif ...) closed by diane
fixed: [452] copies the motifs over to a subanalysis (after clearing) any …
18:37 Ticket #200 (Pushing the threshold change button too fast will cause mussa to crash) closed by diane
fixed: [453] is a good enough solution. Though I might someday want to use …
17:20 Ticket #163 (Motif loading doesn't work with release builds) closed by diane
fixed
17:20 Ticket #200 (Pushing the threshold change button too fast will cause mussa to crash) created by diane
the quick hack i can think of is to disable the widget while the …
16:35 Ticket #199 (After [451] I noticed that subanalyses didn't seem to have motif ...) created by diane
Actually it was even worse in that it had an odd spurious motif added …

10/18/2006:

18:04 Ticket #197 (the subanalysis when using the original mck example draws lines off ...) closed by diane
fixed: Fixed [450]
18:00 Ticket #198 (Document the multi add to sub-analysis feature.) created by king
Document the multi add to sub-analysis feature.
12:33 Ticket #197 (the subanalysis when using the original mck example draws lines off ...) created by diane
11:49 Ticket #196 (Motif editor: document how to delete a motif) closed by king
fixed: Done in changeset [447].
11:47 Ticket #196 (Motif editor: document how to delete a motif) created by king
Motif editor: document how to delete a motif
11:43 Ticket #195 (Disable motif and closing motif editor causes loss of motifs.) created by king
If you disable a motif and then close the motif editor and then reopen …
11:34 Ticket #179 (Add a section on "File > New Mussa Window" feature.) closed by king
fixed: Done in changeset [446].
11:09 Ticket #189 (Document "save on close" section after close of ticket:187) closed by king
fixed: Done in changeset [445].
11:09 Ticket #190 (Update 'save motifs' section after close of ticket #188.) closed by king
fixed: Done in changeset [445].
10:51 Ticket #194 (use window feedback to show that there are unsaved changes) created by king
Editing motif sets dirty flag, but does not include * in title of …
10:50 Ticket #193 (Changing a species name doesn't set dirty flag.) created by king
Changing a species name doesn't set dirty flag.

10/17/2006:

16:27 Ticket #192 (Steven can't save with mussa) closed by diane
fixed: [444] fixes this (and hopefully provides more robust exception …
15:00 Ticket #192 (Steven can't save with mussa) created by diane
I suspect something weird is happening when he tries to save to a …
13:42 Ticket #188 (Save motifs action does not append .mtl or .txt by default) closed by diane
fixed: [438]
12:07 Ticket #187 (Editing a motif does not set dirty flag.) closed by diane
fixed: [436] change add_motif to include dirty = false
12:06 Ticket #186 (Motif dialog on load existing motifs behavior needs update.) closed by diane
fixed
12:03 Ticket #191 (Update "Motif Dialog" section) closed by king
fixed: Done in changeset:435.
11:32 Ticket #191 (Update "Motif Dialog" section) created by king
Update "Motif Dialog" section to be up to date with both screenshots …
11:23 Ticket #175 (Document new 'save motifs' feature.) closed by king
fixed: Done in changeset:433.
11:23 Ticket #176 (Document 'Save Analysis' and 'Save Analysis As' features.) closed by king
fixed: Done in changeset:433.
11:21 Ticket #190 (Update 'save motifs' section after close of ticket #188.) created by king
Update 'save motifs' section after close of ticket #188.
11:19 Ticket #189 (Document "save on close" section after close of ticket:187) created by king
Document "save on close" section after close of ticket:187.
11:06 Ticket #188 (Save motifs action does not append .mtl or .txt by default) created by king
Save motifs action does not append .mtl or .txt by default. If the …
10:43 Ticket #187 (Editing a motif does not set dirty flag.) created by king
Upon editing or adding a new motif, the analysis isn't marked as being …
10:41 Ticket #186 (Motif dialog on load existing motifs behavior needs update.) created by king
When you load an analysis that has saved motifs, say 3 of them, then …
10:32 Ticket #181 (Update 'Load a mussa parameter file' section) closed by king
fixed: Done as of changeset:432.
10:31 Ticket #185 (Update "Load an analysis" section (text/screenshots)) closed by king
fixed: Done as of changeset:432.
10:31 Ticket #169 (Update "New Analysis" section as the Dialog box has changed.) closed by king
fixed: Done as of changeset:432.
10:27 Ticket #185 (Update "Load an analysis" section (text/screenshots)) created by king
Update "Load an analysis" section (text/screenshots)

