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  • 2bae169f38 Annotation display now works (sort of). einarr 2007-02-21 16:39:04 +00:00
  • 28aca8c621 added project to selection controller flatberg 2007-02-21 13:57:48 +00:00
  • 8c03338b75 hypergeometric test (scipy version has errors) flatberg 2007-02-21 13:03:51 +00:00
  • 48165d1aed Updated the selection controller with sorting ++ flatberg 2007-02-21 12:41:37 +00:00
  • f0b2660813 Selection listeners are now notified when new dimensions are added (because this implies that an empty selection is made on the new dimension). einarr 2007-02-21 12:05:08 +00:00
  • 5800e7e362 Fixed a bug that prevented the first selection on a dimension to come from a dataset. einarr 2007-02-21 11:49:43 +00:00
  • a5955f9b59 Now updates the DimListConroller when a CategoryDataset is drag'n'dropped into SelectionListController. einarr 2007-02-21 11:43:00 +00:00
  • c5c4f13a19 Fixed some excessively long lines. einarr 2007-02-21 11:08:20 +00:00
  • 2cc4e86b0a Split selections.py into three different controller classes, one for each list. There is still some work to be done, and bugs to be fixed. einarr 2007-02-21 00:00:26 +00:00
  • a2195bcb4b Added Import annotations option. einarr 2007-02-16 11:23:29 +00:00
  • 93a2f404d2 Data needed if annotationtest should run clean. einarr 2007-02-15 23:09:49 +00:00
  • 6809c1a454 Added some annotation support in selections.py, including the beginning of a menu option to add an arbitrary annotation alongside identifiers. einarr 2007-02-15 22:57:40 +00:00
  • 953662e1fb Added a couple of more assertions to the test of read_annotations_file() einarr 2007-02-15 22:54:08 +00:00
  • e6cf8f765a Added read_annotations_file() einarr 2007-02-15 22:49:40 +00:00
  • b17f04466b Added read_annotations_file() which reads a tab delimited file containing annotations to identifiers along a dimension. einarr 2007-02-15 22:42:55 +00:00
  • 4319e8630e fixed error in typechecking flatberg 2007-02-15 13:36:36 +00:00
  • fc33c2dbfc factored out packer flatberg 2007-02-09 14:02:58 +00:00
  • 15c89fb9b5 Factored out packer A packer.py flatberg 2007-02-09 14:02:39 +00:00
  • 7eb13b14cb Removed resolution arg to Circle to avoid construction of a circlepolygon (deprecated) flatberg 2007-02-02 12:21:19 +00:00
  • 320cd97512 Removed noise generating print statements. einarr 2007-01-31 14:58:37 +00:00
  • 75b66914fd Fixed bug by removing hardcoded filename. einarr 2007-01-31 14:56:43 +00:00
  • 74cb30428c Added annotations to identifiers, and converted the unused annotationtest.py to test the new module. einarr 2007-01-31 14:19:23 +00:00
  • 1863bfc564 Save plot enabled flatberg 2007-01-31 13:26:46 +00:00
  • a7c60ffe64 added venn diagram test plot flatberg 2007-01-31 13:03:27 +00:00
  • 240b0a4a9f New lasso icon flatberg 2007-01-31 13:02:25 +00:00
  • d1205ae67f Removed colorbar flatberg 2007-01-31 13:01:09 +00:00
  • 37feb1c25b bugfix on P scale flatberg 2007-01-31 13:00:36 +00:00
  • 2cfa3ca415 spin on a/o, colorbar on keypress flatberg 2007-01-31 12:59:21 +00:00
  • 63be80aa92 pls options added flatberg 2007-01-31 12:03:11 +00:00
  • 088f180b5d Barplot, lots of changes in scatter, disabled modes, removed labels, bugfix on lasso flatberg 2007-01-31 12:02:11 +00:00
  • e716db3fd2 Added center option to validation, + naming updates flatberg 2007-01-31 11:59:23 +00:00
  • 29509902df bugfix on shape flatberg 2007-01-31 11:57:59 +00:00
  • 8e607c7b1a bugfixed scaling issues flatberg 2007-01-31 11:57:04 +00:00
  • f064b7134d Removed scale option added pack flatberg 2007-01-31 11:56:28 +00:00
