source: trunk/src

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Diff Rev Age Author Log Message
(edit) @3683   15 years Jari Häkkinen Spelling.
(edit) @3680   15 years Nicklas Nordborg Removed explicit call to System.gc(). Better command line parameters …
(edit) @3679   15 years Jari Häkkinen Changing the pesky "a (ä) character to a.
(edit) @3678   15 years Nicklas Nordborg Require DTD files to be encoded in ISO-8859-1
(edit) @3675   15 years Jari Häkkinen Fixing copyright statements. Fixing svn properties.
(edit) @3670   15 years Nicklas Nordborg Included numbers with scientific notation in the test.
(edit) @3668   15 years Martin Svensson Fixes #724 Nullpointer exception when 'overwrite' is not set in …
(edit) @3667   15 years Nicklas Nordborg Display free memory before AND after System.gc().
(edit) @3666   15 years Nicklas Nordborg References #469: Added negative numbers to test case with dirty data
(edit) @3665   15 years Martin Svensson Fixes #514 Change permissions in Power User
(edit) @3664   15 years Nicklas Nordborg Fixes #722: Create DynamicReporterQuery?
(edit) @3663   15 years Nicklas Nordborg Measure performance for reporter migration.
(edit) @3661   15 years Nicklas Nordborg References #720: Progress reporter when emptying trashcan Progress …
(edit) @3659   15 years Nicklas Nordborg References #294: Performance testing Added framework for testing BASE …
(edit) @3657   15 years Nicklas Nordborg Migrate reporters first.
(edit) @3656   15 years Nicklas Nordborg Fixes #719: Add support for JEP if() function
(edit) @3655   15 years Nicklas Nordborg Fixes #720: Progress reporter when emptying trashcan
(edit) @3651   15 years Jari Häkkinen Fixed svn properties issues.
(edit) @3650   15 years Nicklas Nordborg Fixed performance problem with reporter migration. Added support for …
(edit) @3649   15 years Nicklas Nordborg Make sure list of formulas get loaded to avoid …
(edit) @3648   15 years Peter Johansson refs #639 removing the exportPlainMatrix method.
(edit) @3647   15 years Nicklas Nordborg Fixes #718: BioAssaySet? tries to calculate number of spots and …
(edit) @3646   15 years Nicklas Nordborg References #451: Zipped download Fixed test program and added it to …
(edit) @3645   15 years Peter Johansson refs #639 stupid version of exportPureMatrix method that simply …
(edit) @3644   15 years Nicklas Nordborg Fixes #716: Plugin configuration import should be able ot set the …
(edit) @3643   15 years Nicklas Nordborg Fixes #451: Zipped download Added user and plug-in developer documentation
(edit) @3642   15 years Nicklas Nordborg Fixes #715: Install should set same permission on plugin …
(edit) @3641   15 years Nicklas Nordborg References #451: Zipped download Major redesign of the packing …
(edit) @3640   15 years Johan Enell a plugin can have no parameters
(edit) @3639   15 years Johan Enell Fixes #714
(edit) @3638   15 years Nicklas Nordborg Fixes #713: Differences in the configuration file from base1
(edit) @3637   15 years Nicklas Nordborg Fixes #710: Allow subclasses to AbstractFlatFileParser? to participate …
(edit) @3635   15 years Nicklas Nordborg References #358: Better info from Migration tool Show log message …
(edit) @3634   15 years Nicklas Nordborg Fixes #573: Trim whitespace when checking for unique values
(edit) @3633   15 years Nicklas Nordborg References #574. Test program didn't report error properly
(edit) @3632   15 years Johan Enell Fixes #713
(edit) @3631   15 years Nicklas Nordborg Fixes #701: JarClassLoader? should be able to auto-reload based on timestamp
(edit) @3629   15 years Nicklas Nordborg Fixes #712, References #711
(edit) @3628   15 years Nicklas Nordborg References #625: PrintMapFlatFileImporter?.isInContext now checks if …
(edit) @3627   15 years Nicklas Nordborg References #709: Forgot to add predefined query
(edit) @3626   15 years Nicklas Nordborg Fixes #486: Import raw data from the Illumina platform
(edit) @3625   15 years Nicklas Nordborg Fixes #709: Install should install missing plug-in configurations when …
(edit) @3624   15 years Nicklas Nordborg Fixes #708: "NaN" and "Infinity" values in files causes SqlException?
(edit) @3622   15 years Johan Enell Fixes #700, #590
(edit) @3619   15 years Nicklas Nordborg Include test for selecting a parameter expression in SQL: SELECT …
(edit) @3618   15 years Nicklas Nordborg Fixes #702: Add lineNum() function(s) to mapping expressions supported …
(edit) @3617   15 years Nicklas Nordborg Fixes #703: Error message when loading invalid XML files doesn't …
(edit) @3616   15 years Nicklas Nordborg References #698: Fix Javadoc warnings Removed all existing warnings. …
(edit) @3615   15 years Nicklas Nordborg Fixes #691: Make LowessNormalization? and MedianRatioNormalization?
