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40 Commits

Author SHA1 Message Date
Arnar Flatberg 1e0b99f283 small bugfix 2007-01-09 08:53:28 +00:00
Einar Ryeng fa047e0171 Committing non-working code that breaks go workflow. ;) 2007-01-08 21:13:22 +00:00
Einar Ryeng fac9346aad Added very hackish annotation count reader. 2006-12-15 12:53:27 +00:00
Einar Ryeng fb77ddb549 Updated GO workflow. Options class test added. Reading the ontology takes too 
long.
 2006-10-26 16:51:42 +00:00
Einar Ryeng 0b30aeac6f Updated GO workflow. 2006-10-22 23:19:54 +00:00
Einar Ryeng 5491f5ce04 GO workflow. Does not work. 2006-10-22 15:31:36 +00:00
Einar Ryeng 87f87e36c8 * system/fluents.py: Fixed a bug where the the application tried to load 
a toolbar from None

 * system/plots.py: Fixed MainView.insert_view that was a no-op when in large
   view.

 * system/dataset.py: Changed __str__ of dataset to also show names of dimensions.
 2006-07-21 14:30:09 +00:00
Truls Alexander Tangstad 86f89b6ffe Typo. 2006-05-09 13:51:14 +00:00
Truls Alexander Tangstad 5b1af849dc Implemented Limma function for Affy workflow. 
Extended ScatterPlot to take two datasets and updated code using it.
 2006-05-09 13:17:17 +00:00
Truls Alexander Tangstad 0db25f1dd7 Changed use of Dataset.get_matrix() to Dataset.asarray() and removed it. 2006-05-05 14:43:53 +00:00
Reidar Strand Hagen 56a6028547 Validation on number of inputs added 2006-05-03 11:52:54 +00:00
Reidar Strand Hagen 5b2223afcd Multiselection included. (Without input validation). 2006-05-03 11:11:45 +00:00
Einar Ryeng 0df56248ee Removed obsolete module annotations. 2006-04-27 12:41:51 +00:00
Truls Alexander Tangstad 3683f6c2e9 Fixed labels for scatter plots. Set correct labels in go_workflow. Removed extra loadings plot. 2006-04-27 11:38:40 +00:00
Truls Alexander Tangstad 969006015a Added LinePlot used by Affy importer. 2006-04-27 11:03:11 +00:00
Einar Ryeng 251f9d6cf4 Added command line options to create a new project based on a given workflow. 2006-04-25 12:19:25 +00:00
Einar Ryeng 359903c5ab Made system a package. 2006-04-25 09:53:35 +00:00
Einar Ryeng ba2a769f01 Function names are now folders in the navigator. 2006-04-24 15:20:27 +00:00
Einar Ryeng 179a2f88a9 The navigator now displays the plots and data in a tree that shows the ancestry information. 2006-04-24 14:52:21 +00:00
Truls Alexander Tangstad 6c72dec7fa Removed need to provide plots with project/workflow on creation, is instead injected by project itself when added to it. 2006-04-24 14:42:45 +00:00
Truls Alexander Tangstad 97e09b39a1 Added matrix-getter to Dataset. 
Added rma-function to preprocessing incorporated in AffyMatrix-importer.
Added PCAFunction to go_workflow for processing loaded affymatrix data.
 2006-04-24 14:07:34 +00:00
Arnar Flatberg a2e4392a72 Complete rewrite of dataset class, with (all) the necessary updates 2006-04-24 09:53:07 +00:00
Einar Ryeng e762aef882 * system/dialogs.py: Oooops. Forgot this file in the previous commits. Well, 
here it is, currently only with the New Project dialog.
 2006-04-22 22:29:02 +00:00
Einar Ryeng f484ec9945 * workflows/go_workflow.py: Added a workflow name to make it identifiable 
in the "create project" druid.
 2006-04-22 21:48:30 +00:00
Truls Alexander Tangstad 357cd1a1a6 Removed workflow being dependent on rpy by putting the import within the run function of affymatrix import. 2006-04-22 20:48:44 +00:00
Truls Alexander Tangstad 26f16acc9c Made sure pickling use protocol 2 to make it faster and the files smaller (binary). 2006-04-22 18:11:31 +00:00
Truls Alexander Tangstad 553bfbe1ae Big cleanup of affymatrix importer. Now use E@exprs to get matrix from loaded data. 
Also made row and colname import better by ensuring vector-handling, ensuring that getting single column/row data works without being converted into a single string instead of string in a list.
Removed ;1-hack and use NO_CONVERSION to ensure no extra computation is done when calculating r stuff.
Now AffyMatrix data is named as such.
 2006-04-22 17:59:15 +00:00
Truls Alexander Tangstad 5a2a1afe91 Added pickling as a quick and dirty way of loading and saving data in einars workflow. 2006-04-22 16:27:33 +00:00
Truls Alexander Tangstad d123f0e1c1 Added doc-string for CelFileImportFunction. 2006-04-22 15:59:19 +00:00
Truls Alexander Tangstad 23914b2d1e Added support for affy cel files. 2006-04-22 00:17:22 +00:00
Truls Alexander Tangstad c601ad3966 Removed data information as function in workflow and added as default action on datasets double-clicked in navigator. 2006-04-21 15:02:13 +00:00
Truls Alexander Tangstad efcd8c8587 Removed unused code. 2006-04-21 15:00:04 +00:00
Truls Alexander Tangstad 79481ed186 Added plot to output from test-function. 2006-04-21 14:58:42 +00:00
Truls Alexander Tangstad 07ac564668 Changed info function to show dialog instead of returning a view. 2006-04-21 14:12:18 +00:00
Truls Alexander Tangstad c4f9f5c399 Created new workflow for showing information about a dataset as a view. 2006-04-21 13:04:31 +00:00
Arnar Flatberg ccec17262b Added random test data 2006-04-21 10:56:01 +00:00
Einar Ryeng c09f2ceb92 * fluent, *.py: Data and plots returned from functions will now show up in 
the navigator window.
 2006-04-20 14:29:13 +00:00
Arnar Flatberg 6a4ae8ecf1 mainly overhaul of observers, and removal of project singleton 2006-04-20 10:27:58 +00:00
Einar Ryeng f45c9c6bf7 * fluent: General cleanup. 2006-04-19 19:59:55 +00:00
Einar Ryeng c55a39f7f9 * workflows/go_workflow.py: A workflow that makes distance matrices based 
on gene ontology information. Currently only reads gene annotations.
 2006-04-17 20:29:29 +00:00