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194 Commits

Author SHA1 Message Date
Arnar Flatberg 973470b595 stuff 2007-08-02 11:18:18 +00:00
Arnar Flatberg 83d76eac4f Fixed vorrect namespace for scipy funcs 2007-08-02 10:44:06 +00:00
Arnar Flatberg dc3893eecc Fixed a "main.project" bug 2007-08-02 10:19:16 +00:00
Einar Ryeng f12fe23c1b Fixed docstrings. 2007-08-02 10:08:52 +00:00
Einar Ryeng 4c24061575 Fixed docstrings. 2007-08-02 10:08:27 +00:00
Einar Ryeng 6e4db7ebe4 Fixed plot focus signal problem. 2007-07-31 12:25:56 +00:00
Arnar Flatberg 10eba079bc iii 2007-07-30 18:04:42 +00:00
Einar Ryeng aa4007e208 Improved drag'n'drop of data into scatter plots so that it no longer requires 
matching identifiers along dimensions.
 2007-07-30 17:42:48 +00:00
Arnar Flatberg b39e71ca2b Trying to fix cv_pls 2007-07-30 09:46:43 +00:00
Arnar Flatberg 349cab3c51 ups 2007-07-28 16:05:11 +00:00
Arnar Flatberg 9a2e259209 c 2007-07-28 09:19:42 +00:00
Arnar Flatberg df88f44255 clean up 
ups
 2007-07-28 09:18:48 +00:00
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