10/16/2006:

23:57 Ticket #180 (shipit script on os x needs to validate the archive) closed by diane
fixed: [429] provides the more thorough osxdist.py script. At some point its …
23:56 Ticket #184 (Dont link against X11 on OS X) closed by diane
fixed: Fixed [428] Though why did the USE_QT stuff add in X11 in the python …
23:55 Ticket #184 (Dont link against X11 on OS X) created by diane
23:54 Ticket #183 (Seqcomp is case sensitive) closed by diane
fixed: Fixed in [430]
23:49 Ticket #183 (Seqcomp is case sensitive) created by diane
If you load a sequences of different case they seqcomp won't work …
23:02 Ticket #182 (Mussa views need vertical scrolls) created by diane
So if you're comparing enough sequences mussa will run out of vertical …
16:39 Ticket #181 (Update 'Load a mussa parameter file' section) created by king
The 'Load a mussa parameter file' section is out of date. Both the …
13:50 Ticket #180 (shipit script on os x needs to validate the archive) created by diane
Make sure that there's no references to "/usr/local" or X11 libraries.
12:04 Ticket #179 (Add a section on "File > New Mussa Window" feature.) created by king
Add a section on "File > New Mussa Window" feature.
12:02 Ticket #178 (Update all screenshots to latest version of Mussa.) created by king
Update all screenshots to latest version of Mussa, since we are ready …
11:59 Ticket #171 (Remove the "Motif Toggle" button from manual.) closed by king
fixed: Completed in changeset:427.
11:58 Ticket #173 (Update "Sequence Information Bar" section, as it has changed in latest ...) closed by king
fixed: Completed in changeset:427.
11:58 Ticket #172 (Update "Dynamic Threshold" section as the widget has changed.) closed by king
fixed: Completed in changeset:427.
11:58 Ticket #166 (Update Mussa summary screenshot to latest version) closed by king
fixed: Completed in changeset:427.
11:21 Ticket #177 (Confirm description of blue conservation tracks is correct.) created by king
Confirm description of blue conservation tracks is correct and improve …
10:43 Ticket #176 (Document 'Save Analysis' and 'Save Analysis As' features.) created by king
Document 'Save Analysis' and 'Save Analysis As' features.
10:42 Ticket #175 (Document new 'save motifs' feature.) created by king
Document new 'save motifs' feature.
10:40 Ticket #174 (Confirm file formats are documented and correct.) created by king
Confirm file formats are documented and correct.
10:39 Ticket #173 (Update "Sequence Information Bar" section, as it has changed in latest ...) created by king
Update "Sequence Information Bar" section, as it has changed in latest …
10:38 Ticket #172 (Update "Dynamic Threshold" section as the widget has changed.) created by king
Update "Dynamic Threshold" section as the widget has changed.
10:37 Ticket #171 (Remove the "Motif Toggle" button from manual.) created by king
Remove the "Motif Toggle" button from manual as it has been removed …
10:35 Ticket #170 (After implementing ticket:164, update 'Load Mupa' section to link to ...) created by king
After implementing ticket:164, update 'Load Mupa' section to link to …
10:33 Ticket #169 (Update "New Analysis" section as the Dialog box has changed.) created by king
Update "New Analysis" section as the Dialog box has changed.
10:26 Ticket #168 (Mussa manual: Update Mac OS X install instructions) created by king
10:25 Ticket #167 (Add an "Understanding Mussa" section to manual.) created by king
When ever there is a confusing or interesting detail one should know …
10:13 Ticket #166 (Update Mussa summary screenshot to latest version) created by king
Update Mussa summary screenshot to latest version.
10:09 Ticket #161 (Add link to smn1 example data (since the UCSC tutorial is based on it)) closed by king
fixed: Added in changeset:426.
10:03 Ticket #157 (Mussa manual: document 'save to image' feature) closed by king
fixed: Added in changeset:425.
10:01 Ticket #165 (Include a section on creating a motif list file using the smn1 data.) created by king
Include a section on creating a motif list file using the smn1 data.
10:01 Ticket #164 (Include a section on creating a .mupa file using the smn1 data.) created by king
Include a section on creating a .mupa file using the smn1 data.

