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182 Commits

Author SHA1 Message Date
Arnar Flatberg 4b8f594966 app -> main.application 2007-07-27 09:40:58 +00:00
Arnar Flatberg 47b89cc411 Fixed bug in esvd for m>n 2007-07-26 18:32:48 +00:00
Arnar Flatberg 7fd4ac6225 pls opt fix 2007-07-26 18:32:27 +00:00
Arnar Flatberg b35f814ef0 Added center check button on lineview 2007-07-26 18:26:50 +00:00
Einar Ryeng dc7f7dbde2 Added existing_identifiers function to Dataset. 
Added colouring drag'n'drop to DAGPlot in gobrowser module.
 2007-07-26 15:45:42 +00:00
Einar Ryeng a45743c31e Added main.py that now contains the One & Only Singleton instance of these classes: 
- Navigator
 - Aplication
 - Workflow
 - Project
 - Options
Corresponding changes have been added in lots of other files to account for this, but
the access to these objects should now be a lot easier.
 2007-07-26 12:35:59 +00:00
Einar Ryeng 524c90fcf7 Updated to handle new numpy/scipy. 2007-07-24 12:19:13 +00:00
Arnar Flatberg 05274b4f0b confidence 2007-07-23 18:07:10 +00:00
Arnar Flatberg a05d0faa0d Lib updates 2007-07-23 17:33:21 +00:00
Einar Ryeng a503ffcdf8 Fixed linewidth in selection in scatter plots. 2007-07-05 11:57:21 +00:00
Einar Ryeng d29013a863 T-test now works, and outputs a histogram as well as t-values and p-values. 2007-07-03 16:25:38 +00:00
Einar Ryeng 99987999db Broke up a too long line. 2007-07-02 09:54:56 +00:00
Einar Ryeng 4eaea2fe59 Added empty lists as default values for all_data and all_plots in Options, so 
that subclasses of Options will work with the GUI without modifications.
 2007-06-28 21:33:09 +00:00
Einar Ryeng 68cc583d2c Added common_dimensions(ds) that lists common dimensions between two 
datasets.
 2007-06-22 15:35:45 +00:00
Einar Ryeng ff2c42902f Commented out some log lines that just cluttered the log. 2007-06-21 10:25:17 +00:00
Arnar Flatberg ebe7621817 some biocondoctur utilities 2007-05-06 13:51:06 +00:00
Arnar Flatberg a0faed2614 Forgot some ... 2007-04-24 17:21:40 +00:00
Arnar Flatberg 34ae426c86 Added correlation plot and moved colorbar to plots 2007-04-24 17:17:31 +00:00
Arnar Flatberg 90bb25eb55 added default mappable to None 2007-04-24 17:16:34 +00:00
Arnar Flatberg 31ac569c3e Added colorbar shortcut 2007-04-24 17:04:29 +00:00
Arnar Flatberg b02773b4e6 pls loading plot now have correct name 2007-03-15 10:38:52 +00:00
Einar Ryeng 1c48315a0f Added debug output. 2007-03-14 17:26:40 +00:00
Arnar Flatberg 438a268b1d Inserted visible header sort 2007-03-14 16:34:50 +00:00
Arnar Flatberg 3d2492578e whitespace 2007-03-14 16:33:54 +00:00
Arnar Flatberg 3bd21ab089 metric support 2007-03-14 16:33:16 +00:00
Arnar Flatberg 48047f1395 Moved lots of stuff back to sandbox 2007-03-14 16:32:49 +00:00
Arnar Flatberg 7f1f639ee7 Updates on metric, whitespace 2007-03-14 16:31:25 +00:00
Arnar Flatberg 22f6e3284c whitespace 2007-03-14 16:30:18 +00:00
Arnar Flatberg 818dc0b2b0 added a logger for constructor calls 2007-03-14 16:27:23 +00:00
Arnar Flatberg 212da78933 correct comp update 2007-03-14 16:17:21 +00:00
Arnar Flatberg 00dd3e8d9d added validation on identifiers input 2007-03-14 16:06:16 +00:00
Arnar Flatberg 9cbefb5705 in write_ftsv: adjusted so it splits specifically on tab, whitespace allowed in annotations 2007-03-14 10:24:49 +00:00
Einar Ryeng 28e6c52f78 Fixed bug with hidden dimensions. 2007-03-01 15:06:33 +00:00
Arnar Flatberg d699afa6a5 fixed bu when trying to drag anything over an empty view 2007-03-01 15:03:53 +00:00
Einar Ryeng 6101bf850c Changed CategoryDataset ftsv files to be written with 0 and 1 instead of True and False. 2007-02-28 16:33:11 +00:00
Einar Ryeng 89636962a7 Added Workflow.get_data_file_name() which returns the full path to a given 
data file, or None if the file does not exist. This is tested in the test
workflow.
