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
fe0cf736f5
Created affy workflow.
2006-04-27 12:15:30 +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
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
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
3e5be133ad
Fixed the fluents -l bug.
2006-04-25 12:36:38 +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
Arnar Flatberg
cfbb76f25a
import * removed
2006-04-24 16:05:54 +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
Arnar Flatberg
cebf801cf6
bugix on creation of output data (E) from pca
2006-04-24 12:51:43 +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
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
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
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
d26dd54f5b
Label verifier bugged when having generated labels.
2006-04-22 17:30:10 +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
e151e66898
Let log windows always follow changes/new entries.
2006-04-22 15:41:08 +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
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
79481ed186
Added plot to output from test-function.
2006-04-21 14:58:42 +00:00
Truls Alexander Tangstad
Reidar Strand Hagen
Einar Ryeng
Arnar Flatberg