chemaxon.marvin.plugin
Class CalculatorPluginDisplay

java.lang.Object
  chemaxon.marvin.plugin.CalculatorPluginDisplay

public class CalculatorPluginDisplay
extends java.lang.Object

Common base class for calculator plugin displays. Also provides default implementation for molecule display, therefore plugins with molecule / atom data only may use the base class itself.

Since:

Marvin 4.0

Version:

Marvin 5.4, 09/29/2010

Author:

Nora Mate

Field Summary

protected static int	CELLSIZE The default viewer cell size.
protected boolean	displayInMarvinSpace Display in MarvinSpace is enabled or not.
protected static int	HTML Property display type: display in html text.
protected int	icell The viewer cell index (0 for sketcher).
protected static int	LABEL Property display type: display in label.
protected static int	MAX_LINE_LENGTH Maximum desired line length used to form multi-line text.
protected static int	NONE Property display type: no property display.
protected java.awt.Component	parent The parent component.
protected DPoint3[]	reactionArrow The reaction arrow endpoints, null if not a reaction.
protected java.util.ArrayList	resultMolList The result molecules to be displayed.
protected java.util.ArrayList	resultValues The result values to be displayed in MarvinSpace.
protected static int	TEXT Property display type: display in text.
protected java.lang.String	title The result frame title.
protected static java.lang.String	WORD_SEPARATORS Word separators used to form multi-line text if the text is too long.

Constructor Summary

CalculatorPluginDisplay()

Method Summary

protected java.lang.String	appendpHText(java.lang.String text) Appends the pH text.
void	clear() Clears the display.
protected chemaxon.marvin.util.CallbackIface	createMolsFrame()
protected ParameterPanelHandler	createParameterPanel() Creates the parameter panel.
protected chemaxon.marvin.plugin.gui.ResultView	createResultView(java.lang.String title, chemaxon.marvin.common.swing.MolPanel mpan)
protected java.awt.Component	createSpacePanel(Molecule[] mols) Creates space panel with given molecules, creates colored surface to each molecule.
protected chemaxon.marvin.view.swing.ViewPanel	createViewPanel(Molecule[] mols) Creates view panel with given molecules, places molecule properties in formatted texts.
protected chemaxon.marvin.view.swing.ViewPanel	createViewPanel(Molecule[] mols, int rows, int cols, int size, int propertyDisplayType) Creates view panel with given molecules, places molecule properties in formatted texts.
java.awt.Component	getErrorComponent() Returns a component with the appropriate error message.
protected java.lang.Object	getHResult(int i) Returns the sum result of the H neighbours of the given atom.
java.lang.String[]	getLabels(double[] values) Returns formatted array.
ParameterPanelHandler	getParameterPanel() Returns the parameter panel.
protected CalculatorPlugin	getPlugin() Returns the plugin.
chemaxon.common.util.MProgressMonitor	getProgressMonitor(java.awt.Component parent) Creates a progress observer object to be used in CalculatorPlugin.setProgressMonitor(chemaxon.common.util.MProgressMonitor).
protected java.lang.String	getPropertyText(Molecule mol) Returns molecule properties is text form.
java.lang.String	getRemark() Returns the calculation remark.
java.awt.Component	getResultComponent() Returns the result component for display.
protected java.lang.String	getTableText(java.lang.String header, java.lang.String[] labels, double[][] values) Returns table in string form.
java.lang.String	getTitle() Returns the frame title.
protected boolean	isMSpaceDisplayLabelOnlyOnHeavyAtoms() Returns if mspace should display label only on heavy atoms.
boolean	isMultipleDisplay() Returns true if results for more molecules can be displayed in a single component, false if each molecule should be displayed in a separate component.
void	pop() Clears the last stored item from the display.
void	setCellIndex(int icell) Sets the viewer cell index.
void	setParameters(java.util.Properties params) Sets parameters.
void	setParent(java.awt.Component parent) Sets the parent component.
void	setPlugin(CalculatorPlugin plugin) Sets the plugin.
void	setReactionArrow(DPoint3[] reactionArrow) Sets the reaction arrow.
void	setTitle(java.lang.String title) Sets the frame title.
void	store() Stores a new result item.

