Projects/laydi
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  • a613f0a3fa Made scatter use the new methods for index/identifier-conversion. tangstad 2006-05-03 11:40:12 +00:00
  • 5b2223afcd Multiselection included. (Without input validation). reidarst 2006-05-03 11:11:45 +00:00
  • 91c1d8ea8b Fixed getting empty selections. tangstad 2006-05-02 15:40:54 +00:00
  • 56c07c6392 Implemented Dataset.get_indices() and extended Dataset.get_identifiers() to convert between indices and identifiers and subsets thereof. Also added tests. tangstad 2006-05-02 14:06:48 +00:00
  • bda48169fe Fixed imports to make test run. tangstad 2006-05-02 13:21:24 +00:00
  • 2db1fc774e Removed whitespace. tangstad 2006-05-02 13:14:07 +00:00
  • e363f1cd7d Signals for drag'n'drop added to new plots reidarst 2006-05-02 12:38:00 +00:00
  • 4e4150236f Drag'n'drop for plots reidarst 2006-05-02 11:09:55 +00:00
  • a2d3a9d5cc Made PCA more generic, even enable PCA of existing PCA-results as dimension names are modified to handle dimension name component in input. tangstad 2006-04-28 11:44:55 +00:00
  • fa3b1182bc Added font/bg colours to Navigator. (uses coloumns 3,4 in TreeModel, set in projects.py) reidarst 2006-04-27 15:51:25 +00:00
  • 8fd1f4ba83 Renamed module for affy workflow. tangstad 2006-04-27 15:06:01 +00:00
  • 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. tangstad 2006-04-27 14:38:48 +00:00
  • c6ef6cdb07 Added auto-expand and auto-commit reidarst 2006-04-27 14:15:13 +00:00
  • 0df56248ee Removed obsolete module annotations. einarr 2006-04-27 12:41:51 +00:00
  • fe0cf736f5 Created affy workflow. tangstad 2006-04-27 12:15:30 +00:00
  • 06805aa5e4 Changed colormap for LinePlot. tangstad 2006-04-27 12:05:20 +00:00
  • 3683f6c2e9 Fixed labels for scatter plots. Set correct labels in go_workflow. Removed extra loadings plot. tangstad 2006-04-27 11:38:40 +00:00
  • 60c1d19a74 Get correct path for glade file based on the path of the system package. einarr 2006-04-27 11:20:12 +00:00
  • 969006015a Added LinePlot used by Affy importer. tangstad 2006-04-27 11:03:11 +00:00
  • c95c18eb14 fluents.glade is now read from '/system/' under the directory of argv[0]. einarr 2006-04-27 10:54:18 +00:00
  • 959d114774 Changed 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. einarr 2006-04-27 10:06:30 +00:00
  • a92be02e80 Added help index and bug report menu options. einarr 2006-04-27 09:55:19 +00:00
  • 2b0fdc186c Fiexd the cancel button of the new project dialog. Closes #7 einarr 2006-04-26 14:01:46 +00:00
  • a0ad4bdf54 Fixed logger bugs. Closes #6 einarr 2006-04-26 13:29:10 +00:00
  • a9947daf14 Removed debug print statements. einarr 2006-04-26 12:57:00 +00:00
  • 21edeecdc3 Add toolbar support to plots, with home made selection support <phew>. tangstad 2006-04-26 12:11:23 +00:00
  • 490038d9bf Refreshing workflows now works. einarr 2006-04-25 18:06:21 +00:00
  • 3e5be133ad Fixed the fluents -l bug. einarr 2006-04-25 12:36:38 +00:00
  • 251f9d6cf4 Added command line options to create a new project based on a given workflow. einarr 2006-04-25 12:19:25 +00:00
  • 16820cf29e The refresh button in the toolbar reloads the currently active workflow module. einarr 2006-04-25 10:46:06 +00:00
  • 9d7a5ba769 Optimized plot selection. tangstad 2006-04-25 10:08:12 +00:00
  • 359903c5ab Made system a package. einarr 2006-04-25 09:53:35 +00:00
