jigcell.compare.cellcycle
Class CellCycleReportGenerator

java.lang.Object
  javax.swing.TransferHandler
      jigcell.compare.impl.Transferer
          jigcell.compare.impl.DataSource
              jigcell.compare.impl.OwnedDataSource
                  jigcell.compare.impl.PrinterDataSource
                      jigcell.compare.impl.PDFPrinterDataSource
                          jigcell.compare.cellcycle.CellCycleReportGenerator

All Implemented Interfaces:

java.awt.datatransfer.Transferable, java.awt.event.ActionListener, java.awt.event.ItemListener, java.beans.PropertyChangeListener, java.io.Serializable, java.lang.Cloneable, java.util.EventListener, IDataSource, IWriteableDataSource

public final class CellCycleReportGenerator
extends PDFPrinterDataSource
implements java.awt.event.ActionListener, java.awt.event.ItemListener

Prints a summary report of a set of comparisons to a PDF file.

This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.

Author:

Nicholas Allen

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface jigcell.compare.IDataSource

IDataSource.Option

Field Summary

private InterfaceBuilder	builder Builder for current configuration interface
private Compare	compare Comparator of parent window
private ConstantTransform	data Source of data from the currently selected experiment
private static java.lang.String	DESCRIPTION_WRITE Write operation description
private ListComboBoxModel	experimentModel Selection model for prototype experiment
private static java.lang.String	LABEL_EXPERIMENT Label for experimental prototype selection
private static java.lang.String	LABEL_EXPLICITRANGE Label for the explicit range selection option
private static java.lang.String	LABEL_EXPLICITSELECTION Label for the explicit column selection option
private static java.lang.String	LABEL_TRANSFORM Label for column selection transform
private static java.lang.String	LABEL_XAXIS Label for the plotter x-axis option
private static java.lang.String	LABEL_YAXIS Label for the plotter y-axis option
static java.lang.String	OPTION_GENERATORS Option name for generators that the report can be based on
static java.lang.String	OPTION_SELECTION Option name for the plotter column selection
static java.lang.String	OPTION_VIEWRANGE Option name for the plotter view range
private static java.lang.String	TITLE_CONFIGURE Configure window title
private javax.swing.text.Document	xRangeDocument Range of x-axis to use for plots
private javax.swing.text.Document	yRangeDocument Range of y-axis to use for plots

Fields inherited from class jigcell.compare.impl.PDFPrinterDataSource

OPTION_FILESOURCE

Fields inherited from class jigcell.compare.impl.PrinterDataSource

DEFAULT_PAGEHEIGHT, DEFAULT_PAGEWIDTH, DEFAULT_SCREENDPI, MESSAGE_NOFLAVORERROR

Fields inherited from class jigcell.compare.impl.OwnedDataSource

MESSAGE_PACKERROR, MESSAGE_PROXYERROR, OPTION_OWNER, OPTION_TRANSFERCLASS, SIGNATURE_TRANSFER

Fields inherited from class jigcell.compare.impl.DataSource

OPTIONS_LOCK, SEPARATOR_PAIR, SEPARATOR_PART, SEPARATORS

Fields inherited from class jigcell.compare.impl.Transferer

CSV_FOOTER, CSV_LINEPOSTPEND, CSV_LINEPREPEND, CSV_LINESEPARATOR, HTML_FOOTER, HTML_HEADPOSTPEND, HTML_HEADPREPEND, HTML_HEADSEPARATOR, HTML_LINEPOSTPEND, HTML_LINEPREPEND, HTML_LINESEPARATOR

Fields inherited from class javax.swing.TransferHandler

COPY, COPY_OR_MOVE, MOVE, NONE

Fields inherited from interface jigcell.compare.IWriteableDataSource

OPTION_WRITEDESCRIPTION, OPTION_WRITEICON

Fields inherited from interface jigcell.compare.IDataSource

OPTION_NAME

Constructor Summary

CellCycleReportGenerator(Compare compare, IDataGeneratorList experiments)
Constructs a data source that produces a report for a set of generators.

