56c07c6392Implemented Dataset.get_indices() and extended Dataset.get_identifiers() to convert between indices and identifiers and subsets thereof. Also added tests.Truls Alexander Tangstad2006-05-02 14:06:48 +0000
a2d3a9d5ccMade PCA more generic, even enable PCA of existing PCA-results as dimension names are modified to handle dimension name component in input.Truls Alexander Tangstad2006-04-28 11:44:55 +0000
fa3b1182bcAdded font/bg colours to Navigator. (uses coloumns 3,4 in TreeModel, set in projects.py)Reidar Strand Hagen2006-04-27 15:51:25 +0000
5bb93af6f0Changed generic observer pattern and project dependency in plots to be a two-way selection-listener model. The project listens to selections done in plot and broadcasts it back to all plots (including source) which allows them to redraw properly.Truls Alexander Tangstad2006-04-27 14:38:48 +0000
3683f6c2e9Fixed labels for scatter plots. Set correct labels in go_workflow. Removed extra loadings plot.Truls Alexander Tangstad2006-04-27 11:38:40 +0000
60c1d19a74Get correct path for glade file based on the path of the system package.Einar Ryeng2006-04-27 11:20:12 +0000
c95c18eb14fluents.glade is now read from '/system/' under the directory of argv[0].Einar Ryeng2006-04-27 10:54:18 +0000
959d114774Changed from using default python version to python2.4 to make the program work on debian systems. The program does not currently support python 2.3, and probably never will because of the set class that is a built-in only from python 2.4 and up.Einar Ryeng2006-04-27 10:06:30 +0000
a92be02e80Added help index and bug report menu options.Einar Ryeng2006-04-27 09:55:19 +0000
2b0fdc186cFiexd the cancel button of the new project dialog. Closes#7Einar Ryeng2006-04-26 14:01:46 +0000
32fdca837aMoved the generation of workflow list from dialogs.py to workflow.py, as a step in the process of making command line options to the program.Einar Ryeng2006-04-24 21:52:18 +0000
ba2a769f01Function names are now folders in the navigator.Einar Ryeng2006-04-24 15:20:27 +0000
179a2f88a9The navigator now displays the plots and data in a tree that shows the ancestry information.Einar Ryeng2006-04-24 14:52:21 +0000
6c72dec7faRemoved need to provide plots with project/workflow on creation, is instead injected by project itself when added to it.Truls Alexander Tangstad2006-04-24 14:42:45 +0000
97e09b39a1Added matrix-getter to Dataset. Added rma-function to preprocessing incorporated in AffyMatrix-importer. Added PCAFunction to go_workflow for processing loaded affymatrix data.Truls Alexander Tangstad2006-04-24 14:07:34 +0000
e762aef882* system/dialogs.py: Oooops. Forgot this file in the previous commits. Well, here it is, currently only with the New Project dialog.Einar Ryeng2006-04-22 22:29:02 +0000
f484ec9945* workflows/go_workflow.py: Added a workflow name to make it identifiable in the "create project" druid.Einar Ryeng2006-04-22 21:48:30 +0000
efcdafe843* The New project toolbar button now works. A druid will display the available workflows and ask you to select one of them. There are still a couple of unresolved issues, but it works, so i upload it to ease the use of the program.Einar Ryeng2006-04-22 21:46:44 +0000
357cd1a1a6Removed workflow being dependent on rpy by putting the import within the run function of affymatrix import.Truls Alexander Tangstad2006-04-22 20:48:44 +0000
26f16acc9cMade sure pickling use protocol 2 to make it faster and the files smaller (binary).Truls Alexander Tangstad2006-04-22 18:11:31 +0000
553bfbe1aeBig 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.Truls Alexander Tangstad2006-04-22 17:59:15 +0000
c601ad3966Removed data information as function in workflow and added as default action on datasets double-clicked in navigator.Truls Alexander Tangstad2006-04-21 15:02:13 +0000
0918f0019bAdding plots to panes is now done in row_activated_handler again, which makes it respond to double-clicks instead of just being selected in navigator.Truls Alexander Tangstad2006-04-21 14:59:25 +0000
f3a65a3c4fCan now select data in navigator by single-clicking or moving with keyboard, no need to activate (double-click etc.).Truls Alexander Tangstad2006-04-21 14:29:08 +0000
a0d2c0d16d* fluent, system/plots.py: Switching between four and one view now sort of works. Still a bit buggy, and with messy code.Einar Ryeng2006-04-17 22:30:53 +0000
c55a39f7f9* workflows/go_workflow.py: A workflow that makes distance matrices based on gene ontology information. Currently only reads gene annotations.Einar Ryeng2006-04-17 20:29:29 +0000
494aedc1b5* system/plots.py, system/fluent.glade: There is now an active plot.Einar Ryeng2006-04-17 20:27:39 +0000
3668481562* system/workflow.py: Loads and returns gene to GO term mapping.Einar Ryeng2006-04-17 12:35:31 +0000
4bdeef05f6* annotations.py: The Annotations class now work. Querying along any axis is supported, but only two dimensional Annotations can be created.Einar Ryeng2006-04-16 23:30:01 +0000
Truls Alexander Tangstad
Reidar Strand Hagen
Einar Ryeng
Arnar Flatberg