ticket summary component version milestone type owner status created _changetime _description _reporter 81 Storing and searching metadata Qt Gui from __future__ import magic enhancement diane new 2006-04-06T12:06:32-07:00 2006-10-13T13:47:49-07:00 "It'd be really really nice if there was some way that a person could add notes (or perhaps a more controlled ontology of meta-data) to an analysis that was then searchable. Ali suggested that a mussa installation would have some database storing the metadata. I recommended that the metadata be stored in the analysis results but that the application would maintain an index of it." diane 30 "Allow ""leave one out"" nway transitive searches" core release_1.2 enhancement diane new 2006-03-16T15:19:54-08:00 2006-10-20T00:10:03-07:00 It would be really useful if a path could still be drawn even if it one sequence doesn't have a conserved window for it. diane 220 mussa command line seems to be broken... core 1.0 defect diane new 2006-10-25T14:00:01-07:00 2006-10-25T15:05:04-07:00 "I have been trying to run mupa files from the command line, but it keeps throwing the same error... Error: {{{ king@ColossusX:~/proj/mussa_analyses/myogenin$ make cd HuOp; ~/proj/mussa/build/mussagl --no-gui --run myog_w30_t21.mupa I apologize for blocking the gui while running the analysis cd HuCoDoMoRaOp; ~/proj/mussa/build/mussagl --no-gui --run myog_w30_t21.mupa terminate called after throwing an instance of 'annotation_load_error' what(): Error parsing annotation #2 Aborted (core dumped) make: *** [HuCoDoMoRaOp/myog_w30_t21] Error 134 }}}" king 77 Font needs to be better... Qt Gui Standing on our heads enhancement diane new 2006-03-29T15:14:58-08:00 2006-10-13T16:04:09-07:00 Its hard to read... diane 98 QtAssistant needs to be put in the right place on os x. Qt Gui Standing on our heads enhancement diane new 2006-06-06T15:56:58-07:00 2006-10-04T14:58:02-07:00 diane 100 There should be some way to display the annotation name with the annotation track Qt Gui Standing on our heads enhancement diane new 2006-06-06T18:48:36-07:00 2006-10-04T15:13:35-07:00 diane 108 Cancel on the progress bar should do something Qt Gui Standing on our heads enhancement diane new 2006-06-28T17:34:23-07:00 2006-10-13T13:44:06-07:00 A simple answer is to call exit() diane 249 darcs tag mussa_1.1.0 Qt Gui release_1.1 defect diane new 2007-02-22T15:58:43-08:00 2007-02-22T15:58:43-08:00 Make sure to create a tag in darcs with 'mussa_1.1.0' since we used the tag 'mussa_1.0.0' for the first release. king 263 Compile warnings must die! Qt Gui release_1.1 defect diane new 2007-04-19T18:02:39-07:00 2007-04-19T18:14:03-07:00 I noticed compile warnings showed up when compiling MussaGL on Linux, this probably should be fixed before the release, just to make things look and feel like a release. =o) king 82 Unit test python API Qt Gui unit tests enhancement diane new 2006-04-07T00:40:43-07:00 2006-10-20T13:10:30-07:00 With the new cmake system I should make sure that I also test my boost generated python API. diane 268 files that lack a new line would make the mupa parser choke Qt Gui defect diane new 2007-08-02T18:41:48-07:00 2007-08-02T18:41:48-07:00 Steven reported a bug that mussa wouldn't run with some mupa files. It turns out the mupa parser was very cranky if th there wasn't a trailing newline. I briefly tried using spirit to write a parser, but it was easier just to clean up tristan's original parser. (Yay for boost/alg/string.hpp) diane 88 Find titus' paper on FR versus the bacterial genomes other task diane assigned 2006-04-11T14:03:09-07:00 2006-10-13T16:02:36-07:00 "They had some conclusion about different models of evolution for the bacterial genomes when compared to vertibrate genomes... barb thinks it'd be useful to be able to mention this by next group presentation. " diane 7 Reuse seqcomps core Standing on our heads enhancement diane new 2006-03-12T11:49:14-08:00 2006-10-20T13:12:32-07:00 When running a batch of analysis mussa doesn't understand that its already run some of the seqcomps? is there a way to detect if a sequence has already been run? diane 9 Connect to cartwheel Qt Gui Standing on our heads enhancement diane new 2006-03-12T11:52:35-08:00 2006-10-13T13:44:45-07:00 Can we connect to cartwheel and be both a front end for cartwheel and use it for running our own sequence comparisons? diane 13 AnnotationColor mapper needs a user interface