Changes Before Version 5.0.5

Created a compiled version of the budding yeast objective
Wrote help text for budding yeast phenotype objective
Updated tests using sbml files to keep up with sbml2 library changes
Updated data files to work in a single directory per project
Simplified installation instructions on front page
Updated test plan to indicate the new directory for data files
Renamed budding yeast phenotypes to indicate their intended application
Modified budding yeast data files to use new phenotype names and compiled version of the objective function
Added phenotype for the generic cell cycle model
Added transform for the generic cell cycle model
Added objective function for the generic cell cycle model
Wrote help text for generic cell cycle transform and objective
Changed states in generic and budding yeast scan transforms to be 1 based
Modified generic scan transform to flag invalid state transititions
Fixed the add 5 rows option in the table editors
Updated data files for generic budding yeast model
Fixed generic phenotype objective result when the experiment is given as inviable but the number of successful cycles is missing
Created an editor base class for BasicTable
Made the foreground color of unentered data configurable
Converted renderer for BasicTable to use a basic table host
Replaced uses of DefaultCellEditor with BasicEditor
Plotter now validates the input to its public methods
Replaced plotter options with data source options
Broke apart PTPlotBridge.plot
Documented the series combining options in IPlotter
Eliminated static methods for changing options in Plotter
Removed IPlotter.getData
Modified generic objective to accept either real or integral data when real data is expected
Enabled testing of error codes in budding yeast objective
Fixed error codes in budding yeast data
Added two new mutants to budding yeast data and run file
Changed the combine options in IPlotter to be an enumeration
Extended PTPlotBridge to produce an image of the plot window
Made ClipboardDataSource use the name of the clipboard as its name
Added a generic name for data sources based on printers
Created a report generation tool for recording the result of a comparison
Fixed name of menu option for report generator
Fixed name of action button for printing to PDF
Moved constant transform to the public area and added a test for it to the transform tests
Made the plot range configurable with PTPlotBridge
Added a configurable display component to ConstantTransform
Added support for separators to InterfaceBuilder
Created a configuration interfafce for the report generation tool
Made having a computed objective function optional when generating a report
Changed report generator to search for a transform that produces a time course to use
Fixed potential concurrency issue if a report was generated while objectives or transforms were being evaluated
Report generator now gives the names of graph columns when known
Added support for an annotation to ConstantTransform
Added display of column names for the currently selected prototype experiment to report generator
Enabled selection of columns in report generator
Fixed display of available column selections when changing the prototype experiment in report generator
Added specifying the enable state of a component tree rooted with a labeled component in InterfaceBuilder
Changed CachedDataElement to forward getType() calls
Fixed available column selection in report generator when filtering is being performed on the columns using transforms
Fixed bug in Comparator system tests with file paths

Changes Before Version 5.0.4

Prevented subclassing from Blackboard
Changed Blackboard to never directly alter member data after initialization
Prevented subclassing from ClipboardDataSource
Prevented subclassing from ComparatorDataFlavor
Changed ComparatorDataFlavor to never directly alter member data after initialization
Prevented subclassing from DataManager
Changed DataManager to never directly alter member data after initialization
Prevented subclassing from ExceptionRecorder
Changed ExceptionRecorder to never directly alter member data after initialization
Prevented subclassing from SuffixFileFilter
Prevented subclassing from XMLFileEncoder
Change XMLFileEncoder to remove transient declarations and to never alter the data source
Prevented subclassing from PDFPrinterDataSource and SystemPrinterDataSource
Changed ConstantTransform to provide a result name
Added unit tests for TransformEvaluationTransform
Added unit tests for BoxTransformContainer
Fixed initialization of the boxed transform in BoxedTransformContainer
Added unit tests for InputTransform
Fixed propagation of the Comparator root to children of a transform container
Fixed preservation of popup menu flags when copying a transform
Changed frogegg objective function acceptability criterion
Prevented subclassing from JPlot or Ptplot helpers
Minor documentation cleanup in plotter package
Created a PlotException class to distinguish exceptions during plotting
Centralized exception handling for plotting in EditableSeriesView
Improved error message when configuration file is missing
Eliminated peeking into an exception except in showErrorTrace
Added help for BuddingYeastScanTransform
Added stubs for a compiled version of the budding yeast objective

