A panel with a molecular viewer and data table. More...

Inheritance diagram for denoptim.gui.MoleculeViewPanel:

Collaboration diagram for denoptim.gui.MoleculeViewPanel:

Public Member Functions
	MoleculeViewPanel ()
	Constructor. More...

	MoleculeViewPanel (int dividerPosition)
	Constructor that allows to specify whether the data table is editable or not. More...

void	enablePartialData (boolean enable)
	Sets the behavior in case of request to visualize partial data. More...

void	loadChemicalStructure (IAtomContainer mol)
	Loads a structure in the Jmol viewer. More...

void	loadChemicalStructureFromFile (String pathName)
	Loads a structure in the Jmol viewer. More...

void	loadChemicalStructureFromFile (File file)
	Loads a structure in the Jmol viewer. More...

void	clearAll (boolean dataIsComing)
	Removes the currently visualized molecule and AP table. More...

void	cleardataTable ()
	Clears the table of attachment points. More...

void	clearMolecularViewer (boolean dataIsComing)
	Clears the molecular viewer. More...

void	dispose ()

Protected Attributes
DefaultTableModel	dataTabModel

JTable	dataTable

Private Member Functions
void	initialize (int dividerPosition)

void	showPopup (MouseEvent e)

void	fillDataTable (File molFile)

void	fillDataTable (IAtomContainer mol)

void	setJmolViewer ()

Private Attributes
Candidate	item
	The currently loaded item. More...

boolean	toleratePartialData = false
	Flag controlling behavior in case of partial data (e.r., lack of fitness/error) More...

JmolPanel	jmolPanel

JScrollPane	tabPanel

JPopupMenu	dataTabPopMenu

String	tmpSDFFile

final String	NL = System.getProperty("line.separator")

Static Private Attributes
static final long	serialVersionUID = 912850110991449553L
	Version UID. More...

Detailed Description

A panel with a molecular viewer and data table.

Author: Marco Foscato

Definition at line 62 of file MoleculeViewPanel.java.

Constructor & Destructor Documentation

◆ MoleculeViewPanel() [1/2]

denoptim.gui.MoleculeViewPanel.MoleculeViewPanel ( )

Constructor.

Definition at line 95 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.initialize().

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◆ MoleculeViewPanel() [2/2]

denoptim.gui.MoleculeViewPanel.MoleculeViewPanel ( int dividerPosition )

Constructor that allows to specify whether the data table is editable or not.

Parameters

dividerPosition allows to set the initial position of the divide

Definition at line 107 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.initialize().

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Member Function Documentation

◆ clearAll()

void denoptim.gui.MoleculeViewPanel.clearAll ( boolean dataIsComing )

Removes the currently visualized molecule and AP table.

Parameters

dataIsComing set true when there is incoming molecular data to visualize. In such case we do not run the very slow zap script in JMol because the molecular data will be overwritten anyway.

Definition at line 485 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.cleardataTable(), and denoptim.gui.MoleculeViewPanel.clearMolecularViewer().

Referenced by denoptim.gui.GraphVertexMolViewerPanel.clearMolecularViewer(), denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile(), denoptim.gui.GraphVertexMolViewerPanel.renderMolVieverToNeedUpdate(), denoptim.gui.GUIInspectFSERun.renderViewWithoutSelectedItems(), denoptim.gui.GUIInspectGARun.renderViewWithoutSelectedItems(), and denoptim.gui.GraphVertexMolViewerPanel.updateMolevularViewer().

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◆ cleardataTable()

void denoptim.gui.MoleculeViewPanel.cleardataTable ( )

Clears the table of attachment points.

Definition at line 496 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.dataTabModel.

Referenced by denoptim.gui.MoleculeViewPanel.clearAll(), and denoptim.gui.MoleculeViewPanel.fillDataTable().

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◆ clearMolecularViewer()

void denoptim.gui.MoleculeViewPanel.clearMolecularViewer ( boolean dataIsComing )

Clears the molecular viewer.

WARNING: this is VERY SLOW: do not do it unless you are sure you really need to clear the data. Typically, if there is incoming data, you do not need to run this, as the old data will be overwritten anyway.

Parameters

dataIsComing set true when there is incoming molecular data to visualize.

Definition at line 516 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.jmolPanel, and denoptim.gui.JmolPanel.viewer.

Referenced by denoptim.gui.MoleculeViewPanel.clearAll().

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◆ dispose()

void denoptim.gui.MoleculeViewPanel.dispose ( )

Definition at line 538 of file MoleculeViewPanel.java.

References denoptim.gui.JmolPanel.dispose(), and denoptim.gui.MoleculeViewPanel.jmolPanel.

Referenced by denoptim.gui.GraphVertexMolViewerPanel.dispose().

