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147 Commits

Author SHA1 Message Date
Einar Ryeng 44b676f726 system/plots.py: Fixed a few bugs in NetworkPlot. 2006-08-01 14:26:33 +00:00
Einar Ryeng b3d681ef16 * system/plots.py: Added NetworkPlot, which may or may not work correctly. 
* system/dataset.py: Removed a few lines of obsolete code.
 2006-08-01 13:22:39 +00:00
Arnar Flatberg 37b4d55a86 2006-08-01 11:01:52 +00:00
Arnar Flatberg a55a872399 fix output for indices is empty array 2006-08-01 10:53:44 +00:00
Arnar Flatberg 27472defda bugfix in get_identifiers 2006-08-01 10:33:45 +00:00
Arnar Flatberg 676ea4e0b9 removed shape in constructor, added all_dims to dataset base class, updated get_identifiers and get_indices 
Denne linjen og de som er under vil bli ignorert--

M    dataset.py
 2006-08-01 09:45:53 +00:00
Einar Ryeng 61da4f562e Added LICENCE (the pure GPL text copied verbatim from gnu.org) and README. 
Started to add a NetworkX plot in plots.py
 2006-07-31 14:57:24 +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
Einar Ryeng aca9a47f56 Toolbars work again. 2006-06-01 13:51:16 +00:00
Einar Ryeng 0670c42bd4 Drag and drop from the navigator to the viewframes now work. 2006-05-29 19:14:48 +00:00
Einar Ryeng 581cef75ae Fixed plot things. A plot can only be attached to one view now. 2006-05-29 11:24:33 +00:00
Einar Ryeng 62c1d79dac Fixed large/small plot bug by adding ViewFrames that contains plots. 2006-05-22 21:43:24 +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
Reidar Strand Hagen 033d4d5333 removed reorderability 2006-05-09 13:00:16 +00:00
Reidar Strand Hagen 184a49ef9a fixed ordering of multiple selected datasets 2006-05-09 12:22:50 +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
Truls Alexander Tangstad 97f56f66ac Added text-input for contrast-matrix creator for affymetrics workflow. 2006-05-05 14:30:23 +00:00
Truls Alexander Tangstad 98445498b5 If argument 'selection' exists in function.run, pass current selection to it. 2006-05-05 13:10:54 +00:00
Truls Alexander Tangstad aa3a9ab619 Added automagic argument checking when running functions. 2006-05-05 10:10:03 +00:00
Truls Alexander Tangstad 9f7ee74189 Replaced function as button-attribute with lambda as button click handler. 2006-05-04 15:32:59 +00:00
Reidar Strand Hagen 338778d7b1 Functions which doesn't require inputs will now run with data selected 2006-05-03 14:47:55 +00:00
Truls Alexander Tangstad b757da5929 Implemented PhenotypeDataset with tests. 2006-05-03 14:04:28 +00:00
Reidar Strand Hagen 56a6028547 Validation on number of inputs added 2006-05-03 11:52:54 +00:00
Truls Alexander Tangstad a613f0a3fa Made scatter use the new methods for index/identifier-conversion. 2006-05-03 11:40:12 +00:00
Reidar Strand Hagen 5b2223afcd Multiselection included. (Without input validation). 2006-05-03 11:11:45 +00:00
Truls Alexander Tangstad 91c1d8ea8b Fixed getting empty selections. 2006-05-02 15:40:54 +00:00
Truls Alexander Tangstad 56c07c6392 Implemented Dataset.get_indices() and extended Dataset.get_identifiers() to convert between indices and identifiers and subsets thereof. 
Also added tests.
 2006-05-02 14:06:48 +00:00
Truls Alexander Tangstad 2db1fc774e Removed whitespace. 2006-05-02 13:14:07 +00:00
Reidar Strand Hagen e363f1cd7d Signals for drag'n'drop added to new plots 2006-05-02 12:38:00 +00:00
Reidar Strand Hagen 4e4150236f Drag'n'drop for plots 2006-05-02 11:09:55 +00:00
Truls Alexander Tangstad a2d3a9d5cc Made PCA more generic, even enable PCA of existing PCA-results as dimension names are modified to handle dimension name component in input. 2006-04-28 11:44:55 +00:00
Reidar Strand Hagen fa3b1182bc Added font/bg colours to Navigator. (uses coloumns 3,4 in TreeModel, set in projects.py) 2006-04-27 15:51:25 +00:00
Truls Alexander Tangstad 5bb93af6f0 Changed 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.
 2006-04-27 14:38:48 +00:00
Reidar Strand Hagen c6ef6cdb07 Added auto-expand and auto-commit 2006-04-27 14:15:13 +00:00
Einar Ryeng 0df56248ee Removed obsolete module annotations. 2006-04-27 12:41:51 +00:00
Truls Alexander Tangstad 06805aa5e4 Changed colormap for LinePlot. 2006-04-27 12:05:20 +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
Einar Ryeng 60c1d19a74 Get correct path for glade file based on the path of the system package. 2006-04-27 11:20:12 +00:00
Truls Alexander Tangstad 969006015a Added LinePlot used by Affy importer. 2006-04-27 11:03:11 +00:00
Einar Ryeng c95c18eb14 fluents.glade is now read from '/system/' under the directory of argv[0]. 2006-04-27 10:54:18 +00:00
Einar Ryeng a92be02e80 Added help index and bug report menu options. 2006-04-27 09:55:19 +00:00
Einar Ryeng 2b0fdc186c Fiexd the cancel button of the new project dialog. Closes #7 2006-04-26 14:01:46 +00:00
Einar Ryeng a0ad4bdf54 Fixed logger bugs. Closes #6 2006-04-26 13:29:10 +00:00
Einar Ryeng a9947daf14 Removed debug print statements. 2006-04-26 12:57:00 +00:00
Truls Alexander Tangstad 21edeecdc3 Add toolbar support to plots, with home made selection support <phew>. 2006-04-26 12:11:23 +00:00
Einar Ryeng 490038d9bf Refreshing workflows now works. 2006-04-25 18:06:21 +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 16820cf29e The refresh button in the toolbar reloads the currently active workflow module. 2006-04-25 10:46:06 +00:00
Truls Alexander Tangstad 9d7a5ba769 Optimized plot selection. 2006-04-25 10:08:12 +00:00
Einar Ryeng 359903c5ab Made system a package. 2006-04-25 09:53:35 +00:00
Einar Ryeng 32fdca837a Moved 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.