Method Summary

void	actionPerformed(java.awt.event.ActionEvent e)
private ITransform	applyColumnSelection(ITransform transform, IDataElement columnSelection) Applies the column selection to a transform.
private IDataElement	buildRangeElement() Constructs a data element with the user's plotter range.
boolean	configure() Does whatever configuration this data source requires and returns whether the configuration was completed successfully.
private ITransform	findLastTransform(IDataGenerator experiment, boolean useFirst) Picks a transform to use as input to the report plotter.
private static com.lowagie.text.Image	generatePlotImage(IDataElement viewRange, ITransform transform) Produces a plot image of the time series data in the transform.
IDataElement	getColumnSelection() The column selection option.
boolean	getPredictedCompatibility(java.lang.Class clazz) A prediction on whether this data source can hold a particular type.
boolean	getPredictedCompatibility(java.lang.Object instance) A prediction on whether this data source can hold a particular type.
private IDataGeneratorList	getPrototypeExperiments() The list of experimental prototypes to select from.
IDataElement	getViewRange() The view range option.
void	itemStateChanged(java.awt.event.ItemEvent e)
void	propertyChange(java.beans.PropertyChangeEvent e)
void	setColumnSelection(IDataElement selection) The column selection option.
private void	setPrototypeExperiments(IDataGeneratorList experiments) Sets the list of experimental prototypes to select from.
private void	setUseRangeControls(boolean enabled) Sets whether the view range controls should be enabled.
private void	setUseSelectionControls(boolean enabled) Sets whether the column selection controls should be enabled.
void	setViewRange(IDataElement range) Sets the view range option.
private javax.swing.JComponent	smashTransformDisplayComponent(javax.swing.JComponent component) Heavily constrains the dimensions of most of the components in a transform display.
private void	updateColumnSelector() Places the columns of the latest experiment selection into the column selector.
void	write(java.lang.Object data) Writes data to the source destroying the previous contents if multiple objects are not supported.

Methods inherited from class jigcell.compare.impl.PDFPrinterDataSource

getFileSourceOption, initializeSource, setFileSourceOption

Methods inherited from class jigcell.compare.impl.OwnedDataSource

encode, getOwnerOption, getTransferClassOption, setOwnerOption, setTransferClassOption

Methods inherited from class jigcell.compare.impl.DataSource

addOption, addPropertyChangeListener, addPropertyChangeListener, clone, getName, getOption, getOptions, getOptionType, getPropertyChangeListeners, getPropertyChangeListeners, getReadDescriptionOption, getReadIconOption, getState, getWriteDescriptionOption, getWriteIconOption, persistSource, removePropertyChangeListener, removePropertyChangeListener, setName, setOption, setOptions, setOptionType, setReadDescriptionOption, setReadIconOption, setState, setWriteDescriptionOption, setWriteIconOption, toString, unpersistSource

Methods inherited from class jigcell.compare.impl.Transferer

addExtension, addFlavor, createCSVTable, createFormattedTable, createHTMLTable, getExceptionRecorder, getExpectedClasses, getExpectedClasses, getExpectedClasses, getFlavors, getFlavors, getPreferredExtensions, getPreferredExtensions, getTransferClass, getTransferData, getTransferDataFlavors, getTransferFlavor, isDataFlavorSupported, transfer

Methods inherited from class javax.swing.TransferHandler

canImport, createTransferable, exportAsDrag, exportDone, exportToClipboard, getCopyAction, getCutAction, getPasteAction, getSourceActions, getVisualRepresentation, importData

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface jigcell.compare.IWriteableDataSource

getWriteDescriptionOption, getWriteIconOption, setWriteDescriptionOption, setWriteIconOption

Methods inherited from interface jigcell.compare.IDataSource

addOption, clone, getName, getOption, getState, setOption, setState

Methods inherited from interface java.awt.datatransfer.Transferable

getTransferData, getTransferDataFlavors, isDataFlavorSupported

Field Detail

OPTION_GENERATORS

public static final java.lang.String OPTION_GENERATORS

Option name for generators that the report can be based on

See Also:

Constant Field Values

OPTION_SELECTION

public static final java.lang.String OPTION_SELECTION

Option name for the plotter column selection

See Also:

Constant Field Values

OPTION_VIEWRANGE

public static final java.lang.String OPTION_VIEWRANGE

Option name for the plotter view range

See Also:

Constant Field Values

DESCRIPTION_WRITE

private static final java.lang.String DESCRIPTION_WRITE

Write operation description

See Also:

Constant Field Values

LABEL_EXPERIMENT

private static final java.lang.String LABEL_EXPERIMENT

Label for experimental prototype selection

See Also:

Constant Field Values

LABEL_EXPLICITRANGE

private static final java.lang.String LABEL_EXPLICITRANGE

Label for the explicit range selection option

See Also:

Constant Field Values

LABEL_EXPLICITSELECTION

private static final java.lang.String LABEL_EXPLICITSELECTION

Label for the explicit column selection option

See Also:

Constant Field Values

LABEL_TRANSFORM

private static final java.lang.String LABEL_TRANSFORM

Label for column selection transform

See Also:

Constant Field Values

LABEL_XAXIS

private static final java.lang.String LABEL_XAXIS

Label for the plotter x-axis option

See Also:

Constant Field Values

LABEL_YAXIS

private static final java.lang.String LABEL_YAXIS

Label for the plotter y-axis option

See Also:

Constant Field Values

TITLE_CONFIGURE

private static final java.lang.String TITLE_CONFIGURE

Configure window title

See Also:

Constant Field Values

compare

private transient Compare compare

Comparator of parent window

data

private transient ConstantTransform data

Source of data from the currently selected experiment

xRangeDocument

private transient javax.swing.text.Document xRangeDocument

Range of x-axis to use for plots

yRangeDocument

private transient javax.swing.text.Document yRangeDocument

Range of y-axis to use for plots

builder

private transient InterfaceBuilder builder

Builder for current configuration interface

experimentModel

private transient ListComboBoxModel experimentModel

Selection model for prototype experiment

Constructor Detail

CellCycleReportGenerator

public CellCycleReportGenerator(Compare compare,
                                IDataGeneratorList experiments)

Constructs a data source that produces a report for a set of generators.

