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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 …

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 …

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 …

18:05 Ticket #122 (Motif editor needs to support more than 10 motifs) closed by diane: fixed

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 …

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 …

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

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)

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 …

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 …

17:14 Ticket #105 (Load Analysis should spawn a new window) closed by diane: fixed: Technically the create from mupa file should open a new window too, …
17:09 Ticket #132 (Make open saved analysis open a new window) closed by diane: duplicate: duplicate of ticket:105
17:02 Ticket #132 (Make open saved analysis open a new window) created by diane: I can make open saved analysis open a new window if the window isn't …
15:55 Ticket #131 (When closing an analysis window, cancel doesn't prevent the close) created by diane: Brandon tried to close a subanalysis window that hadn't been saved. It …
15:34 Ticket #130 (Save is relative to the current directory) closed by diane: fixed: implemented [370] though I started [372] because I forgot that I'd …
11:52 Ticket #130 (Save is relative to the current directory) created by diane: Mussa doesn't save the path it was loaded from, so when save a …
11:11 Ticket #129 (Subseq doesn't support trees correctly) closed by diane: fixed: Implemented [367]

17:47 Ticket #129 (Subseq doesn't support trees correctly) created by diane: Currently subseq's start/count is always relative to the seq_string, …
14:12 Ticket #127 (The sidebar layout isn't right after loading a second analysis into ...) closed by diane: fixed: fixed in [363]
13:12 Ticket #128 (the editable sequence name only shows the end of long names.) closed by diane: fixed: fixed [362] ( I think I spent more time on bug tracking than bug …
13:06 Ticket #128 (the editable sequence name only shows the end of long names.) created by diane: Not terribly important but a long name like "tetraodon" only shows the …
13:05 Ticket #127 (The sidebar layout isn't right after loading a second analysis into ...) created by diane: The layout doesn't put the first description block at the very top …

18:38 Ticket #126 (Figure out how to get the spirit parsers to report parse errors) created by diane: The annotation parser and the motif parser are now both using the …
18:36 Ticket #116 (Perhaps the motif file should have a name field.) closed by diane: fixed: implmented in [361] with the caveat that my spirit parsers don't throw …
15:52 Ticket #73 (Performance problems doing analysis) closed by diane: invalid: This ticket was mostly gathering information about what influences …
15:36 Ticket #125 (autodetect if python needs -lutil) created by diane: On Fedora core the version of python requires being linked with …
15:35 Ticket #124 (report patch version) created by diane: Brandon suggested that it'd be useful for mussa to have some version …
15:33 Ticket #123 (Allow hiding sidebars) created by diane: Tristan complained briefly about the sidebars taking up too much …

18:21 Ticket #101 (On windows, the file browse button doesn't remember the previous path) closed by diane: fixed: Actually this applied to the os x (and probably linux) versions as …
17:31 Ticket #122 (Motif editor needs to support more than 10 motifs) created by diane: I really should be using one of the Qt MVC classes to let the number …
17:13 Ticket #107 (Motifs don't show up on the Mussa Aligned Sequence window anymore.) closed by diane: worksforme: I'm going to pretend this is working at the moment. If someone …
17:11 Ticket #27 (Collect example sequences) closed by diane: fixed: i've got lots of example sequence now... I don't think this is …
17:10 Ticket #114 (Location analyses are saved to is ill-defined on OS X.) closed by diane: fixed: [358] sets the default save as directory to the users home directory, …
16:57 Ticket #119 (Add dependencies to MussaglBuild page) closed by diane: fixed: I think I've added the current set of dependencies.

22:13 Ticket #121 (the load_mupa function choaks when given something other than a file) closed by diane: fixed: Fixed in [352]
17:01 Ticket #121 (the load_mupa function choaks when given something other than a file) created by diane: The load_mussa code hangs when you run mussa --run <directoy name>.

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