10/15/2006:

13:35 MussaglBuild edited by diane
(diff)

10/13/2006:

18:53 Milestone Few Small Repairs completed
(Ok so it was more than a few small repairs) This was to implement …
18:51 Ticket #150 (Example data for 1.0 release) closed by diane
fixed
18:26 Ticket #163 (Motif loading doesn't work with release builds) created by diane
For some reason motifs aren't loading any more.
18:15 Ticket #156 (Mussa manual - meta ticket) closed by king
invalid: No longer needed since we have a new milestone for 1.0 documentation.
18:14 Ticket #162 (Mussa manual: Update major new features section) created by king
Mussa manual: Update major new features section
18:13 Ticket #161 (Add link to smn1 example data (since the UCSC tutorial is based on it)) created by king
Add link to smn1 example data (since the UCSC tutorial is based on it)
18:09 Ticket #151 (Crash is possible when creating a subanalysis smaller than the window) closed by diane
fixed
17:33 Ticket #160 (error: default argument for parameter of type ‘MussaRef’ has type ‘int’) closed by king
fixed: Fixed by changeset:422.
17:30 Ticket #160 (error: default argument for parameter of type ‘MussaRef’ has type ‘int’) created by king
Mussa refused to build in Ubuntu with gcc 4.0.3. Error: […] gcc …
17:27 Ticket #153 (Allow users to specify the file load file mask) closed by king
fixed: Closed by changeset:422
17:24 Ticket #159 (Create track macro to display changelog with build numbers) created by king
The change log is too long to display in the Manual. The Manual should …
17:14 Ticket #131 (When closing an analysis window, cancel doesn't prevent the close) closed by diane
worksforme: At least on OS X and Linux there are no problems, perhaps windows has …
16:53 Ticket #158 (When unable to parse a fasta file report its name) created by diane
It would also be useful to report what characters it failed on.
16:44 OverlappingWindows edited by diane
(diff)
16:44 OverlappingWindows edited by diane
(diff)
16:42 OverlappingWindows edited by diane
(diff)
16:35 sequence_alignment_far.png attached to OverlappingWindows by diane
far away second window
16:34 sequence_alignment_close.png attached to OverlappingWindows by diane
close windows
16:34 OverlappingWindows edited by diane
(diff)
16:22 overlapping_windows.zip attached to OverlappingWindows by diane
Example data to illustrate how a distant match can be confusing
16:22 OverlappingWindows created by diane
16:13 Ticket #157 (Mussa manual: document 'save to image' feature) created by king
Mussa manual needs the 'save to image' feature documented.
16:08 Ticket #156 (Mussa manual - meta ticket) created by king
Tasks for updating Mussa Manual: * #137 * #152 * #153 * #157
15:17 Ticket #96 (Save to image broken) closed by king
fixed: Fixed by changeset:419.
13:51 Ticket #49 (QAssistant Mussa Docs) closed by diane
fixed: Brandon has been working on a tutorial. It's not done, but since we …
13:49 Ticket #155 (Include a simple repeat filter) created by diane
It would be nice if mussa had an option to perform some type of repeat …

10/12/2006:

22:54 Ticket #133 (Should be able to save motifs) closed by diane
fixed: Patche [404] added the lowest level save motif code [408] connected …
22:23 Ticket #154 (off by one error when drawing segments) closed by diane
fixed: [411] fixed it (and widened the glyphs a little)
22:22 Ticket #154 (off by one error when drawing segments) created by diane
I think [397] introduced an error where line segments were being drawn …
16:00 Ticket #120 (Windows doesn't have python installed by default) closed by diane
fixed
15:48 Ticket #153 (Allow users to specify the file load file mask) created by diane
Currently its somewhat mysterious what file masks we allow for mussa …
15:18 Ticket #152 (Update mussa_manual.adp to latest tutorial version) created by king
The QtAssistant .adp file for the mussa_manual needs to be updated to …
02:04 Ticket #151 (Crash is possible when creating a subanalysis smaller than the window) created by diane

10/11/2006:

16:15 Ticket #150 (Example data for 1.0 release) created by diane
After talking to Barbara, since our release is timed with Libera's …
15:57 Ticket #149 (Handle " in motif names) closed by diane
fixed: [405] adds validation code to prevent users from entering bad data.
15:56 Ticket #126 (Figure out how to get the spirit parsers to report parse errors) closed by diane
fixed: [403] fixes this. Admittedly my count variable in my functor structs …
14:41 Ticket #149 (Handle " in motif names) created by diane
I need to do something with " in a motif name, as if its left in it'll …

10/10/2006:

