Timeline
10/27/2006:
- 18:57 Ticket #182 (Mussa views need vertical scrolls) closed by
- 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
- fixed: [469] brute forces a sizeHint to make this work.
- 18:22 Ticket #235 (set version to 1.0 in version.h) created by
- when releasing lets set the version number.
- 18:08 Ticket #213 (Document how to deselect tracks/paths) closed by
- fixed: Done in change set [467].
- 18:08 Ticket #170 (After implementing ticket:164, update 'Load Mupa' section to link to ...) closed by
- fixed: Done in change set [467].
- 17:58 Ticket #225 (Document mussagl command line option) closed by
- fixed: Done in change set [465].
- 17:56 Ticket #162 (Mussa manual: Update major new features section) closed by
- fixed
- 17:55 Ticket #168 (Mussa manual: Update Mac OS X install instructions) closed by
- fixed: Done in change set [466].
- 17:55 Ticket #214 (Document why sub-analysis exists) closed by
- fixed: Done in change set [466].
- 17:54 Ticket #234 (Document * in title when there are unsaved changes) created by
- See ticket:194.
- 17:53 Ticket #233 (when first displaying mussa the tracks aren't sized to the available ...) created by
- 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
- See ticket #211 for more information.
- 17:50 Ticket #231 (Document copy and paste into motif editor now functional.) created by
- 17:31 Ticket #137 (Document why Base pair match lines on the sequence view don't always ...) closed by
- fixed: Done in change set [465].
- 17:30 Ticket #227 (Document Python useage in Mussagl) closed by
- fixed: Done in change set [465].
- 17:30 Ticket #167 (Add an "Understanding Mussa" section to manual.) closed by
- fixed: Done in change set [465].
- 17:29 Ticket #164 (Include a section on creating a .mupa file using the smn1 data.) closed by
- fixed: Done in change set [465].
- 17:24 Ticket #178 (Update all screenshots to latest version of Mussa.) closed by
- fixed: Done
- 16:37 MussaglAnimated edited by
- (diff)
- 16:33 MussaglAnimated created by
- 16:26 WikiStart edited by
- testing (diff)
- 15:37 Ticket #230 (shipit script should ship source distribution too.) created by
- 15:36 Ticket #229 (Package Everything for 1.0) created by
- Include documentation and a source distribution.
- 14:22 Ticket #228 (Allow more vertical collapse of description widgets) created by
- 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
- 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
- fixed: [463] implemented
- 10:48 WikiStart edited by
- Added some contact information. (diff)
- 10:44 Ticket #227 (Document Python useage in Mussagl) created by
- It might be useful to let people know there is some features for …
- 10:33 WikiStart edited by
- Try to include some contact information... js test. (diff)
- 10:17 Ticket #226 (QtTest is now a framework) created by
- Need to update cmakes scripts to handle qt 4.2
10/26/2006:
- 16:13 Ticket #225 (Document mussagl command line option) created by
- 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
- 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
- I'm starting to duplicate code between the two classes like copying …
- 13:47 Ticket #211 (Report how many basepairs are copied) closed by
- 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
- fixed: Done in change set [459].
- 10:13 Ticket #223 (Set the Window Icon to be the Mussa icon) created by
- 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
- 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
- Discover/document effect of ordering species on analysis run times.
- 14:00 Ticket #220 (mussa command line seems to be broken...) created by
- 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
- Gee I wish I could click on a sequence track and drag it into a …
- 14:25 Ticket #207 (Reenable GUI tests) closed by
- fixed
- 14:21 Ticket #218 (Qt4.2 has a platform independent way to place Ok/Cancel buttons in dialog) created by
- 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
- 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
- fixed: fixed in [456]
10/20/2006:
- 17:51 Ticket #216 (subanalysis doesn't call setSoftThreshold to after finishing analysis) created by
- 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
- 17:07 Ticket #214 (Document why sub-analysis exists) created by
- Document the reason for sub-analysis. Meaning mention that you can run …
- 16:44 Ticket #213 (Document how to deselect tracks/paths) created by
- 16:43 Ticket #212 (ESC key should by bound to 'deselect' current selection.) created by
- 13:22 Ticket #211 (Report how many basepairs are copied) created by
- 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
- 13:19 Ticket #209 (Extend the command line parsing to allow fully specifying an analysis) created by
- 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
- ./alg/test/unittest is taking too long to run, I should probably split …
- 13:15 Ticket #207 (Reenable GUI tests) created by
- 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
- 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
- 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
- 10:15 Ticket #203 (Unit test the code that generates all the mussa filename) created by
- This will require pulling the naming code out into seperate functions …
- 00:27 Ticket #202 (Investigate SIP instead of boost::python) created by
- 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
- [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
- 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
- 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
- fixed
- 17:20 Ticket #200 (Pushing the threshold change button too fast will cause mussa to crash) created by
- 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
- 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
- fixed: Fixed [450]
- 18:00 Ticket #198 (Document the multi add to sub-analysis feature.) created by
- 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
- 11:49 Ticket #196 (Motif editor: document how to delete a motif) closed by
- fixed: Done in changeset [447].