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◆ enablePartialData()

void denoptim.gui.MoleculeViewPanel.enablePartialData ( boolean enable )

Sets the behavior in case of request to visualize partial data.

E.g., SDF files that have neither fitness nor error field.

Definition at line 260 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.toleratePartialData.

Referenced by denoptim.gui.GraphVertexMolViewerPanel.initialize().

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◆ fillDataTable() [1/2]

void denoptim.gui.MoleculeViewPanel.fillDataTable ( File molFile )

private

Parameters

molFile can be null, used only to get more data than what already collected in the DNEOPTIMMolecule class.

Definition at line 382 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.fillDataTable(), and denoptim.io.DenoptimIO.readAllAtomContainers().

Referenced by denoptim.gui.MoleculeViewPanel.fillDataTable(), denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile(), and denoptim.gui.MoleculeViewPanel.showPopup().

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◆ fillDataTable() [2/2]

void denoptim.gui.MoleculeViewPanel.fillDataTable ( IAtomContainer mol )

private

Parameters

molFile can be null, used only to get more data than what already collected in the DNEOPTIMMolecule class.

Definition at line 403 of file MoleculeViewPanel.java.

References denoptim.gui.GUIPreferences.chosenSDFTags, denoptim.gui.MoleculeViewPanel.cleardataTable(), denoptim.gui.MoleculeViewPanel.dataTabModel, denoptim.gui.GUIPreferences.defualtSDFTags, denoptim.constants.DENOPTIMConstants.FITNESSTAG, denoptim.graph.Candidate.getComments(), denoptim.graph.Candidate.getError(), denoptim.graph.Candidate.getFitness(), denoptim.graph.Candidate.getGeneration(), denoptim.graph.Candidate.getName(), denoptim.graph.Candidate.getUID(), denoptim.graph.Candidate.hasFitness, denoptim.gui.MoleculeViewPanel.item, denoptim.constants.DENOPTIMConstants.MOLERRORTAG, denoptim.constants.DENOPTIMConstants.PROVENANCE, and denoptim.constants.DENOPTIMConstants.UNIQUEIDTAG.

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◆ initialize()

void denoptim.gui.MoleculeViewPanel.initialize ( int dividerPosition )

private

Definition at line 115 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.dataTable, denoptim.gui.MoleculeViewPanel.dataTabModel, denoptim.gui.Utils.getTempFile(), denoptim.gui.MoleculeViewPanel.jmolPanel, denoptim.gui.MoleculeViewPanel.showPopup(), denoptim.gui.MoleculeViewPanel.tabPanel, and denoptim.gui.MoleculeViewPanel.tmpSDFFile.

Referenced by denoptim.gui.MoleculeViewPanel.MoleculeViewPanel().

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◆ loadChemicalStructure()

void denoptim.gui.MoleculeViewPanel.loadChemicalStructure ( IAtomContainer mol )

Loads a structure in the Jmol viewer.

Parameters

mol	the structure to load

Definition at line 271 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile(), denoptim.gui.MoleculeViewPanel.tmpSDFFile, and denoptim.io.DenoptimIO.writeSDFFile().

Referenced by denoptim.gui.GraphVertexMolViewerPanel.loadDnGraphToViewer(), and denoptim.gui.GraphVertexMolViewerPanel.updateMolevularViewer().

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◆ loadChemicalStructureFromFile() [1/2]

void denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile ( File file )

Loads a structure in the Jmol viewer.

Parameters

file	the file to open

Definition at line 302 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.clearAll(), denoptim.gui.MoleculeViewPanel.fillDataTable(), denoptim.graph.Candidate.fromAtomContainerNoGraph(), denoptim.gui.MoleculeViewPanel.item, denoptim.gui.MoleculeViewPanel.jmolPanel, denoptim.io.DenoptimIO.readAllAtomContainers(), denoptim.io.DenoptimIO.readCandidates(), denoptim.gui.MoleculeViewPanel.setJmolViewer(), denoptim.gui.MoleculeViewPanel.toleratePartialData, and denoptim.gui.JmolPanel.viewer.

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◆ loadChemicalStructureFromFile() [2/2]

void denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile ( String pathName )

Loads a structure in the Jmol viewer.

Parameters

fitProvMol the structure to load

Definition at line 290 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile().

Referenced by denoptim.gui.MoleculeViewPanel.loadChemicalStructure(), denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile(), denoptim.gui.GUIInspectFSERun.renderViewWithSelectedItem(), and denoptim.gui.GUIInspectGARun.renderViewWithSelectedItem().

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◆ setJmolViewer()

void denoptim.gui.MoleculeViewPanel.setJmolViewer ( )

private

Definition at line 524 of file MoleculeViewPanel.java.