Changes Before Version 5.0.3

Updated data files used in benchmarks
Used proxy builder to eliminate inner classes in debug console
Used proxy builder to eliminate most public interface from debug console
Added display of evaluation result after command echo to debug console
Cleaned up debug console code to make reading easier
Debug console now displays the exception trace when an error occurs
Added the ability to run scripts from files when the program starts
Updated data files used in budding yeast model
Added scaling by wildtype mass to budding yeast scan transform
Allowed state checking to be done on the first step of a new cycle in budding yeast scan transform
Skipped the check for ORI inactivation in first cycle of budding yeast scan transform
Simplified cycle scanning in budding yeast scan transform
Reduced the budding threshold to 0.8 in budding yeast scan transform
Made references to non-static inner classes from static inner classes in the same containing class be fully qualified to satisfy stricter compiler
Fixed sort order of results in Compare^2 when loading a result set group before loading the objective set
Fixed Compare^2 crunching the columns when it tries to update the layout
Fixed new compiler warnings identified by jikes 1.22

Changes Before Version 5.0.2

Added a new suite of unit tests for data elements of all types
Made the property checked for by system tests volatile to prevent optimizing out of loop
Added a new suite of unit tests for tab functions
Fixed an exception caused by setting a source without a location
Cleaned up system unit tests and added several new ones
Added help descriptions for ScriptEvaluationTransform and ScriptEvaluationObjective
Fixed missing documentation in constructors for RawFileDataSource and XMLFileDataSource
Budding yeast scan interface now displays all of the threshold and limit values being used