(edit) @3614   15 years Johan Enell Fixes #699
(edit) @3613   15 years Johan Enell Fixes #673
(edit) @3610   15 years Nicklas Nordborg References #360: Make subsections on view pages hideable …
(edit) @3607   15 years Nicklas Nordborg References #551: Write "Plugin developer" section Now ready for reading.
(edit) @3606   15 years Nicklas Nordborg Fixes #697: Uploading and unpacking a compressed file corrupts the file
(edit) @3604   15 years Nicklas Nordborg Fixes #257: Fix the Jep.nodeToExpression method
(edit) @3603   15 years Nicklas Nordborg Undo last commit which was done by accident.
(edit) @3602   15 years Nicklas Nordborg
(edit) @3601   15 years Nicklas Nordborg References #692: Fixes possible NullPointerException? in update
(edit) @3600   15 years Nicklas Nordborg Fixes #480: Verify values in extended-properties.xml and raw-data-types.xml
(edit) @3598   15 years Nicklas Nordborg Fixes #566: Plugins using the flat file parser should warn about …
(edit) @3597   15 years Nicklas Nordborg Fixes #655: Plugins -> defintions fails with 'illegal attempt to …
(edit) @3596   15 years Nicklas Nordborg Fixes #654: Batch deletion of reporters
(edit) @3594   15 years Nicklas Nordborg Fixes #626: Remove base1executor any to any links
(edit) @3593   15 years Nicklas Nordborg Fixes #692: Jobs that are part of an experiment should use permissions …
(edit) @3592   15 years Nicklas Nordborg Fixes #687: Make it possible for other plug-ins than the FormulaFilter?
(edit) @3590   15 years Nicklas Nordborg Fixes #688: Don't use Float.valueOf() or Float.parseString() to parse …
(edit) @3588   15 years Nicklas Nordborg Fixes #326: Mass annotation plug-in
(edit) @3587   15 years Martin Svensson References #686 Two more coreplugins are updated …
(edit) @3586   15 years Nicklas Nordborg References #326: Mass annotation plug-in Major features in place. …
(edit) @3585   15 years Martin Svensson Fixes #685 The documentation is done
(edit) @3584   15 years Martin Svensson References #686 Updated gui contexts in JepExtraValueCalculator? to …
(edit) @3583   15 years Martin Svensson References #686 Jep Formula Filter and JepExtraValueCalculator? can now …
(edit) @3580   15 years Nicklas Nordborg Fixes #690: Not allowed to read Extra value type
(edit) @3576   15 years Martin Svensson References #451 Avoid null pointer exception
(edit) @3575   15 years Martin Svensson Fixes #685 Add plugin parameter asking for bioassays to …
(edit) @3572   15 years Martin Svensson Fixes #451 This plugin is now installed with BASE as a core plugin and …
(edit) @3571   15 years Martin Svensson References #451 Some minor bugs are fixed.
(edit) @3569   15 years Nicklas Nordborg Fixes #684: AbstractAnalysisPlugin? should not include [Item.BIOASSAYS, …
(edit) @3568   15 years Martin Svensson References #451 Packer plugin for zip, tar.gz and tar.bz2 format …
(edit) @3564   15 years Nicklas Nordborg Fixes #675, #676 and #677
(edit) @3562   15 years Nicklas Nordborg Fixes #649 and #674
(edit) @3561   15 years Nicklas Nordborg Fixes #672: Enable AnnotationRestriction? to be used on joined tables
(edit) @3560   15 years Nicklas Nordborg References #573. Must also trim annotation values or the filter will …
(edit) @3558   15 years Nicklas Nordborg Fixes #669
(edit) @3557   15 years Nicklas Nordborg Fixes #648
(edit) @3556   15 years Nicklas Nordborg Fixes #648 and #650
(edit) @3555   15 years Martin Svensson Reference #451 The actual compression is not quite written yet.
(edit) @3554   15 years Johan Enell Fixes #671, References #590 Test for BioAssaySetExporter? added which …
(edit) @3552   15 years Martin Svensson References #375. Only wants to do a commit before the weekend.
(edit) @3547   15 years Martin Svensson References #375. The first part is done, listing which …
(edit) @3545   15 years Johan Enell Merged log:branches/2.3.2#3537:3542 to trunk.
(edit) @3544   15 years Martin Svensson Fixes #191. Updating schema version and added since(javadoc) to new methods
(edit) @3536   15 years Martin Svensson References #625. This will correct the issue related to #657
(edit) @3535   15 years Martin Svensson References #191
(edit) @3534   15 years Martin Svensson References #657
(edit) @3532   15 years Martin Svensson Fixes #358 Better info from migration tool
(edit) @3531   15 years Martin Svensson References #358. Some changes on the log statements
(edit) @3530   15 years Johan Enell some admin changes
(edit) @3529   15 years Martin Svensson References #358. Use log4j properly in migration. Updated more …
(edit) @3528   15 years Johan Enell AverageMethod? added Fixes #648
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