  • 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. einarr 2006-04-24 21:52:18 +00:00
  • cfbb76f25a import * removed flatberg 2006-04-24 16:05:54 +00:00
  • ba2a769f01 Function names are now folders in the navigator. einarr 2006-04-24 15:20:27 +00:00
  • 179a2f88a9 The navigator now displays the plots and data in a tree that shows the ancestry information. einarr 2006-04-24 14:52:21 +00:00
  • 6c72dec7fa Removed need to provide plots with project/workflow on creation, is instead injected by project itself when added to it. tangstad 2006-04-24 14:42:45 +00:00
  • b807f27874 Fixed deselection in scatterplot. tangstad 2006-04-24 14:28:30 +00:00
  • 3fb7d06f4e Fixed problem with plots accumulating. tangstad 2006-04-24 14:25:24 +00:00
  • 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. tangstad 2006-04-24 14:07:34 +00:00
  • cebf801cf6 bugix on creation of output data (E) from pca flatberg 2006-04-24 12:51:43 +00:00
  • 2bddb22867 Fixed navigator after changes in Dataset. tangstad 2006-04-24 11:39:11 +00:00
  • 6356e2ebd6 get_dim_names and get_identifiers added in dataset flatberg 2006-04-24 11:23:30 +00:00
  • a2e4392a72 Complete rewrite of dataset class, with (all) the necessary updates flatberg 2006-04-24 09:53:07 +00:00
  • 53d0228074 * Added the full text of the GNU GPL. einarr 2006-04-22 22:46:10 +00:00
  • e762aef882 * system/dialogs.py: Oooops. Forgot this file in the previous commits. Well, here it is, currently only with the New Project dialog. einarr 2006-04-22 22:29:02 +00:00
  • 2da88a5128 * Fixed a couple of menu items. einarr 2006-04-22 21:56:30 +00:00
  • f484ec9945 * workflows/go_workflow.py: Added a workflow name to make it identifiable in the "create project" druid. einarr 2006-04-22 21:48:30 +00:00
  • 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. einarr 2006-04-22 21:46:44 +00:00
  • 357cd1a1a6 Removed workflow being dependent on rpy by putting the import within the run function of affymatrix import. tangstad 2006-04-22 20:48:44 +00:00
  • 26f16acc9c Made sure pickling use protocol 2 to make it faster and the files smaller (binary). tangstad 2006-04-22 18:11:31 +00:00
  • 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. tangstad 2006-04-22 17:59:15 +00:00
  • d26dd54f5b Label verifier bugged when having generated labels. tangstad 2006-04-22 17:30:10 +00:00
  • 5a2a1afe91 Added pickling as a quick and dirty way of loading and saving data in einars workflow. tangstad 2006-04-22 16:27:33 +00:00
  • d123f0e1c1 Added doc-string for CelFileImportFunction. tangstad 2006-04-22 15:59:19 +00:00
  • e151e66898 Let log windows always follow changes/new entries. tangstad 2006-04-22 15:41:08 +00:00
  • 23914b2d1e Added support for affy cel files. tangstad 2006-04-22 00:17:22 +00:00
  • c601ad3966 Removed data information as function in workflow and added as default action on datasets double-clicked in navigator. tangstad 2006-04-21 15:02:13 +00:00
  • efcd8c8587 Removed unused code. tangstad 2006-04-21 15:00:04 +00:00
  • 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. tangstad 2006-04-21 14:59:25 +00:00
  • 79481ed186 Added plot to output from test-function. tangstad 2006-04-21 14:58:42 +00:00
  • 832827bd5a Removed unused code. tangstad 2006-04-21 14:45:01 +00:00
  • 95eb78bf0d Use name of data in navigator. tangstad 2006-04-21 14:30:10 +00:00