Qt Gui Standing on our heads enhancement diane new 2006-03-14T00:10:47-08:00 2006-10-20T00:09:15-07:00 "One might imagine that users would actually like to edit colors by doing something other than changing a text file. The difficulty is deciding if annotations and motifs should be lumped together? and if so does the UI let you add motifs and annotations or just motifs? This is a bit harder as the definition of a motif and the generic annotation is very different. Motifs are defined by a sequence, while generic annotations are start/stop locations--so they definitely need different sets of input controls." diane 17 Allow user to specify an offset for base pair location label Qt Gui Standing on our heads enhancement diane new 2006-03-15T02:09:25-08:00 2006-11-22T11:41:30-08:00 "In order to make it easer to map some random fasta file back to the genome, it'd be useful to provide a way to add some constant offset to the indexes reported in the user interface. For example if you've got a 100 base pair long sequence, the values reported for its position might be 32113100, 32113199 (assuming the offset was 32113100). (Actually we might want to think about if it should be 0 based or 1 based?)" diane 61 For mac users it'd be useful to make double clicking on a data file actually load mussagl Qt Gui Standing on our heads enhancement diane new 2006-03-24T17:30:37-08:00 2006-10-13T13:45:26-07:00 Of course somehow we'd need to make an analysis actually be represented by a file instead of a directory. diane 65 It'd be neat if you could select a region and go to ucsc Qt Gui Standing on our heads enhancement diane new 2006-03-24T18:07:26-08:00 2006-08-23T17:52:18-07:00 This is also useful for fixing annotation problems diane 141 Vector output Qt Gui Standing on our heads enhancement diane new 2006-10-02T14:55:29-07:00 2006-10-02T14:55:29-07:00 It'd be really nice if we could generate vector output, both for better fonts and higher resolution output. Mozilla is using [http://cairographics.org/introduction cairo] diane 145 Use titus' paircomp and motility core Standing on our heads enhancement diane new 2006-10-04T15:11:50-07:00 2006-10-04T15:11:50-07:00 One of my concerns is how to pull his code into mussa in a way that is easy to install but still doesn't fork. diane 201 Run analyses in worker thread core Standing on our heads enhancement diane new 2006-10-20T00:11:33-07:00 2006-10-20T00:11:33-07:00 [108] depends on this. Allow at leas some actions to run in seperate threads. diane 204 When you resize a mussa window, resize the drawing too. Qt Gui Standing on our heads enhancement diane new 2006-10-20T11:08:12-07:00 2006-10-27T14:19:46-07:00 diane 209 Extend the command line parsing to allow fully specifying an analysis Qt Gui Standing on our heads enhancement diane new 2006-10-20T13:19:03-07:00 2006-10-20T13:19:03-07:00 This would be useful so I could use make to more easily run/update analyses. diane 224 Define a common base class between MussaWindow and MussAlignedWindow Qt Gui Standing on our heads enhancement diane new 2006-10-26T15:05:48-07:00 2006-10-26T15:05:48-07:00 I'm starting to duplicate code between the two classes like copying the copy action and reporting how many basepairs were copied. This and other duplications should be shared. diane 6 Analysis saving is smelly core Standing on our heads task diane new 2006-03-12T11:47:46-08:00 2006-10-13T13:45:45-07:00 "Analysis saving uses system calls to make a directory and splatter a bunch of files in it. This makes loading an analysis a bit odd as you need to load a directory, and you get a bunch of errors on standard out. It'd be nice if everything was saved into a single file? or at least used a more multiplatform way for creating directories." diane 21 Implement a better way of handling the GL selection buffer core Standing on our heads task diane new 2006-03-15T17:50:59-08:00 2006-10-13T13:54:01-07:00 "The current opengl selection code uses a hard coded buffer size, which can probably overflow in some situation. There are two solutions, either make a buffer big enough to select everything, or figure out how to parse multiple calls to glRenderMode. At the very least I need to make sure that I don't walk outside the buffer." diane 202 Investigate SIP instead of boost::python Qt Gui Standing on our heads task king new 2006-10-20T00:27:27-07:00 2007-05-15T15:58:59-07:00 The hope is that perhapis