Parameters:

compare - Comparator

experiments - Experimental prototypes

Method Detail

generatePlotImage

private static com.lowagie.text.Image generatePlotImage(IDataElement viewRange,
                                                        ITransform transform)

Produces a plot image of the time series data in the transform.

Parameters:

viewRange - Extent of plot region

transform - Transform

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent e)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

configure

public boolean configure()

Does whatever configuration this data source requires and returns whether the configuration was completed successfully.

Specified by:

configure in interface IDataSource

Overrides:

configure in class PDFPrinterDataSource

getColumnSelection

public IDataElement getColumnSelection()

The column selection option. The column selection is either null (use source data) or in the form (column1, column2, ...).

getPredictedCompatibility

public boolean getPredictedCompatibility(java.lang.Class clazz)

A prediction on whether this data source can hold a particular type.

Specified by:

getPredictedCompatibility in interface IWriteableDataSource

Overrides:

getPredictedCompatibility in class OwnedDataSource

Parameters:

clazz - Type

getPredictedCompatibility

public boolean getPredictedCompatibility(java.lang.Object instance)

A prediction on whether this data source can hold a particular type.

Specified by:

getPredictedCompatibility in interface IWriteableDataSource

Overrides:

getPredictedCompatibility in class OwnedDataSource

Parameters:

instance - Type

getViewRange

public IDataElement getViewRange()

The view range option. The range is either null (fit to data) or in the form ((xmin, ymin), (xmax, ymax)).

itemStateChanged

public void itemStateChanged(java.awt.event.ItemEvent e)

Specified by:

itemStateChanged in interface java.awt.event.ItemListener

setColumnSelection

public void setColumnSelection(IDataElement selection)

The column selection option. The column selection is either null (use source data) or in the form (column1, column2, ...).

Parameters:

selection - Column selection

setViewRange

public void setViewRange(IDataElement range)

Sets the view range option. The range must be either null (fit to data) or in the form ((xmin, ymin), (xmax, ymax)).

Parameters:

range - View range

propertyChange

public void propertyChange(java.beans.PropertyChangeEvent e)

Specified by:

propertyChange in interface java.beans.PropertyChangeListener

Overrides:

propertyChange in class DataSource

write

public void write(java.lang.Object data)
           throws java.lang.Exception

Writes data to the source destroying the previous contents if multiple objects are not supported.

Specified by:

write in interface IWriteableDataSource

Overrides:

write in class PDFPrinterDataSource

Parameters:

data - Data

Throws:

java.lang.Exception

applyColumnSelection

private ITransform applyColumnSelection(ITransform transform,
                                        IDataElement columnSelection)

Applies the column selection to a transform.

Parameters:

transform - Transform

columnSelection - Column selection

buildRangeElement

private IDataElement buildRangeElement()

Constructs a data element with the user's plotter range.

findLastTransform

private ITransform findLastTransform(IDataGenerator experiment,
                                     boolean useFirst)

Picks a transform to use as input to the report plotter.

Parameters:

experiment - Experiment line containing transform

useFirst - Whether the scan should stop at the first eligible transform to use

getPrototypeExperiments

private IDataGeneratorList getPrototypeExperiments()

The list of experimental prototypes to select from.

setPrototypeExperiments

private void setPrototypeExperiments(IDataGeneratorList experiments)

Sets the list of experimental prototypes to select from.

Parameters:

experiments - Experimental prototypes

setUseRangeControls

private void setUseRangeControls(boolean enabled)

Sets whether the view range controls should be enabled.

Parameters:

enabled - Range control enabled state

setUseSelectionControls

private void setUseSelectionControls(boolean enabled)

Sets whether the column selection controls should be enabled.

Parameters:

enabled - Selection control enabled state

smashTransformDisplayComponent

private javax.swing.JComponent smashTransformDisplayComponent(javax.swing.JComponent component)

Heavily constrains the dimensions of most of the components in a transform display. Works around a display bug where the transform interface size breaks when scrollbars are added.

Parameters:

component - Transform interface component

updateColumnSelector

private void updateColumnSelector()

Places the columns of the latest experiment selection into the column selector.