Package com.chemaxon.calculations.gui

Class CalculatorPluginDisplay<P extends CalculatorPlugin>

java.lang.Object
chemaxon.marvin.plugin.CalculatorPluginService<P>
com.chemaxon.calculations.gui.CalculatorPluginDisplay<P>
Direct Known Subclasses:
CalculatorPluginDisplay
@PublicAPI public class CalculatorPluginDisplay<P extends CalculatorPlugin> extends CalculatorPluginService<P>
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

  • Field Details

    • CELLSIZE

      protected static final int CELLSIZE
      The default viewer cell size.
      See Also:

    • NONE

      protected static final int NONE
      Property display type: no property display.
      See Also:

    • LABEL

      protected static final int LABEL
      Property display type: display in label.
      See Also:

    • TEXT

      protected static final int TEXT
      Property display type: display in text.
      See Also:

    • HTML

      protected static final int HTML
      Property display type: display in html text.
      See Also:

    • WORD_SEPARATORS

      protected static final String WORD_SEPARATORS
      Word separators used to form multi-line text if the text is too long.
      See Also:

    • MAX_LINE_LENGTH

      protected static final int MAX_LINE_LENGTH
      Maximum desired line length used to form multi-line text.
      See Also:

    • parent

      protected Component parent
      The parent component.

    • title

      protected 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 ArrayList resultMolList
      The result molecules to be displayed.

    • resultValues

      protected ArrayList resultValues
      The result values to be displayed in MarvinSpace.

    • reactionArrow

      protected DPoint3[] reactionArrow
      The reaction arrow endpoints, null if not a reaction.

  • Constructor Details

    • CalculatorPluginDisplay

      public CalculatorPluginDisplay()

  • Method Details

    • setPlugin

      @Deprecated public void setPlugin(CalculatorPlugin plugin)
      Deprecated.
      use setPluginChecked(CalculatorPlugin) instead
      Sets the plugin.
      Parameters:
      plugin - is the plugin

    • setPluginChecked

      public void setPluginChecked(P plugin)
      Sets the plugin.
      Parameters:
      plugin - is the plugin

    • getPlugin

      protected final P getPlugin()
      Description copied from class: CalculatorPluginService
      Returns the calculator plugin object.
      Specified by:
      getPlugin in class CalculatorPluginService<P extends CalculatorPlugin>
      Returns:
      the calculator plugin object

    • setParent

      public final void setParent(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(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(String title)
      Sets the frame title.
      Parameters:
      title - is the frame title

    • getTitle

      public 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 MProgressMonitor getProgressMonitor(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 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 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(String title, chemaxon.marvin.common.swing.MolPanel mpan) throws PluginException
      Throws:
      PluginException

    • getErrorComponent

      public 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 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 String getPropertyText(Molecule mol)
      Returns molecule properties is text form.
      Parameters:
      mol - is the molecule
      Returns:
      molecule properties in text form

    • appendpHText

      protected String appendpHText(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 String[] getLabels(double[] values)
      Returns formatted array.
      Parameters:
      values - is the numerical array
      Returns:
      the formatted array

    • getTableText

      protected final String getTableText(String header, 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 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