Changes Before Version 6.0.5
- Updated benchmarks to work with latest Model Builder and Run Manager
- Added a better way to register simulators for use in the Comparator
- Added a command to import the names from a list of runs for use as experiments
- Fixed loss of focus from Evaluate Script transform after typing characters
- Fixed help text for WOSS objective
- Added support for running Oscill8 simulations from the Comparator
Changes Before Version 6.0.4
- Fixed display bug in report generator when adding a custom column selection
- Made the wildtype properties automatically computed for the generic and budding yeast models
- Restored benchmarks for Model Builder and Run Manager
- Changed report generator to use selected columns instead of all columns when no explicit column selection is made
- Changed order of cell cycle checking events to be more favorable for closely spaced events
- Fixed NullPointerException when starting the report generator
- Added interface display of the optional Esp1 check in BuddingYeastScanTransform
- Make the checking of Esp1 in BuddingYeastScanTransform optional
- Change the storage class for points in GenericScanTransform and BuddingYeastScanTransform to eliminate outer class reference
- Eliminated dependency from RawFileDataSource and PDFPrinterDataSource to InterfaceBuilder
- Eliminated dependency from DataGeneratorEvaluator to ProgressMonitor
- Moved all user interface handling from ProgrammableDataGenerator to CustomizableInterface
- Fixed initialization of known transforms in TransformEvaluationTransform
- Eliminated ICustomizableDataGenerator
- Created interface classes for Transform, TransformContainer, Objective, and BoxTransformContainer and moved all user interface handling to these new classes
- Rename getInnerCustomizer to createCustomizer
- Moved tracking of customizers from data generators to their interfaces
- Moved indication of multiple user interface view support from data generators to their interfaces
- Eliminated marker interface for multiple view support
- Created dummy interface in ProgrammableDataGenerator for data generators that don't implement their own interface class
- Moved all support for customizable interface managing from EditableDataGenerator to ProgrammableDataGenerator
- Moved automatic run file generators from compare to runsupport
- Prevented objective result from being cut off when there was a large number of significant digits
- Sorted and made unique the list of installed look and feels displayed in the Comparator configuration editor
- Changed configuration setting for look and feels to use the name instead of the class
- Added automatic registration of known external look and feels
- Fixed spacing in menu entries without icons on Java 6.0
- Change benchmarking to use system timer instead of high precision timer to allow running on non-Sun JVMs
- Moved automatic SBML model generators from compare to sbml2
Changes Before Version 6.0.3
- Fixed plotting of series that contained integer coefficients
- Simplified the way overloaded types are accessed in the configuration
- Changed CompareFrontEnd to record the last maximized state of the display frame and restore on startup
- Added an overload to Config for working with rectangles
- Changed CompareFrontEnd to record the last normal window dimensions of the display frame and restore on startup
Changes Before Version 6.0.2
- Sped up retrieval of slices from PackedDoubleDataElement
- Fixed doubled error report when viewing details in EvaluationErrorViewer
- Fixed adding a transform or objective function with the same name as an experiment
- Fixed adding 5 rows when in a popup list editor
- Added support for specifying an arrest stage but not arrest type for generic and budding yeast objective functions
- Fixed documentation errors
- Changed TimeSeriesTypeChecker to give a default name to all entries
- Created a new variant of TimeSeriesTypeChecker that allows user specified column names
- Added time series splitting to Plotter that converts Combine.ACROSS formatted data to Combine.NONE
- Added support for multiple series plots in the transform and objective tabs
- Moved shared plotting support to EditableSeriesView
- Fixed Compare^2 zoom view not updating when the order of columns was changed
- Added plotter support for customizing the plot title
- Added plotter support for customizing the series colors
Changes Before Version 6.0.1
- Updated about dialog
- Made the creation of the data manager overridable in Compare
- Change NullPointerExceptions to InvalidArgumentExceptions for argument validation
- Improved argument validation in Compare, XMLFormatter, and ConfigEditor
