Commit Graph

87 Commits

Author SHA1 Message Date
8fd1f4ba83 Renamed module for affy workflow. 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.
2006-04-27 14:38:48 +00:00
c6ef6cdb07 Added auto-expand and auto-commit 2006-04-27 14:15:13 +00:00
0df56248ee Removed obsolete module annotations. 2006-04-27 12:41:51 +00:00
fe0cf736f5 Created affy workflow. 2006-04-27 12:15:30 +00:00
06805aa5e4 Changed colormap for LinePlot. 2006-04-27 12:05:20 +00:00
3683f6c2e9 Fixed labels for scatter plots. Set correct labels in go_workflow. Removed extra loadings plot. 2006-04-27 11:38:40 +00:00
60c1d19a74 Get correct path for glade file based on the path of the system package. 2006-04-27 11:20:12 +00:00
969006015a Added LinePlot used by Affy importer. 2006-04-27 11:03:11 +00:00
c95c18eb14 fluents.glade is now read from '/system/' under the directory of argv[0]. 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.
2006-04-27 10:06:30 +00:00
a92be02e80 Added help index and bug report menu options. 2006-04-27 09:55:19 +00:00
2b0fdc186c Fiexd the cancel button of the new project dialog. Closes #7 2006-04-26 14:01:46 +00:00
a0ad4bdf54 Fixed logger bugs. Closes #6 2006-04-26 13:29:10 +00:00
a9947daf14 Removed debug print statements. 2006-04-26 12:57:00 +00:00
21edeecdc3 Add toolbar support to plots, with home made selection support <phew>. 2006-04-26 12:11:23 +00:00
490038d9bf Refreshing workflows now works. 2006-04-25 18:06:21 +00:00
3e5be133ad Fixed the fluents -l bug. 2006-04-25 12:36:38 +00:00
251f9d6cf4 Added command line options to create a new project based on a given workflow. 2006-04-25 12:19:25 +00:00
16820cf29e The refresh button in the toolbar reloads the currently active workflow module. 2006-04-25 10:46:06 +00:00
9d7a5ba769 Optimized plot selection. 2006-04-25 10:08:12 +00:00
359903c5ab Made system a package. 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.
2006-04-24 21:52:18 +00:00
cfbb76f25a import * removed 2006-04-24 16:05:54 +00:00
ba2a769f01 Function names are now folders in the navigator. 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. 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. 2006-04-24 14:42:45 +00:00
b807f27874 Fixed deselection in scatterplot. 2006-04-24 14:28:30 +00:00
3fb7d06f4e Fixed problem with plots accumulating. 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.
2006-04-24 14:07:34 +00:00
cebf801cf6 bugix on creation of output data (E) from pca 2006-04-24 12:51:43 +00:00
2bddb22867 Fixed navigator after changes in Dataset. 2006-04-24 11:39:11 +00:00
6356e2ebd6 get_dim_names and get_identifiers added in dataset 2006-04-24 11:23:30 +00:00
a2e4392a72 Complete rewrite of dataset class, with (all) the necessary updates 2006-04-24 09:53:07 +00:00
53d0228074 * Added the full text of the GNU GPL. 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.
2006-04-22 22:29:02 +00:00
2da88a5128 * Fixed a couple of menu items. 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.
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.
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. 2006-04-22 20:48:44 +00:00
26f16acc9c Made sure pickling use protocol 2 to make it faster and the files smaller (binary). 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.
2006-04-22 17:59:15 +00:00
d26dd54f5b Label verifier bugged when having generated labels. 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. 2006-04-22 16:27:33 +00:00
d123f0e1c1 Added doc-string for CelFileImportFunction. 2006-04-22 15:59:19 +00:00
e151e66898 Let log windows always follow changes/new entries. 2006-04-22 15:41:08 +00:00
23914b2d1e Added support for affy cel files. 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. 2006-04-21 15:02:13 +00:00
efcd8c8587 Removed unused code. 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. 2006-04-21 14:59:25 +00:00