 2007-02-28 14:56:24 +00:00
Arnar Flatberg 281337251d Added selection of lines in network plot 2007-02-27 21:19:24 +00:00
Arnar Flatberg 78183df0e9 Alignment of function boxes 2007-02-27 18:14:58 +00:00
Arnar Flatberg b754a5df44 Update from change of plots/view 2007-02-27 16:31:18 +00:00
Arnar Flatberg 61cfd00558 Division of plots -> view/plots 2007-02-27 16:28:03 +00:00
Arnar Flatberg 059cddbc16 Division of plots -> view/plots 2007-02-27 16:27:39 +00:00
Arnar Flatberg 686a1fdcd1 network/venn plot now maximizes the space available 2007-02-27 15:42:27 +00:00
Arnar Flatberg d27278241c oops ... (broken code fixed) 2007-02-27 15:08:00 +00:00
Arnar Flatberg 4de65f1085 Clean up 2007-02-27 15:05:21 +00:00
Einar Ryeng f73a6db0ee Added ctrl+arrows to navigate between plots. 2007-02-26 23:00:25 +00:00
Einar Ryeng eacb44f32a Removed "Edit" menu. 2007-02-26 22:12:32 +00:00
Einar Ryeng d040f11c2f Added identifier list update on selection changed. 2007-02-26 18:02:34 +00:00
Einar Ryeng 537dc9f0ec Cleanup of selection browser module. Added comments, fixed some bits of code. 2007-02-26 14:35:31 +00:00
Arnar Flatberg c0bbe24c39 No selections in scatter marker now updates to no selection instead of last selection 2007-02-26 12:11:28 +00:00
Arnar Flatberg a6fbef9cfa scatter plot selected markers are now on top (visible) 2007-02-26 11:20:02 +00:00
Arnar Flatberg 2f60d0663d Clean up of import statements 2007-02-26 09:08:50 +00:00
Arnar Flatberg 5ed602f355 Lots of changes .... (new selector, mode updates, histogram selection, ++) 2007-02-26 08:00:36 +00:00
Arnar Flatberg 3ee8439e07 Added selection listeners to plots in context menu 2007-02-26 07:58:33 +00:00
Arnar Flatberg a614908436 Size of current selection is now updated in details 2007-02-23 11:12:03 +00:00
Arnar Flatberg 41e8ed511b Fixed dim_cursor_changed to to use the correct treemodel, and added show/hide on selection details 2007-02-23 10:46:04 +00:00
Arnar Flatberg 0d8702bb71 added show/hide on dimensions 2007-02-21 19:57:27 +00:00
Einar Ryeng 2bae169f38 Annotation display now works (sort of). 2007-02-21 16:39:04 +00:00
Arnar Flatberg 28aca8c621 added project to selection controller 2007-02-21 13:57:48 +00:00
Arnar Flatberg 8c03338b75 hypergeometric test (scipy version has errors) 2007-02-21 13:03:51 +00:00
Arnar Flatberg 48165d1aed Updated the selection controller with sorting ++ 2007-02-21 12:41:37 +00:00
Einar Ryeng f0b2660813 Selection listeners are now notified when new dimensions are added (because 
this implies that an empty selection is made on the new dimension).
 2007-02-21 12:05:08 +00:00
Einar Ryeng 5800e7e362 Fixed a bug that prevented the first selection on a dimension to come from a 
dataset.
 2007-02-21 11:49:43 +00:00
Einar Ryeng a5955f9b59 Now updates the DimListConroller when a CategoryDataset is drag'n'dropped into 
SelectionListController.
 2007-02-21 11:43:00 +00:00
Einar Ryeng c5c4f13a19 Fixed some excessively long lines. 2007-02-21 11:08:20 +00:00
Einar Ryeng 2cc4e86b0a Split selections.py into three different controller classes, one for each list. There 
is still some work to be done, and bugs to be fixed.
 2007-02-21 00:00:26 +00:00
Einar Ryeng a2195bcb4b Added Import annotations option. 2007-02-16 11:23:29 +00:00
Einar Ryeng 6809c1a454 Added some annotation support in selections.py, including the beginning of a 
menu option to add an arbitrary annotation alongside identifiers.
 2007-02-15 22:57:40 +00:00
Einar Ryeng b17f04466b Added read_annotations_file() which reads a tab delimited file containing 
annotations to identifiers along a dimension.