- Moved handling of the flavor and file extension maps from Compare to Transferer
- Eliminated unneeded getFlavors method from Config and SeriesView
- Added new model benchmarks and updated the benchmark data files
- Fixed property descriptions for BuddingYeastWildtypeProperties
- Improved how DataGeneratorList and DataGeneratorMap look when printed
- Changed BuddingYeastScanTransform and GenericScanTransform to scale according to a wildtype transform instead of using hardcoded values
- Fixed reporting of dependencies for TransformEvaluationTransform
- Expanded size of transform and objective help windows
- Added error codes to help of generic and budding yeast scan transforms
- Centralized handling of InvocationTargetExceptions for unwrapping and display
- Added the ability to retrieve the names of all top-level resources
- Added support for scanning the top-level resources to Compare and Blackboard
- Renamed scanResource to scanResourceCatalog and added better documentation
- Added support for scanning a resource map that isn't a catalog
- Moved many strings from compare2 package into resource bundles
- Made the use of EventQueue instead of SwingUtilities consistent when invoking runnables
- Improved error checking in Blackboard, ThresholdEditor, and ThresholdRelativeViewColorer
- Added support for using multiple resource bundles
- Changed Compare to be pickier about whether parameters can be null
- Hid the use of a Runnable to add new tabs in CompareFrontEnd
- Moved many strings from views package into resource bundles
- Added toArray method to IDataGeneratorList
- Added the ability to pick from the current list of experiments when choosing a transform or objective function name
- Added support for selecting a choice from a combo box to ConfigEditor
- Made the look-and-feel selectable from the list of currently installed looks
- Fixed bug in CompareFrontEnd that caused readConfiguration to never be called
- Made the look-and-feel dynamically update when the option is changed
- Moved many strings from plotter package into resource bundles
- Extended support for setting the plotter range to all plotters
- Fixed configuration editors not changing look-and-feel dynamically
- Added icons for error history, importing, and preferences
- Redesigned menus to better categorize choices
- Created an accessory area for tabs to display an accessory component
- Removed FrontEndTabInfo from public access
- Fixed some incorrect usages of the tab map to look up tab infos and added a getTabInfo method to remove the confusion
- Created a memory monitor accessory to act as the default accessory
- Improved the API for working with tabs that support searching
- Created a search accessory
- Made it possible to not have a tab accessory installed
- Added an interface for tab accessories and support for installation notifications
- Improved handling of HTML components used for help
- Added a lightweight data generator list for use with objectives
- Added a copy constructor to DataGeneratorList
- Added additional input validation to DataGeneratorList
- Improved DataGeneratorList indices to keep up to date with list mutations
- Changed ObjectiveSeriesView to not replace generator evaluation events with generator edit events
Changes Before Version 6.0.0
- Added support for creating proxies of property change listeners
- Improved error handling of Blackboard and DataGeneratorEvaluator
- Converted DataGeneratorEvaluator to use a proxy for property change events
- Converted Compare and CompareFrontEnd to use external resource bundle for strings
- Added replacements for assertException, logException, logMessage, and logMessageAndAssert with better API for error handling
- Updated Compare and CompareFrontEnd to describe errors better
- Eliminated logMessage and logMessageAndAssert
- Eliminated logException
- Fixed two errors in budding yeast phenotype objective that happened when the experimental result indicated an inviable mutant
- Fixed incorrect NaN result of objective function for benchmark runs
- Eliminated assertException
- Added a custom error message to every exception handler
- Fixed documentation errors
- Fixed race condition in DataEditorPanelTab.ReadHelper
- Fixed two rare text alignment problems in Compare^2 caused by reordering columns
- Made it easier to get the view column index from a model column marker
- Fixed incorrect cell editor bug when comparison type column was moved in Compare^2 before an objective set was loaded
- Fixed two incorrect result coloring bugs when objective result column was moved in objective view and the row is not evaluated