17:55 Ticket #148 (setup_analysis dialog should make sure that the threshold is not ...) closed by diane
fixed: fixed by [402] by using spinboxes instead of qlineedits.
17:16 ExampleData edited by king
(diff)
17:16 ExampleData edited by king
(diff)
17:15 smn1_example_data_v1_0_1.zip attached to ExampleData by king
Removed html formatting that snuck into the files.
17:09 Ticket #147 (Sometimes the width of a quadrallateral is too small) closed by diane
fixed: [400] fixed this. yay pixel width computations.
16:35 Ticket #146 (Win32: Create new analysis mystery crash) closed by king
fixed: Surprisingly, changeset:398 fixed this problem... Apparently the motif …
16:29 Ticket #148 (setup_analysis dialog should make sure that the threshold is not ...) created by diane
16:25 Ticket #139 (Edit motif window looses motif information when closed) closed by diane
fixed: fixed [399]
15:46 Ticket #147 (Sometimes the width of a quadrallateral is too small) created by diane
On some larger views the quads used for when widths are greater than 1 …
15:45 Ticket #134 (Width of seqcomp match line is wrong) closed by diane
fixed: [397] uses line drawing code when the length of a segment is <= 1.
15:43 Ticket #144 (IUPAC codes are destroyed by the sequence normalization code) closed by diane
fixed: [398] added general sequence alphabet handling. (Using a subset of …
13:33 ExampleData edited by king
(diff)
13:32 ExampleData edited by king
(diff)
13:27 ExampleData edited by king
(diff)
13:27 ExampleData edited by king
(diff)
13:26 ExampleData edited by king
(diff)

10/06/2006:

16:53 ExampleData edited by king
(diff)
16:52 ExampleData edited by king
(diff)
16:44 ExampleData edited by king
Link to information about SMN1 & SMN2 at OMIM. (diff)
15:27 Ticket #146 (Win32: Create new analysis mystery crash) created by king
I discovered that when you create a new analysis with Mussa in windows …
10:46 ExampleData edited by king
(diff)
10:44 ExampleData edited by king
(diff)
10:41 ExampleData edited by king
Added zip of example data. (diff)
10:39 smn1_example_data_v1_0.zip attached to ExampleData by king
SMN1 example data v1.0
10:38 ExampleData created by king
Adding smn1 example data
10:10 WikiStart edited by king
Adding a page for posting example data. (diff)

10/05/2006:

00:50 Ticket #103 (Motifs need a name field) closed by diane
fixed: I think this works now. Motifs are sequences, and the name is set. …

10/04/2006:

15:20 Ticket #10 (Integrate motifs with annotations) closed by diane
duplicate: The move to turn motifs and annotations into specializations of …
15:11 Ticket #145 (Use titus' paircomp and motility) created by diane
One of my concerns is how to pull his code into mussa in a way that is …
15:02 Ticket #143 (add command line option to annotate an analysis with a motif file.) closed by diane
fixed: [395] added the command line option.
10:09 Ticket #144 (IUPAC codes are destroyed by the sequence normalization code) created by diane
when searching for a motif the sequence class feeds things through a …

10/03/2006:

18:17 Ticket #142 (It'd be really useful to trigger a subanalysis from an aligned ...) closed by diane
fixed: [388] implements this.
18:17 Ticket #140 (Load Motifs doesn't do anything) closed by diane
fixed: [394] and [393] fix this. The parser wasn't working and then the …
18:16 Ticket #138 (Sequence view window needs a title) closed by diane
fixed: [391] implements this and also fills in the other window titles.
15:19 Ticket #143 (add command line option to annotate an analysis with a motif file.) created by diane
since you can load an analysis and create a new analysis from the …

10/02/2006:

14:56 Ticket #142 (It'd be really useful to trigger a subanalysis from an aligned ...) created by diane
14:55 Ticket #141 (Vector output) created by diane
It'd be really nice if we could generate vector output, both for …
14:54 Ticket #140 (Load Motifs doesn't do anything) created by diane
It appears that the Load Motif menu option either doesn't load motifs …
14:46 Ticket #139 (Edit motif window looses motif information when closed) created by diane
It really should reload the motif information from the analysis when …

09/29/2006:

13:46 Ticket #138 (Sequence view window needs a title) created by diane

09/28/2006:

18:05 Ticket #122 (Motif editor needs to support more than 10 motifs) closed by diane
fixed
Note: See TracTimeline for information about the timeline view.