Changes Before Version 5.0.1

Added proxy for creating Comparator objects
Removed Comparator implementations from ProgrammableDataGeneratorEditor, TransformEditor, ObjectiveEditor
Refactored the event handling in TransformEditor and ObjectiveEditor to use delegate methods
Moved duplicated code for name updates in TransformEditor and ObjectiveEditor to ProgrammableDataGeneratorEditor
Refactored name updates in ProgrammableDataGeneratorEditor to make most of the code reusable
Fixed name of property fired when an objective is edited
Changed order in PanelTab constructor to not add a property listener until the tab has been initialized
Merged code for handling property change events in TransformEditor and ObjectiveEditor to ProgrammableDataGeneratorEditor
Merged code for reading primitive objects in TransformEditor and ObjectiveEditor to ProgrammableDataGeneratorEditor
Fixed possible interface freeze when updating the list of transforms in TransformEditor
Made the file filters in ObjectiveSeriesView public to reuse them in ObjectiveEditor and Compare2
Fixed display bug in the finished toggle of transforms that caused changes to be ignored
Exposed the non-prompting versions of add and duplicate to the public API in ProgrammableDataGeneratorEditor
Changed about dialog to be updated automatically with the version number
Removed Comparator implementations from CellCycleTransformView, ObjectiveSeriesView, and Compare2
Moved IStructuredTypeChecker to compare to break dependency from ui package to data package
Replaced runnables in DataGeneratorEvaluator using ProxyBuilder and eliminated the need for execution modes
Fixed debug assertion when trying to compute the threshold for an equivalence comparison
Made read helpers handle required threading internally
Replaced runnables in ReadHelper using ProxyBuilder and eliminated the need for run states
Redesigned Compare2ReadHelper to use separate classes for each readable type
Changed when read helpers cleared the current source from before the read started to just before the newly read data is committed
Converted type checkers to supply a Comparator using ProxyBuilder instead of implementing Comparable
Changed sorting in CellCycleExperimentView to use the appropriate Comparator for the type
Fixed recording recently used sources in ProgrammaticDataGeneratorEditor
Fixed what the current source got set to after an import in ProgrammaticDataGeneratorEditor
Made support for changing the XML formatting a standalone class from Compare
Added support for creating sliders to InterfaceBuilder
Created interface for threshold editor in Compare^2
Limited the number of digits that the threshold editor displays
Changed IDataGeneratorMap and DataGeneratorMap to provide services by composition rather than inheritance
Cleaned all the cruft out of existing persistence delegates
Added a persistence delegate to DataGeneratorMap to duplicate the format used by a regular map
Made searching for generators in DataGeneratorList when an index has been created more likely to match expectations
Required that the compatible transform list be an IDataGeneratorList
Required that the contained transform list be an IDataGeneratorList
Changed IDataGeneratorList and DataGeneratorList to provide services by composition rather than inheritance
Required that the list of transform dependencies be an IDataGeneratorList
Added a persistence delegate to DataGeneratorList to duplicate the format used by a regular list
Fixed some documentation errors in Compare, Compare2, and ProgrammableDataGeneratorEditor
Changed IResultSetMap and ResultSetMap to provide services by composition rather than inheritance
Added explicit checks for null to ThresholdAbsoluteViewColorer and ThresholdRelativeViewColorer in case their threshold comparison color is the default
Fixed view colorers to explicitly read the configuration on initialization
Added documentation to Compare^2 about the data types that are expected in collections
Added persistence delegates to ResultSetMap and ResultSetGroupMap to duplicate the format used by a regular map
Updated example files in installation to the format used in current versions
Exposed the original Comparator and configuration markers used to start a tab in PanelTab
Exposed the table being displayed in BasicTableView
Eliminated the package level access methods used by ViewColorer that prevented creating an independent colorer implementation
Moved the prompt for the result set name in Compare^2 to before loading the set
Changed Compare2Model to only announce that a threshold has changed after an edit
Fixed the criteria for when the threshold editor slider would be disabled
Made ThresholdEditor listen for property change events about thresholds to update the display when Compare^2 loads a new threshold set
Fixed the default selection in threshold editor when first opened
Changed setting a threshold in the threshold editor to notify the table model of the update
Improved update speed when dragging the threshold editor after a view zoom is created by batching updates
Moved the event posting for updating the view zoom inside the batching to improve update speed even further
Cleaned the cruft out of the persistence delegate for objective comparisons
Converted the table column size computation methods in BasicTable to be static
Changed the default constructor of IDataGeneratorCollection.Key to invoke the normal constructor
Changed the persistence of DataGeneratorList, DataGeneratorMap, ResultSetGroupMap, and ResultSetMap to initialize the data structure for the number of elements that will be added
Fixed class cast exception when importing a transform or objective set into the editor
Fixed persistence for data maps which take a 4 byte real parameter but were being given an 8 byte real value
Fixed interface freeze when a customizer view was created for the first time while the data generator was locked
Added new transform to perform the budding yeast scan
Fixed transform editor to not disable the context menu remove option from all primitive transforms on load
Added documentation for the file formats used by the Comparator
Fixed link in documentation to XMLFormatter in Compare
Updated documentation links on the Comparator front page
Added documentation for debugging problems in the Comparator
Renamed the configuration property used to toggle exception debugging
Organized list of blue sky changes and pitched a few out that aren't needed any more or were actually done
OAA Connector now registers solvables for doing dispatch operations on public objects
Fixed generation of munged names for tabs in OAAConnector dispatches
Fixed double underscores in OAAConnector dispatch function names
Updated the Comparator dashboard analyzer to be an actual working component instead of a demo
Updated the dashboard analyzer to support the new format for run files
Removed the code in the dashboard analyzer only needed for connecting with NCA
Added documentation for using the dashboard analyzer
Finished implementing the actual execution of an arbitrary dispatch over OAA
Added static method to OAAConnector to make running a dispatch easier
Added tests for dispatching to OAAConnectorTest
Consolidated the execution of solvables in OAAConnector to use a helper method
Updated documentation style
Added cleanup for the dashboard analyzer in the build system