Methods inherited from class java.lang.Object

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

Field Detail

CELLSIZE

protected static final int CELLSIZE

The default viewer cell size.

See Also:

Constant Field Values

NONE

protected static final int NONE

Property display type: no property display.

See Also:

Constant Field Values

LABEL

protected static final int LABEL

Property display type: display in label.

See Also:

Constant Field Values

TEXT

protected static final int TEXT

Property display type: display in text.

See Also:

Constant Field Values

HTML

protected static final int HTML

Property display type: display in html text.

See Also:

Constant Field Values

WORD_SEPARATORS

protected static final java.lang.String WORD_SEPARATORS

Word separators used to form multi-line text if the text is too long.

See Also:

Constant Field Values

MAX_LINE_LENGTH

protected static final int MAX_LINE_LENGTH

Maximum desired line length used to form multi-line text.

See Also:

Constant Field Values

parent

protected java.awt.Component parent

The parent component.

title

protected java.lang.String title

The result frame title.

icell

protected int icell

The viewer cell index (0 for sketcher).

displayInMarvinSpace

protected boolean displayInMarvinSpace

Display in MarvinSpace is enabled or not.

resultMolList

protected java.util.ArrayList resultMolList

The result molecules to be displayed.

resultValues

protected java.util.ArrayList resultValues

The result values to be displayed in MarvinSpace.

reactionArrow

protected DPoint3[] reactionArrow

The reaction arrow endpoints, null if not a reaction.

Constructor Detail

CalculatorPluginDisplay

public CalculatorPluginDisplay()

Method Detail

setPlugin

public void setPlugin(CalculatorPlugin plugin)

Sets the plugin.

Parameters:

plugin - is the plugin

getPlugin

protected final CalculatorPlugin getPlugin()

Returns the plugin.

Returns:

the plugin

setParent

public final void setParent(java.awt.Component parent)

Sets the parent component.

Parameters:

parent - is the parent component

setCellIndex

public final void setCellIndex(int icell)

Sets the viewer cell index.

Parameters:

icell - is the viewer cell index

setParameters

public void setParameters(java.util.Properties params)

Sets parameters. The default implementation checks whether displaying in MarvinSpace is required and possible, descendant classes may fetch display parameters.

Parameters:

params - is the parameter table

setTitle

public void setTitle(java.lang.String title)

Sets the frame title.

Parameters:

title - is the frame title

getTitle

public java.lang.String getTitle()

Returns the frame title.

Returns:

the frame title

setReactionArrow

public void setReactionArrow(DPoint3[] reactionArrow)

Sets the reaction arrow. If set then molecules stored by store() will be taken as reaction components. The next clear() resets this reaction mode.

Parameters:

reactionArrow - is the reaction arrow endpoint array

getProgressMonitor

public chemaxon.common.util.MProgressMonitor getProgressMonitor(java.awt.Component parent)

Creates a progress observer object to be used in CalculatorPlugin.setProgressMonitor(chemaxon.common.util.MProgressMonitor). Short calculations do not need this object. The default implementation returns null, subclasses may return MProgressMonitor or any other progress monitor implemeting MProgressMonitor.

Parameters:

parent - is the parent component (centralize relative to)

Returns:

a progress observer object

getParameterPanel

public final ParameterPanelHandler getParameterPanel()
                                              throws PluginException

Returns the parameter panel.

Returns:

the parameter panel

Throws:

PluginException - on error

createParameterPanel

protected ParameterPanelHandler createParameterPanel()
                                              throws PluginException

Creates the parameter panel. The default implementation creates a ParameterPanel object from the <plugin class name>Parameters.xml configuration XML read from CalculatorPlugin.PLUGIN_DIR with user parameter settings read from $HOME/chemaxon/<plugin class name>Parameters.properties (Windows), or $HOME/.chemaxon/<plugin class name>Parameters.properties (UNIX / Linux). Returns null (no paramter panel for this plugin) if the configuration XML is not found.