  • f3a65a3c4f Can now select data in navigator by single-clicking or moving with keyboard, no need to activate (double-click etc.). tangstad 2006-04-21 14:29:08 +00:00
  • 07ac564668 Changed info function to show dialog instead of returning a view. tangstad 2006-04-21 14:12:18 +00:00
  • c4f9f5c399 Created new workflow for showing information about a dataset as a view. tangstad 2006-04-21 13:04:31 +00:00
  • e4831ada13 Now can get and set name in Dataset. Also added getter for dim_names. tangstad 2006-04-21 12:28:29 +00:00
  • 33c9da117c Typo. tangstad 2006-04-21 10:56:56 +00:00
  • ccec17262b Added random test data flatberg 2006-04-21 10:56:01 +00:00
  • facf706420 * Removed PCA workflow dependence. einarr 2006-04-21 09:55:50 +00:00
  • fc4e62f799 current datset selection fix flatberg 2006-04-21 09:23:05 +00:00
  • 7851048fb6 workflow update flatberg 2006-04-21 08:34:08 +00:00
  • aa6f598f87 workflow update flatberg 2006-04-21 08:30:37 +00:00
  • 2e53626393 s flatberg 2006-04-21 08:29:43 +00:00
  • 800e7dc42e New pca workflow and datset updates flatberg 2006-04-20 15:30:29 +00:00
  • c09f2ceb92 * fluent, *.py: Data and plots returned from functions will now show up in the navigator window. einarr 2006-04-20 14:29:13 +00:00
  • 78ecadb3ab Fixed label of menu item. tangstad 2006-04-20 14:11:52 +00:00
  • f394610724 * fluent: removed old, non-working code. einarr 2006-04-20 10:34:50 +00:00
  • 6a4ae8ecf1 mainly overhaul of observers, and removal of project singleton flatberg 2006-04-20 10:27:58 +00:00
  • f45c9c6bf7 * fluent: General cleanup. einarr 2006-04-19 19:59:55 +00:00
  • 4541716f90 small fix flatberg 2006-04-19 19:26:14 +00:00
  • 0eebd9436c object selection fix flatberg 2006-04-19 18:50:10 +00:00
  • 56dac31529 Updated plots to demonstrate current selection update flatberg 2006-04-19 18:25:44 +00:00
  • 1091bea0e9 category data and plot selection update| flatberg 2006-04-19 10:37:44 +00:00
  • a8937ededb mainly play in plots flatberg 2006-04-18 14:25:46 +00:00
  • 1d48bd85c5 added scatter flatberg 2006-04-18 09:19:59 +00:00
  • a0d2c0d16d * fluent, system/plots.py: Switching between four and one view now sort of works. Still a bit buggy, and with messy code. einarr 2006-04-17 22:30:53 +00:00
  • c55a39f7f9 * workflows/go_workflow.py: A workflow that makes distance matrices based on gene ontology information. Currently only reads gene annotations. einarr 2006-04-17 20:29:29 +00:00
  • 494aedc1b5 * system/plots.py, system/fluent.glade: There is now an active plot. einarr 2006-04-17 20:27:39 +00:00
  • 3668481562 * system/workflow.py: Loads and returns gene to GO term mapping. einarr 2006-04-17 12:35:31 +00:00
  • 2f2d54e5c8 op flatberg 2006-04-17 09:08:40 +00:00
  • adc3bf6bb1 * project.py: Added comments. einarr 2006-04-17 00:29:00 +00:00
  • 4bdeef05f6 * annotations.py: The Annotations class now work. Querying along any axis is supported, but only two dimensional Annotations can be created. einarr 2006-04-16 23:30:01 +00:00
  • 23fb12f53a First commit flatberg 2006-04-16 22:57:50 +00:00
  • eb45c125aa * annotations.py: Annotation class for two-way annotations. Does only support exactly two dimensions. einarr 2006-04-16 22:06:29 +00:00
  • 5853216df4 Initial import. * fluent: The application program. * system: The core system. * workflows: Directory for workflow modules. einarr 2006-04-16 18:25:54 +00:00
  • bb246a77d7 Initial directory creation. einarr 2006-04-16 18:18:22 +00:00