- 11:47 Ticket #196 (Motif editor: document how to delete a motif) created by
- Motif editor: document how to delete a motif
- 11:43 Ticket #195 (Disable motif and closing motif editor causes loss of motifs.) created by
- 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
- fixed: Done in changeset [446].
- 11:09 Ticket #189 (Document "save on close" section after close of ticket:187) closed by
- fixed: Done in changeset [445].
- 11:09 Ticket #190 (Update 'save motifs' section after close of ticket #188.) closed by
- fixed: Done in changeset [445].
- 10:51 Ticket #194 (use window feedback to show that there are unsaved changes) created by
- 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
- Changing a species name doesn't set dirty flag.
10/17/2006:
- 16:27 Ticket #192 (Steven can't save with mussa) closed by
- fixed: [444] fixes this (and hopefully provides more robust exception …
- 15:00 Ticket #192 (Steven can't save with mussa) created by
- 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
- fixed: [438]
- 12:07 Ticket #187 (Editing a motif does not set dirty flag.) closed by
- fixed: [436] change add_motif to include dirty = false
- 12:06 Ticket #186 (Motif dialog on load existing motifs behavior needs update.) closed by
- fixed
- 12:03 Ticket #191 (Update "Motif Dialog" section) closed by
- fixed: Done in changeset:435.
- 11:32 Ticket #191 (Update "Motif Dialog" section) created by
- Update "Motif Dialog" section to be up to date with both screenshots …
- 11:23 Ticket #175 (Document new 'save motifs' feature.) closed by
- fixed: Done in changeset:433.
- 11:23 Ticket #176 (Document 'Save Analysis' and 'Save Analysis As' features.) closed by
- fixed: Done in changeset:433.
- 11:21 Ticket #190 (Update 'save motifs' section after close of ticket #188.) created by
- 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
- 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
- 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
- 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
- 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
- fixed: Done as of changeset:432.
- 10:31 Ticket #185 (Update "Load an analysis" section (text/screenshots)) closed by
- fixed: Done as of changeset:432.
- 10:31 Ticket #169 (Update "New Analysis" section as the Dialog box has changed.) closed by
- fixed: Done as of changeset:432.
- 10:27 Ticket #185 (Update "Load an analysis" section (text/screenshots)) created by
- 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
- 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
- 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
- 23:54 Ticket #183 (Seqcomp is case sensitive) closed by
- fixed: Fixed in [430]
- 23:49 Ticket #183 (Seqcomp is case sensitive) created by
- If you load a sequences of different case they seqcomp won't work …
- 23:02 Ticket #182 (Mussa views need vertical scrolls) created by
- 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
- 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
- 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
- Add a section on "File > New Mussa Window" feature.
- 12:02 Ticket #178 (Update all screenshots to latest version of Mussa.) created by
- 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
- fixed: Completed in changeset:427.
- 11:58 Ticket #173 (Update "Sequence Information Bar" section, as it has changed in latest ...) closed by
- fixed: Completed in changeset:427.
- 11:58 Ticket #172 (Update "Dynamic Threshold" section as the widget has changed.) closed by
- fixed: Completed in changeset:427.
- 11:58 Ticket #166 (Update Mussa summary screenshot to latest version) closed by
- fixed: Completed in changeset:427.
- 11:21 Ticket #177 (Confirm description of blue conservation tracks is correct.) created by
- Confirm description of blue conservation tracks is correct and improve …
- 10:43 Ticket #176 (Document 'Save Analysis' and 'Save Analysis As' features.) created by
- Document 'Save Analysis' and 'Save Analysis As' features.
- 10:42 Ticket #175 (Document new 'save motifs' feature.) created by
- Document new 'save motifs' feature.
- 10:40 Ticket #174 (Confirm file formats are documented and correct.) created by
- Confirm file formats are documented and correct.
- 10:39 Ticket #173 (Update "Sequence Information Bar" section, as it has changed in latest ...) created by
- 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
- Update "Dynamic Threshold" section as the widget has changed.
- 10:37 Ticket #171 (Remove the "Motif Toggle" button from manual.) created by
- 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
- 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
- Update "New Analysis" section as the Dialog box has changed.
- 10:26 Ticket #168 (Mussa manual: Update Mac OS X install instructions) created by
- 10:25 Ticket #167 (Add an "Understanding Mussa" section to manual.) created by
- 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
- 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
- fixed: Added in changeset:426.
- 10:03 Ticket #157 (Mussa manual: document 'save to image' feature) closed by
- fixed: Added in changeset:425.