 2006-04-24 21:52:18 +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 b807f27874 Fixed deselection in scatterplot. 2006-04-24 14:28:30 +00:00
Truls Alexander Tangstad 3fb7d06f4e Fixed problem with plots accumulating. 2006-04-24 14:25:24 +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
Truls Alexander Tangstad 2bddb22867 Fixed navigator after changes in Dataset. 2006-04-24 11:39:11 +00:00
Arnar Flatberg 6356e2ebd6 get_dim_names and get_identifiers added in dataset 2006-04-24 11:23:30 +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 53d0228074 * Added the full text of the GNU GPL. 2006-04-22 22:46:10 +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 2da88a5128 * Fixed a couple of menu items. 2006-04-22 21:56:30 +00:00
Einar Ryeng 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.
 2006-04-22 21:46:44 +00:00
Truls Alexander Tangstad d26dd54f5b Label verifier bugged when having generated labels. 2006-04-22 17:30:10 +00:00
Truls Alexander Tangstad e151e66898 Let log windows always follow changes/new entries. 2006-04-22 15:41:08 +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 0918f0019b Adding 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. 2006-04-21 14:59:25 +00:00
Truls Alexander Tangstad 832827bd5a Removed unused code. 2006-04-21 14:45:01 +00:00
Truls Alexander Tangstad 95eb78bf0d Use name of data in navigator. 2006-04-21 14:30:10 +00:00
Truls Alexander Tangstad f3a65a3c4f Can now select data in navigator by single-clicking or moving with keyboard, no need to activate (double-click etc.). 2006-04-21 14:29:08 +00:00
Truls Alexander Tangstad e4831ada13 Now can get and set name in Dataset. Also added getter for dim_names. 2006-04-21 12:28:29 +00:00
Truls Alexander Tangstad 33c9da117c Typo. 2006-04-21 10:56:56 +00:00
Arnar Flatberg fc4e62f799 current datset selection fix 2006-04-21 09:23:05 +00:00
Arnar Flatberg 7851048fb6 workflow update 2006-04-21 08:34:08 +00:00
Arnar Flatberg 2e53626393 s 2006-04-21 08:29:43 +00:00
Arnar Flatberg 800e7dc42e New pca workflow and datset updates 2006-04-20 15:30:29 +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
Truls Alexander Tangstad 78ecadb3ab Fixed label of menu item. 2006-04-20 14:11:52 +00:00
Einar Ryeng f394610724 * fluent: removed old, non-working code. 2006-04-20 10:34:50 +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
Arnar Flatberg 4541716f90 small fix 2006-04-19 19:26:14 +00:00
Arnar Flatberg 0eebd9436c object selection fix 2006-04-19 18:50:10 +00:00
Arnar Flatberg 56dac31529 Updated plots to demonstrate current selection update 2006-04-19 18:25:44 +00:00
Arnar Flatberg 1091bea0e9 category data and plot selection update| 2006-04-19 10:37:44 +00:00
Arnar Flatberg a8937ededb mainly play in plots 2006-04-18 14:25:46 +00:00
Arnar Flatberg 1d48bd85c5 added scatter 2006-04-18 09:19:59 +00:00
Einar Ryeng a0d2c0d16d * fluent, system/plots.py: Switching between four and one view now sort of 
works. Still a bit buggy, and with messy code.
 2006-04-17 22:30:53 +00:00
Einar Ryeng 494aedc1b5 * system/plots.py, system/fluent.glade: There is now an active plot. 2006-04-17 20:27:39 +00:00
Einar Ryeng 3668481562 * system/workflow.py: Loads and returns gene to GO term mapping. 2006-04-17 12:35:31 +00:00
Arnar Flatberg 2f2d54e5c8 op 2006-04-17 09:08:40 +00:00
Einar Ryeng adc3bf6bb1 * project.py: Added comments. 2006-04-17 00:29:00 +00:00
Einar Ryeng 4bdeef05f6 * annotations.py: The Annotations class now work. Querying along any 
axis is supported, but only two dimensional Annotations can be created.
 2006-04-16 23:30:01 +00:00
Arnar Flatberg 23fb12f53a First commit 2006-04-16 22:57:50 +00:00
Einar Ryeng eb45c125aa * annotations.py: Annotation class for two-way annotations. Does only support 
exactly two dimensions.
 2006-04-16 22:06:29 +00:00
Einar Ryeng 5853216df4 Initial import. 
* fluent: The application program.
 * system: The core system.
 * workflows: Directory for workflow modules.
 2006-04-16 18:25:54 +00:00