  • 1d5929f14c pls options glade file flatberg 2007-01-31 11:55:43 +00:00
  • ed2848beb3 Errors when identifers dont match shape, + whitespace flatberg 2007-01-31 11:54:54 +00:00
  • 48bb47ec86 Bugfixed pca flatberg 2007-01-25 12:36:32 +00:00
  • aeb37cf4cd Added supportp for tall X in PCA flatberg 2007-01-25 12:17:16 +00:00
  • fa3722600c pca options glade file flatberg 2007-01-25 12:15:30 +00:00
  • 61bfc236e6 Changed location of PCA options glade file. einarr 2007-01-25 12:15:19 +00:00
  • 7a204a3426 Added option page to option dialog flatberg 2007-01-25 12:10:18 +00:00
  • 1c2c2c8895 Multiple lib changes flatberg 2007-01-25 11:58:10 +00:00
  • a65d79697f Added Expand/Collapse menu choices to the GO browser context menu. This is particularly useful when searching for GO terms, because the gtk TreeView widget does not do interactive search in collapsed parts of the tree. einarr 2007-01-21 16:16:37 +00:00
  • e03cc4ed4c Added a ScrolledWindow around the navigator. einarr 2007-01-19 14:00:10 +00:00
  • 7693f336ba Added a singleton project in the project module, so that the current project is easily accessible from anywhere in the code. As there is only one project at any given time this should not be a problem. einarr 2007-01-18 15:45:48 +00:00
  • f533344242 Added histogram in plot menu flatberg 2007-01-17 15:40:54 +00:00
  • 7c20e6d780 Added simple histogram flatberg 2007-01-17 15:40:33 +00:00
  • 1ffbf4f9e7 Added default implementation of set_current_selection in Plot, so that plots can safely ignore selections without adding any code to the plot. einarr 2007-01-17 15:35:12 +00:00
  • 06591e301e Added "Plot" submenu in navigator context menu. Can create an ImagePlot of a dataset. einarr 2007-01-17 14:06:07 +00:00
  • c3c6e85044 Added ImagePlot, which displays a dataset as an image. einarr 2007-01-17 13:20:04 +00:00
  • 33c51505c4 Fixed the dataset loading so that it returns a correctly named Dataset. einarr 2007-01-16 12:41:29 +00:00
  • f612dda72f Fixed bug in ftsv save and open dialogs. The save dialog now looks as intended. Added the possibility to load several datasets at once. Error handling should still be improved. einarr 2007-01-16 12:28:56 +00:00
  • ea4c0af6de fixed shift/control on lasso flatberg 2007-01-15 15:46:24 +00:00
  • cacb0a27b7 Added "Save dataset" option to navigator context menu. einarr 2007-01-15 13:58:56 +00:00
  • 476c830a5e lasso flatberg 2007-01-15 13:47:47 +00:00
  • 0a38cb7d4a added lasso flatberg 2007-01-15 13:47:18 +00:00
  • ee447b688c Added context menu to NavigatorView that allows reading FTSV datasets directly, i.e. without adding a function in the workflow for this. einarr 2007-01-12 14:37:44 +00:00
  • 58886726d8 Small updates. einarr 2007-01-12 10:50:55 +00:00
  • ae3aa7e4aa Create Resnik distances and save them as ftsv. einarr 2007-01-12 00:00:56 +00:00
  • 08b7d8dd85 Added function to save fluents tab separated values (ftsv) files. einarr 2007-01-11 23:24:05 +00:00
  • e4d7f8e5a2 Resnik distances between GO terms work now. einarr 2007-01-11 22:01:31 +00:00
  • 4b1d16ea78 Updated go-workflow. einarr 2007-01-11 18:57:45 +00:00
  • 3340b1b7ac Added support for union/intersection selections flatberg 2007-01-11 13:07:54 +00:00
  • d4f5a92010 Fixed typo. einarr 2007-01-11 13:07:03 +00:00
  • 9274b044b7 Added read_ftsv in dataset.py. This method reads fluents tab separated values files and returns a dataset. einarr 2007-01-10 17:35:58 +00:00
  • 060732d980 More persumably non-working stuff. einarr 2007-01-10 15:33:19 +00:00
  • 1e0b99f283 small bugfix flatberg 2007-01-09 08:53:28 +00:00