it'd be easier to export mussa classes to pyqt? diane 242 make really sure people understand how repeatmasking prevents motifs from being shown. Qt Gui document_1.1 defect diane new 2006-11-27T17:10:19-08:00 2006-11-27T17:10:19-08:00 "CANNTG Human/Mouse Mask one of them, and both of them... connections should match, but the motifs shown should be very different because the motif finder wont find anything in the N regions." diane 198 Document the multi add to sub-analysis feature. Qt Gui 1.0 document_1.1 task king new 2006-10-18T18:00:05-07:00 2006-10-27T17:56:44-07:00 Document the multi add to sub-analysis feature. king 221 Discover/document effect of ordering species on analysis run times. core 1.0 document_1.1 task king new 2006-10-25T15:30:30-07:00 2006-10-27T17:57:00-07:00 Discover/document effect of ordering species on analysis run times. king 232 Document the report bp copied number. Qt Gui document_1.1 task king new 2006-10-27T17:52:19-07:00 2006-10-27T17:52:29-07:00 See ticket #211 for more information. king 234 Document * in title when there are unsaved changes Qt Gui document_1.1 task king new 2006-10-27T17:54:20-07:00 2006-10-27T17:54:20-07:00 See ticket:194. king 258 document new escape to clear selection Qt Gui document_1.1 task king new 2007-04-16T16:57:21-07:00 2007-04-16T16:57:21-07:00 we might want to tell people that if you press the escape key while something is selected, the selection is cleared. diane 264 Document sequence properties other document_1.1 task king new 2007-04-20T11:19:06-07:00 2007-04-20T11:19:06-07:00 Document sequence properties (Edit > Sequence Properties) king 8 Per species thresholds core from __future__ import magic enhancement diane new 2006-03-12T11:50:35-08:00 2006-10-04T15:17:26-07:00 One requested feature was that one could set the threshold of comparison on a per sequence comparison. E.g. A-B is 25/30 while B-C is 20/30. diane 28 Allow user to force a loaded sequence to be reverse complimented. Qt Gui from __future__ import magic enhancement diane new 2006-03-16T11:14:00-08:00 2006-10-04T15:14:50-07:00 When loading a sequence, it'd be nice to be able indicate that it should be reverse complimented. diane 80 Difference between analyses Qt Gui from __future__ import magic enhancement diane new 2006-03-30T15:50:04-08:00 2006-10-13T13:48:02-07:00 It would be useful if you could load an analysis and then load a second analysis and see what items are different. diane 87 Autodetect threshold Qt Gui from __future__ import magic enhancement diane new 2006-04-11T13:54:42-07:00 2006-10-13T13:48:14-07:00 It might be useful to autodetect a reasonable threshold... diane 219 Reordering sequences in an analysis would be really nice Qt Gui from __future__ import magic enhancement diane new 2006-10-24T17:12:02-07:00 2006-10-24T17:12:02-07:00 Gee I wish I could click on a sequence track and drag it into a different order. diane 222 Allow hyperlink annotations for CDS to PyMol rendering of protein structure Qt Gui from __future__ import magic enhancement diane new 2006-10-25T17:12:57-07:00 2006-10-25T17:12:57-07:00 Especially with highlighting where the chunk of dna shows up on protein. diane 238 Set left offset graphically Qt Gui from __future__ import magic enhancement diane new 2006-11-22T12:33:42-08:00 2006-11-22T12:33:42-08:00 Setting the left edge of a sequence numerically ticket:111 is hopefully acceptable as a first pass, though it would be quite useful for there to be some graphical way of setting the position of the track. Either clicking to say center here, or dragging a track around. diane 245 Implement back_inserter for sequence type core from __future__ import magic enhancement diane new 2007-01-04T13:15:11-08:00 2007-01-04T13:15:11-08:00 It'd be useful for paircomp's reverse_complement code if mussa's Sequence class had a back inserter. Currently sequences need be completely immutable. diane 266 Sub-analysis drawing bug (see attached screenshots) Qt Gui release_1.1 defect diane new 2007-07-16T15:57:44-07:00 2007-07-16T15:57:44-07:00 I did a sequence view on a conserved region up stream of the annotated gene, including the first exon (see attached screenshots). I then did a 8 out of 10 sub-analysis which was drawn incorrectly (see attached screenshot). The analysis was from mck_full_repeatmasked/HuCoDoMoRa/mck_w30_t21/. king 267 Sequence View soft threshold control non-responsive Qt Gui release_1.1 