Truls Alexander Tangstad
8fd1f4ba83
Renamed module for affy workflow.
2006-04-27 15:06:01 +00:00
Truls Alexander Tangstad
5bb93af6f0
Changed generic observer pattern and project dependency in plots to be a two-way selection-listener model.
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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
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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
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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.
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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,
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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
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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
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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.
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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
Reidar Strand Hagen
Einar Ryeng
Arnar Flatberg