References denoptim.gui.MoleculeViewPanel.jmolPanel, denoptim.gui.MoleculeViewPanel.NL, and denoptim.gui.JmolPanel.viewer.

Referenced by denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile().

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◆ showPopup()

void denoptim.gui.MoleculeViewPanel.showPopup ( MouseEvent e )

private

Definition at line 187 of file MoleculeViewPanel.java.

References denoptim.gui.GUIPreferences.chosenSDFTags, denoptim.gui.MoleculeViewPanel.dataTabPopMenu, denoptim.gui.GUIPreferences.defualtSDFTags, denoptim.gui.MoleculeViewPanel.fillDataTable(), denoptim.graph.Candidate.getSDFFile(), denoptim.gui.MoleculeViewPanel.item, and denoptim.io.DenoptimIO.readAllAtomContainers().

Referenced by denoptim.gui.MoleculeViewPanel.initialize().

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Member Data Documentation

◆ dataTable

JTable denoptim.gui.MoleculeViewPanel.dataTable

protected

Definition at line 83 of file MoleculeViewPanel.java.

Referenced by denoptim.gui.MoleculeViewPanel.initialize().

◆ dataTabModel

DefaultTableModel denoptim.gui.MoleculeViewPanel.dataTabModel

protected

Definition at line 82 of file MoleculeViewPanel.java.

Referenced by denoptim.gui.MoleculeViewPanel.cleardataTable(), denoptim.gui.MoleculeViewPanel.fillDataTable(), and denoptim.gui.MoleculeViewPanel.initialize().

◆ dataTabPopMenu

JPopupMenu denoptim.gui.MoleculeViewPanel.dataTabPopMenu

private

Definition at line 84 of file MoleculeViewPanel.java.

Referenced by denoptim.gui.MoleculeViewPanel.showPopup().

◆ item

Candidate denoptim.gui.MoleculeViewPanel.item

private

The currently loaded item.

Definition at line 72 of file MoleculeViewPanel.java.

Referenced by denoptim.gui.MoleculeViewPanel.fillDataTable(), denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile(), and denoptim.gui.MoleculeViewPanel.showPopup().

◆ jmolPanel

JmolPanel denoptim.gui.MoleculeViewPanel.jmolPanel

private

Definition at line 80 of file MoleculeViewPanel.java.

Referenced by denoptim.gui.MoleculeViewPanel.clearMolecularViewer(), denoptim.gui.MoleculeViewPanel.dispose(), denoptim.gui.MoleculeViewPanel.initialize(), denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile(), and denoptim.gui.MoleculeViewPanel.setJmolViewer().

◆ NL

final String denoptim.gui.MoleculeViewPanel.NL = System.getProperty("line.separator")

private

Definition at line 88 of file MoleculeViewPanel.java.

Referenced by denoptim.gui.MoleculeViewPanel.setJmolViewer().

◆ serialVersionUID

final long denoptim.gui.MoleculeViewPanel.serialVersionUID = 912850110991449553L

staticprivate

Version UID.

Definition at line 67 of file MoleculeViewPanel.java.

◆ tabPanel

JScrollPane denoptim.gui.MoleculeViewPanel.tabPanel

private

Definition at line 81 of file MoleculeViewPanel.java.

Referenced by denoptim.gui.MoleculeViewPanel.initialize().

◆ tmpSDFFile

String denoptim.gui.MoleculeViewPanel.tmpSDFFile

private

Definition at line 86 of file MoleculeViewPanel.java.

Referenced by denoptim.gui.MoleculeViewPanel.initialize(), and denoptim.gui.MoleculeViewPanel.loadChemicalStructure().

◆ toleratePartialData

boolean denoptim.gui.MoleculeViewPanel.toleratePartialData = false

private

Flag controlling behavior in case of partial data (e.r., lack of fitness/error)

Definition at line 78 of file MoleculeViewPanel.java.

Referenced by denoptim.gui.MoleculeViewPanel.enablePartialData(), and denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/gui/MoleculeViewPanel.java

Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MoleculeViewPanel() [1/2]

◆ MoleculeViewPanel() [2/2]

Member Function Documentation

◆ clearAll()

◆ cleardataTable()

◆ clearMolecularViewer()

◆ dispose()

◆ enablePartialData()

◆ fillDataTable() [1/2]

◆ fillDataTable() [2/2]

◆ initialize()

◆ loadChemicalStructure()

◆ loadChemicalStructureFromFile() [1/2]

◆ loadChemicalStructureFromFile() [2/2]

◆ setJmolViewer()

◆ showPopup()

Member Data Documentation

◆ dataTable

◆ dataTabModel

◆ dataTabPopMenu

◆ item

◆ jmolPanel

◆ NL

◆ serialVersionUID

◆ tabPanel

◆ tmpSDFFile

◆ toleratePartialData