defect diane new 2007-07-17T11:21:56-07:00 2007-07-17T11:21:56-07:00 "The soft threshold control in the Sequence View is non-responsive even though it does not look to be disabled. Mussa Version Info: Windows build 571 Qt 4.3.0 OpenGL 2.0.3" king 248 Test latest build on all platforms Qt Gui release_1.1 task diane new 2007-02-22T15:55:29-08:00 2007-02-22T15:55:29-08:00 Test latest build on all platforms. king 205 Add button for autofitting sequence to window Qt Gui release_1.2 enhancement diane new 2006-10-20T11:40:00-07:00 2006-10-20T11:40:00-07:00 Brandon even reminded me that there's even code for it, we just need to hook it up to the zoom widget. diane 218 Qt4.2 has a platform independent way to place Ok/Cancel buttons in dialog Qt Gui release_1.2 enhancement diane new 2006-10-24T14:21:21-07:00 2006-10-27T14:14:04-07:00 One fo the neat new features of 4.2 was it had a way of putting Ok/Cancel in different places depending on the conventions for that OS. diane 228 Allow more vertical collapse of description widgets Qt Gui release_1.2 enhancement diane new 2006-10-27T14:22:21-07:00 2006-11-22T11:44:46-08:00 In order to cram more tracks on a screen, we might want to be allowed to collapse at least some of the information in the sidebars. diane 241 One of the annotations needed is to show where the start of the gene is Qt Gui release_1.2 enhancement diane new 2006-11-27T16:29:42-08:00 2006-11-27T16:29:42-08:00 diane 106 Figure out how to test copySelectedTracks core unit tests enhancement diane new 2006-06-20T19:17:01-07:00 2006-10-20T13:12:56-07:00 I need to figure out some way to programmatically set a selection so I can write unittests for all the copySelectedTrack functions diane 203 Unit test the code that generates all the mussa filename core unit tests enhancement diane new 2006-10-20T10:15:21-07:00 2006-10-24T14:26:06-07:00 "This will require pulling the naming code out into seperate functions especially the ""automatic"" add the extension "".mtl"" that recently appeared in the gui." diane 48 Automate win32 installer build other enhancement diane new 2006-03-22T01:47:49-08:00 2006-10-13T16:03:03-07:00 "Wouldn't it be nice if a new build of the win32 installer could be me made using a script in Linux? Inno Setup will need to be installed and run using wine probably. The following win32 .dlls are needed... * mingwm10.dll * QtCore4.dll * QtGui4.dll * QtOpenGL4.dll There is a slim chance mussagl.exe might need some boost libraries as well... but it looks like the boost libs may have been included statically (worth dubble checking). Either way, a win32 build of Qt4.1 and boost will be needed for cross compiling using mingw." king 11 create unifed sequence type core Standing on our heads enhancement diane new 2006-03-13T17:54:41-08:00 2006-10-20T00:09:46-07:00 "There are many different types of things that we attach to a sequence, like seqcomp windows, motifs, annotations, etc. It'd be nice if all of these things shared a common ""location"" type that understood the start/stop/strand addressing. I got the idea because I was feeling annoyed that motif searching returned matches for both forward and reverse compliment matches but gave me no indication that they'd done this." diane 29 Connect to Core Match core Standing on our heads enhancement diane new 2006-03-16T15:18:12-08:00 2006-10-13T13:47:21-07:00 "Integrate tony's core match algorithm. (Hmm... might also want to switch to paircomp?) Barbara also wants an estimate of how long to implement." diane 136 allow absolute positioning Qt Gui Standing on our heads enhancement diane new 2006-09-27T00:22:41-07:00 2006-10-04T15:16:46-07:00 "I think i can allow absolute positioning if I made the ""location"" base pairs in the info sidebars editable." diane 253 Show conserved window on local alignment display Qt Gui Standing on our heads enhancement diane new 2007-03-02T15:25:23-08:00 2007-03-02T15:25:23-08:00 "It might be useful to show the windows that were aligned on the local alignment display, since the local alignments are only done within those windows. This might make it a bit easier to see the limitations of what was matched." diane 231 Document copy and paste into motif editor now functional. Qt Gui document_1.1 task king new 2006-10-27T17:50:56-07:00 2006-10-27T17:50:56-07:00 king 159 Create track macro to display changelog with build numbers other 1.0 from __future__ import docs task king