Changes Before Version 5.0.0

Created a factory class for proxying method calls to arbitrary methods in existing objects
Changed several inner classes to use the ProxyBuilder factory
Cleaned up the names and packages for all interfaces and classes
Removed all deprecated API methods
Updated all attribute, configuration, and option names to follow the Comparator naming convention
Updated all frogegg data files
Added index to data generator lists to speed up searches for many generators
Changed CellCycleTransformView and ObjectiveSeriesView to switch on the index of data generator lists when loading
Updated documentation for changed class, method, and field names
Assigned input and output types to existing transforms and objective functions
Fixed null pointer exception when opening a debugging console
Added a name for debugging console tabs to the configuration file
Fixed propogation of types through a MetricDataGenerator
Added type checking for transforms and objectives to views
Did a lot of minor cleanup to all classes
Reduced the number of places in TransformDebugger that directly touched a debugger thread
Fixed some potential deadlocks with TransformDebugger and moved more debugging handling into debugger thread
Fixed a proxy that wrapped a ThreadDeath in another exception
Created a simple generator for SBML models
Cleaned up the way the SBML parser generates output
Added many convenience functions to the SBML parser
Added more convenience functions to the ModelBuilderPlugin
Created a benchmark routine for evaluating model loading performance in the model builder
Added ability to start the OAA Connector from the Comparator menu
Added some convenience functions to OAAConnector for sending requests
Fixed old script code in OAAConnectorTests and modified it to use convenience functions in OAAConnector
Converted benchmarks to use a proxy for thread creation
Added more convenience functions for running benchmarks
Added more documentation for creating benchmarks
Reduced the number of places exceptions can be thrown in benchmarks
Added more relationals to BooleanRelationalDataGenerator
Changed benchmarks to indicate completion by firing a property on the Comparator
Fixed bug when moving a group selection down in EditableSeriesView
Created a transform that runs a script during evaluation
Added support for text areas to InterfaceBuilder
Shifted some of the logic for performing comparisons to ObjectiveSeriesView.comparison
Changed ObjectiveSeriesView.Comparison to return IGNORE when null is given to findComparison
Fixed bug where some views would not repaint the display after the renderer colors changed
Removed the Compare2ViewRenderer in favor of allowing ViewColorer to paint the comparison type column
Removed some unused methods from Compare
Added benchmark for measuring the time required to add a new experiment
Added benchmark for measuring the time required to configure a new experiment
Fixed bug where transform and objective scripts containing | or @ would not be loadable
Fixed bug where deleting a comment would cause the generator to incorrectly be persisted
Fixed bug where deleting the type would not cause the type checker to recheck the generator
Made it easier to get timings for a large number of values from benchmarks
Fixed bug where using a menu shortcut while an editable table cell was selected would start editing the cell
Updated transforms and objective for running benchmarks
Fixed bug where creating a customizer for a script evaluation transform or objective required acquiring a lock
Converted references to menu item commands to use fixed command names
Simplified option in objective renderers for changing text alignment
Fixed bug in installer script that tried to make a non-existant file executable
Updated build configuration to support subversion
Updated experiment data types for budding yeast
Fixed bug in script based transforms and objectives that caused setting the script after editing to loop once
Added additional variables to the environment for script based transforms and objectives
Moving rows up or down no longer clears the selection
Updated support for running external programs as plugins in the Comparator
Simplified the callback from DataGeneratorEvaluator
Added a call stack to data generator evaluation allowing for traces along the execution path
EvaluationErrorViewer uses the call stack if available to help find the originating generator
Fixed bug in FlippedDataElement to better handle unflippable elements
Added a benchmark for measuring reaction entry speed
Fixed bug in SeriesDialog where the location of the popup was not recorded
Fixed bug in SeriesEditorDialog where filling list selections did not work
Fixed bug in DimensionWeightEditorDialog and ElementWeightEditorDialog where value updates would stop being displayed
Converted special run selection numbers in JigCellRunManagerTransform to constants
Added designation for automatically selecting a run to JigCellRunManagerTransform
Added support for radio buttons to InterfaceBuilder
Fixed bug in InterfaceBuilder where listeners weren't attached to buttons that didn't descend from JButton
Fixed bug in JigCellRunManagerTransform that would attempt to select the first run even if it didn't exist
Added interface to toggle between user or automatic selection of a run in JigCellRunManagerInterface
Made automatic run selection the default in JigCellRunManagerInterface
Changed JigCellRunManagerTransform to record the last run automatically selected
Made the annotation for JigCellRunManagerTransform use the last run automatically selected if needed
Fixed bug in JigCellRunManagerTransform where updating the last run automatically selected would not potentially clear the transform chain when needed to notify later transforms that state had changed
Added support for getColumnCount and getRowCount to BasicTableView
Separated the display of a zoomed view to a new class out of Compare2
Fixed bug in Compare^2 where an exception occured in the zoom view when the number of columns changed
Fixed bug in Compare^2 where an exception occured in the zoom view when no colorer was available
Fixed bug in Compare^2 where the toolbar icon for the popup threshold editor had the wrong command name
Consolidated several implementations of fillSelected to BasicTableView
Created documentation for adding a tab to the Comparator
Added new benchmarks for measuring Run Manager performance
Updated data files for budding yeast and frogegg models
Change path to website in installer
New logging information for benchmarks
Stubbed out remaining Run Manager benchmarks