- 10:01 Ticket #165 (Include a section on creating a motif list file using the smn1 data.) created by
- 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
- Include a section on creating a .mupa file using the smn1 data.
10/15/2006:
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
- fixed
- 18:26 Ticket #163 (Motif loading doesn't work with release builds) created by
- For some reason motifs aren't loading any more.
- 18:15 Ticket #156 (Mussa manual - meta ticket) closed by
- 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
- 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
- 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
- fixed
- 17:33 Ticket #160 (error: default argument for parameter of type ‘MussaRef’ has type ‘int’) closed by
- fixed: Fixed by changeset:422.
- 17:30 Ticket #160 (error: default argument for parameter of type ‘MussaRef’ has type ‘int’) created by
- 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
- fixed: Closed by changeset:422
- 17:24 Ticket #159 (Create track macro to display changelog with build numbers) created by
- 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
- 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
- It would also be useful to report what characters it failed on.
- 16:44 OverlappingWindows edited by
- (diff)
- 16:44 OverlappingWindows edited by
- (diff)
- 16:42 OverlappingWindows edited by
- (diff)
- 16:34 OverlappingWindows edited by
- (diff)
- 16:22 OverlappingWindows created by
- 16:13 Ticket #157 (Mussa manual: document 'save to image' feature) created by
- Mussa manual needs the 'save to image' feature documented.
- 16:08 Ticket #156 (Mussa manual - meta ticket) created by
- Tasks for updating Mussa Manual: * #137 * #152 * #153 * #157
- 15:17 Ticket #96 (Save to image broken) closed by
- fixed: Fixed by changeset:419.
- 13:51 Ticket #49 (QAssistant Mussa Docs) closed by
- 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
- 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
- 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
- fixed: [411] fixed it (and widened the glyphs a little)
- 22:22 Ticket #154 (off by one error when drawing segments) created by
- 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
- fixed
- 15:48 Ticket #153 (Allow users to specify the file load file mask) created by
- 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
- 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
10/11/2006:
- 16:15 Ticket #150 (Example data for 1.0 release) created by
- After talking to Barbara, since our release is timed with Libera's …
- 15:57 Ticket #149 (Handle " in motif names) closed by
- 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
- fixed: [403] fixes this. Admittedly my count variable in my functor structs …
- 14:41 Ticket #149 (Handle " in motif names) created by
- 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
- fixed: fixed by [402] by using spinboxes instead of qlineedits.
- 17:16 ExampleData edited by
- (diff)
- 17:16 ExampleData edited by
- (diff)
- 17:09 Ticket #147 (Sometimes the width of a quadrallateral is too small) closed by
- fixed: [400] fixed this. yay pixel width computations.
- 16:35 Ticket #146 (Win32: Create new analysis mystery crash) closed by
- 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
- 16:25 Ticket #139 (Edit motif window looses motif information when closed) closed by
- fixed: fixed [399]
- 15:46 Ticket #147 (Sometimes the width of a quadrallateral is too small) created by
- 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
- 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
- fixed: [398] added general sequence alphabet handling. (Using a subset of …
- 13:33 ExampleData edited by
- (diff)
- 13:32 ExampleData edited by
- (diff)
- 13:27 ExampleData edited by
- (diff)
- 13:27 ExampleData edited by
- (diff)
- 13:26 ExampleData edited by
- (diff)
10/06/2006:
- 16:53 ExampleData edited by
- (diff)
- 16:52 ExampleData edited by
- (diff)
- 16:44 ExampleData edited by
- Link to information about SMN1 & SMN2 at OMIM. (diff)
- 15:27 Ticket #146 (Win32: Create new analysis mystery crash) created by
- I discovered that when you create a new analysis with Mussa in windows …
- 10:46 ExampleData edited by
- (diff)
- 10:44 ExampleData edited by
- (diff)
- 10:41 ExampleData edited by
- Added zip of example data. (diff)
- 10:38 ExampleData created by
- Adding smn1 example data
- 10:10 WikiStart edited by
- Adding a page for posting example data. (diff)
10/05/2006:
- 00:50 Ticket #103 (Motifs need a name field) closed by
- 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
- duplicate: The move to turn motifs and annotations into specializations of …
- 15:11 Ticket #145 (Use titus' paircomp and motility) created by
- 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
- fixed: [395] added the command line option.
- 10:09 Ticket #144 (IUPAC codes are destroyed by the sequence normalization code) created by
- 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
- fixed: [388] implements this.
- 18:17 Ticket #140 (Load Motifs doesn't do anything) closed by
- 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
- 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
- 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
- 14:55 Ticket #141 (Vector output) created by
- 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
- 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
- It really should reload the motif information from the analysis when …
09/29/2006:
09/28/2006:
Note:
See TracTimeline
for information about the timeline view.
