Timeline



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The 'Load a mussa parameter file' section is out of date.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

09/27/2006:

17:38 Ticket #137 (Document why Base pair match lines on the sequence view don't always ...) created by diane
in cases where there's a match between the first and second sequence …
00:22 Ticket #136 (allow absolute positioning) created by diane
I think i can allow absolute positioning if I made the "location" base …

09/25/2006:

10:14 Ticket #135 (Win32: Save as not working... causes crash.) closed by king
fixed: Fixed in changeset:381. boost::filesystem needed to be told to use …

09/22/2006:

16:30 Ticket #135 (Win32: Save as not working... causes crash.) created by king
On windows the Save As feature causes a crash.

09/21/2006:

14:26 Ticket #134 (Width of seqcomp match line is wrong) created by diane
It might be useful if the seqcomp match lines being drawn were …
13:23 OSXUniversalDependencies edited by diane
(diff)

09/19/2006:

16:49 Ticket #133 (Should be able to save motifs) created by diane
It looks like the best path is that when saving an analysis it'll also …

09/18/2006:

16:24 Ticket #125 (autodetect if python needs -lutil) closed by diane
fixed: Fixed with [375] and [376] Pretty nice of distutils to provide a way …
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