 2007-02-15 22:42:55 +00:00
Arnar Flatberg 4319e8630e fixed error in typechecking 2007-02-15 13:36:36 +00:00
Arnar Flatberg fc33c2dbfc factored out packer 2007-02-09 14:02:58 +00:00
Arnar Flatberg 15c89fb9b5 Factored out packer 
A    packer.py
 2007-02-09 14:02:39 +00:00
Arnar Flatberg 7eb13b14cb Removed resolution arg to Circle to avoid construction of a circlepolygon (deprecated) 2007-02-02 12:21:19 +00:00
Einar Ryeng 320cd97512 Removed noise generating print statements. 2007-01-31 14:58:37 +00:00
Einar Ryeng 75b66914fd Fixed bug by removing hardcoded filename. 2007-01-31 14:56:43 +00:00
Einar Ryeng 74cb30428c Added annotations to identifiers, and converted the unused annotationtest.py to 
test the new module.
 2007-01-31 14:19:23 +00:00
Arnar Flatberg 1863bfc564 Save plot enabled 2007-01-31 13:26:46 +00:00
Arnar Flatberg d1205ae67f Removed colorbar 2007-01-31 13:01:09 +00:00
Arnar Flatberg 37feb1c25b bugfix on P scale 2007-01-31 13:00:36 +00:00
Arnar Flatberg 2cfa3ca415 spin on a/o, colorbar on keypress 2007-01-31 12:59:21 +00:00
Arnar Flatberg 63be80aa92 pls options added 2007-01-31 12:03:11 +00:00
Arnar Flatberg 088f180b5d Barplot, lots of changes in scatter, disabled modes, removed labels, bugfix on lasso 2007-01-31 12:02:11 +00:00
Arnar Flatberg e716db3fd2 Added center option to validation, + naming updates 2007-01-31 11:59:23 +00:00
Arnar Flatberg 29509902df bugfix on shape 2007-01-31 11:57:59 +00:00
Arnar Flatberg 8e607c7b1a bugfixed scaling issues 2007-01-31 11:57:04 +00:00
Arnar Flatberg f064b7134d Removed scale option added pack 2007-01-31 11:56:28 +00:00
Arnar Flatberg 1d5929f14c pls options glade file 2007-01-31 11:55:43 +00:00
Arnar Flatberg ed2848beb3 Errors when identifers dont match shape, + whitespace 2007-01-31 11:54:54 +00:00
Arnar Flatberg 48bb47ec86 Bugfixed pca 2007-01-25 12:36:32 +00:00
Arnar Flatberg aeb37cf4cd Added supportp for tall X in PCA 2007-01-25 12:17:16 +00:00
Arnar Flatberg fa3722600c pca options glade file 2007-01-25 12:15:30 +00:00
Einar Ryeng 61bfc236e6 Changed location of PCA options glade file. 2007-01-25 12:15:19 +00:00
Arnar Flatberg 7a204a3426 Added option page to option dialog 2007-01-25 12:10:18 +00:00
Arnar Flatberg 1c2c2c8895 Multiple lib changes 2007-01-25 11:58:10 +00:00
Einar Ryeng e03cc4ed4c Added a ScrolledWindow around the navigator. 2007-01-19 14:00:10 +00:00
Einar Ryeng 7693f336ba Added a singleton project in the project module, so that the current project is 
easily accessible from anywhere in the code. As there is only one project at
any given time this should not be a problem.

The Gene Ontology browser needed this to be able to set the selection without
passing the current project through several constructors. 

Added a context menu in the GO browser that allows the user to select all GO
terms in the subgraph that starts on the current node.
 2007-01-18 15:45:48 +00:00
Arnar Flatberg f533344242 Added histogram in plot menu 2007-01-17 15:40:54 +00:00
Arnar Flatberg 7c20e6d780 Added simple histogram 2007-01-17 15:40:33 +00:00
Einar Ryeng 1ffbf4f9e7 Added default implementation of set_current_selection in Plot, so that plots can safely 
ignore selections without adding any code to the plot.

Rectangle select mode, lasso select mode and freeze are now grayed out in ImagePlot.
 2007-01-17 15:35:12 +00:00
Einar Ryeng 06591e301e Added "Plot" submenu in navigator context menu. Can create an ImagePlot of a dataset. 2007-01-17 14:06:07 +00:00
Einar Ryeng c3c6e85044 Added ImagePlot, which displays a dataset as an image. 2007-01-17 13:20:04 +00:00