new 2006-10-13T17:24:05-07:00 2006-10-27T17:47:55-07:00 The change log is too long to display in the Manual. The Manual should only display the last 10 or 20 and then link to the full change log, or maybe just link to the full change log. king 165 Include a section on creating a motif list file using the smn1 data. other 1.0 from __future__ import docs task king new 2006-10-16T10:01:52-07:00 2006-10-27T17:48:32-07:00 Include a section on creating a motif list file using the smn1 data. king 18 segments should indicate if they're both forward and reveresed core from __future__ import magic enhancement diane new 2006-03-15T02:37:08-08:00 2006-10-13T13:48:33-07:00 "a segment should track forward and reverse compliment separately, as perhaps it is possible that the same segment will match both forwards and reversed in different paths. It be neat to draw those cases as alternating blue/red stippled lines" diane 54 Allow compressing repeat regions Qt Gui from __future__ import magic enhancement diane new 2006-03-23T10:24:28-08:00 2006-10-13T13:48:50-07:00 For MEME Ali compressed reprat regions and replaced them with a small chunk of Ns. It might be interesting to do the same for mussa. (as a visualization aid). diane 112 Sequence logo Qt Gui from __future__ import magic enhancement diane new 2006-07-11T16:10:21-07:00 2006-10-04T15:03:44-07:00 "It'd be neat if the mussa analysis could show a ""sequence logo"", the different sized fonts for the frequence of base pair occurence." diane 155 Include a simple repeat filter core from __future__ import magic enhancement diane new 2006-10-13T13:49:49-07:00 2006-10-13T13:49:57-07:00 It would be nice if mussa had an option to perform some type of repeat filtering. diane 262 ThresholdWidget.reset() SIGNAL/SLOTS issue. Qt Gui release_1.2 defect diane new 2007-04-19T17:52:46-07:00 2007-04-19T17:52:46-07:00 "When working towards a fix for ticket:257, I added a reset() function to the ThresholdWidget, with the hope of avoiding emiting a changedValue, but this fails because the ThresholdWidget.setRange(min,max) code which is called by reset, ends up calling the basepair_spinner->setRange(min,max) function, which triggers a valueChanged emit, because by default the basepair_spinner's value is 0, and therefor gets bummed up to the new minimum. This then calls ThresholdWidget.setBasePairThreshold(min), which causes the analysis to be set to the minimum instead of the soft threshold, therefore triggering an nway analysis. Then the soft threshold gets set to the correct soft threshold triggering another loop and and another nway. The fix for ticket:257, fixes the problem by disconnecting the MussaWindow from the ThresholdWidget while the ThresholdWidget is being updated and then reconnects afterwards. There is probably a way of having the ThresholdWidget break it's signals/slots at the correct times to get it to function properly without triggering an emit which ends up being sent back to the MussaWindow. For now, the fix to ticket:257 breaks the SIGNAL/SLOT loop (in MussaWindow.setAnalysis), just not in the ideal spot (ThresholdWidget)." king 123 Allow hiding sidebars Qt Gui release_1.2 enhancement diane new 2006-09-13T15:33:14-07:00 2006-10-20T00:25:26-07:00 Tristan complained briefly about the sidebars taking up too much space. Might be useful to be able to hide them, or perhaps hide one or the other. diane 124 report patch version core release_1.2 enhancement diane new 2006-09-13T15:35:27-07:00 2006-10-20T15:50:23-07:00 "Brandon suggested that it'd be useful for mussa to have some version number... perhaps the count of darcs patches? Though there's a problem with that in that its relative to a particular darcs repository." diane 230 shipit script should ship source distribution too. other release_1.2 enhancement diane new 2006-10-27T15:37:22-07:00 2006-10-27T15:37:22-07:00 diane 89 Blast to find mussa regions core Standing on our heads enhancement diane new 2006-04-11T15:55:59-07:00 2006-10-13T13:47:08-07:00 its unclear if this is a good idea or not, but it might be interesting. Given a sequence and a target genome, blast to find the few best hits and then do a paircomp style comparision to analyze more deeply. diane 193 Changing a species name doesn't set dirty flag. Qt Gui 1.0 release_1.2 enhancement diane new 2006-10-18T10:50:07-07:00 2006-10-20T00:06:54-07:00 Changing a species name doesn't set dirty flag. king