Returns:

the parameter panel

Throws:

PluginException - on error

isMultipleDisplay

public boolean isMultipleDisplay()

Returns true if results for more molecules can be displayed in a single component, false if each molecule should be displayed in a separate component. The default implementation returns true.

Returns:

true if results for more molecules can be displayed in a single component

pop

public void pop()

Clears the last stored item from the display. The default implemetation clears the top element in resultMolList and resets reactionArrow.

clear

public void clear()

Clears the display. The default implemetation clears resultMolList and resets reactionArrow.

store

public void store()
           throws PluginException

Stores a new result item. The default implementation adds the current result molecule returned by CalculatorPlugin.getResultMolecule() to resultMolList.

Throws:

PluginException

getHResult

protected java.lang.Object getHResult(int i)
                               throws PluginException

Returns the sum result of the H neighbours of the given atom.

Parameters:

i - index of the atom

Returns:

result the result item for the specified index

Throws:

PluginException

Since:

Marvin 4.1

getResultComponent

public java.awt.Component getResultComponent()
                                      throws PluginException

Returns the result component for display. The default implementation places the molecules stored in resultMolList in a viewer and displays molecular results (stored in molecule properties) in text fields.

Returns:

the result component

Throws:

PluginException - on error

Since:

Marvin 4.0

createResultView

protected chemaxon.marvin.plugin.gui.ResultView createResultView(java.lang.String title,
                                                                 chemaxon.marvin.common.swing.MolPanel mpan)
                                                          throws PluginException

Throws:

PluginException

createMolsFrame

protected chemaxon.marvin.util.CallbackIface createMolsFrame()
                                                      throws PluginException

Throws:

PluginException

getErrorComponent

public java.awt.Component getErrorComponent()
                                     throws PluginException

Returns a component with the appropriate error message. Relevant if CalculatorPlugin.run(), or equivalently CalculatorPlugin.isOK() returns false.

Returns:

the error component

Throws:

PluginException

getRemark

public java.lang.String getRemark()
                           throws PluginException

Returns the calculation remark.

Returns:

the calculation remark

Throws:

PluginException

createViewPanel

protected chemaxon.marvin.view.swing.ViewPanel createViewPanel(Molecule[] mols)
                                                        throws PluginException

Creates view panel with given molecules, places molecule properties in formatted texts. Fuses molecules if no properties to be displayed.

Parameters:

mols - is the molecule array

Returns:

the view panel

Throws:

PluginException

createViewPanel

protected chemaxon.marvin.view.swing.ViewPanel createViewPanel(Molecule[] mols,
                                                               int rows,
                                                               int cols,
                                                               int size,
                                                               int propertyDisplayType)

Creates view panel with given molecules, places molecule properties in formatted texts.

Parameters:

mols - is the molecule array

rows - the number of visible rows

cols - the number of columns

propertyDisplayType - is TEXT, LABEL, HTML or NONE

Returns:

the view panel

getPropertyText

protected java.lang.String getPropertyText(Molecule mol)

Returns molecule properties is text form.

Parameters:

mol - is the molecule

Returns:

molecule properties in text form

appendpHText

protected java.lang.String appendpHText(java.lang.String text)

Appends the pH text.

Parameters:

text - is the text

Returns:

the text + the pH text

isMSpaceDisplayLabelOnlyOnHeavyAtoms

protected boolean isMSpaceDisplayLabelOnlyOnHeavyAtoms()

Returns if mspace should display label only on heavy atoms.

Since:

Marvin 5.4

getLabels

public final java.lang.String[] getLabels(double[] values)

Returns formatted array.

Parameters:

values - is the numerical array

Returns:

the formatted array

getTableText

protected final java.lang.String getTableText(java.lang.String header,
                                              java.lang.String[] labels,
                                              double[][] values)

Returns table in string form.

Parameters:

header - is the header (the first char is the separator)

labels - is the first column

values - is the value column array

createSpacePanel

protected java.awt.Component createSpacePanel(Molecule[] mols)
                                       throws PluginException

Creates space panel with given molecules, creates colored surface to each molecule.

Parameters:

mols - is the molecule array

Returns:

the space panel

Throws:

PluginException

Since:

Marvin 4.1