  • fa047e0171 Committing non-working code that breaks go workflow. ;) einarr 2007-01-08 21:13:22 +00:00
  • 6f050d4f10 Fixed error in docstring. einarr 2007-01-08 19:31:19 +00:00
  • 1371bc1b1a Added function menu. Clicking the items still does not work, though. einarr 2007-01-05 14:42:22 +00:00
  • f7fe171896 Added Optionsdialog for pca and pls flatberg 2007-01-04 13:53:47 +00:00
  • e08a8377ed Added Options and OptionsDialog flatberg 2007-01-04 13:53:03 +00:00
  • ebd4fdae7b Changed all places that load icons to do it through IconFactory. einarr 2007-01-03 17:30:27 +00:00
  • 57e58e3910 Renamed IconFactory.get_icon() -> IconFactory.get() einarr 2007-01-03 13:46:39 +00:00
  • d45ae4f480 Added icon factory to ensure that all icons are loaded exactly once. This also cleans up code and saves X pixmap memory. einarr 2007-01-03 13:34:40 +00:00
  • 75447d8840 Fixed function output bug. Datasets now appear as children of their first parent, also in gtk 2.10 einarr 2007-01-03 13:05:37 +00:00
  • c34f23190b init flatberg 2007-01-02 15:10:59 +00:00
  • 3ef5522dd0 First import of chemometrics utils flatberg 2006-12-18 11:59:12 +00:00
  • fac9346aad Added very hackish annotation count reader. einarr 2006-12-15 12:53:27 +00:00
  • 6aa1a1a817 Code upgraded to adjust for new version of networkx flatberg 2006-11-24 13:29:09 +00:00
  • 880509f8a9 Removed whitespace that broke plots. einarr 2006-10-31 14:35:12 +00:00
  • fb77ddb549 Updated GO workflow. Options class test added. Reading the ontology takes too long. einarr 2006-10-26 16:51:42 +00:00
  • 438dbd358b Dataset to colour of dragndrop in dataset + minor addjustments in networkplot flatberg 2006-10-25 12:56:21 +00:00
  • 0b30aeac6f Updated GO workflow. einarr 2006-10-22 23:19:54 +00:00
  • 5491f5ce04 GO workflow. Does not work. einarr 2006-10-22 15:31:36 +00:00
  • de4a65e7b3 Added the svg format icon for move flatberg 2006-10-18 12:47:01 +00:00
  • cdb8d1b026 Removed unit test for workflows. The only test file in the directory is for a workflow that is not used. einarr 2006-10-17 17:53:52 +00:00
  • 1f9a400057 Added docstrings. einarr 2006-10-17 17:50:42 +00:00
  • f7ededa451 Removed executable bit. einarr 2006-10-17 17:50:18 +00:00
  • fe96772319 Expanded some documentation. einarr 2006-10-17 17:18:46 +00:00
  • 5d4700da20 Removed some example rubbish that was placed after the GPL and had gotten inside the file due to sloppy cut-n-paste. einarr 2006-10-17 17:17:50 +00:00
  • fb3d9f2050 Added documentation directory with a Makefile to generate source code documentation. This adds python-epydoc as a build dependency. einarr 2006-10-17 15:06:24 +00:00
  • 4153f06c60 Added start-up script that sets PYTHONPATH and starts fluents. einarr 2006-10-17 14:43:57 +00:00
  • 375d45e0cc Updated import statements, and removed the workflows pca_workflow and affy_workflow. einarr 2006-10-17 14:42:27 +00:00
  • 610812f265 Started to rename "system" package to "fluents". Repository will be broken until this is completed. einarr 2006-10-17 14:28:35 +00:00
  • c40f9a2947 Added a LineViewPlot in GenerateData flatberg 2006-10-17 13:59:31 +00:00
  • bf951990f5 Comments and cleanup in LineViewPlot flatberg 2006-10-17 13:58:33 +00:00
  • ba55678472 Added documentation strings and removed some unused code. einarr 2006-10-17 12:33:30 +00:00
  • 42f6fd7440 Yet another bugfix on the plot updates. View frames will now be updated from the upper left corner, horizontally first. einarr 2006-10-17 10:37:46 +00:00
  • 4b8ff16bbf Another bug fix. Double-clicking function output works, also after changing table size. einarr 2006-10-17 10:32:53 +00:00