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[Cdk-commits] CVS: cdk/org/openscience/cdk/renderer MoleculeViewer2D.java,1.17,1.18
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From: Christoph S. <ste...@us...> - 2002-05-31 21:26:17
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Update of /cvsroot/cdk/cdk/org/openscience/cdk/renderer
In directory usw-pr-cvs1:/tmp/cvs-serv4509/openscience/cdk/renderer
Modified Files:
MoleculeViewer2D.java
Log Message:
Bug fixes in Aromaticity detection and Fingerprinting
Index: MoleculeViewer2D.java
===================================================================
RCS file: /cvsroot/cdk/cdk/org/openscience/cdk/renderer/MoleculeViewer2D.java,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -r1.17 -r1.18
*** MoleculeViewer2D.java 1 Mar 2002 17:20:10 -0000 1.17
--- MoleculeViewer2D.java 31 May 2002 21:26:14 -0000 1.18
***************
*** 1,28 ****
! /* MoleculeViewer2D.java
! *
! * $RCSfile$ $Author$ $Date$ $Revision$
! *
! * Copyright (C) 1997-2001 The Chemistry Development Kit (CDK) project
! *
! * Contact: ste...@ic..., ge...@ma..., eg...@sc...
! *
! * This program is free software; you can redistribute it and/or
! * modify it under the terms of the GNU Lesser General Public License
! * as published by the Free Software Foundation; either version 2.1
! * of the License, or (at your option) any later version.
! *
! * This program is distributed in the hope that it will be useful,
! * but WITHOUT ANY WARRANTY; without even the implied warranty of
! * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
! * GNU Lesser General Public License for more details.
! *
! * You should have received a copy of the GNU Lesser General Public License
! * along with this program; if not, write to the Free Software
! * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
-
package org.openscience.cdk.renderer;
-
import org.openscience.cdk.*;
import org.openscience.cdk.renderer.*;
--- 1,27 ----
! /*
! * MoleculeViewer2D.java
! *
! * $RCSfile$ $Author$ $Date$ $Revision$
! *
! * Copyright (C) 1997-2001 The Chemistry Development Kit (CDK) project
! *
! * Contact: ste...@ic..., ge...@ma..., eg...@sc...
! *
! * This program is free software; you can redistribute it and/or
! * modify it under the terms of the GNU Lesser General Public License
! * as published by the Free Software Foundation; either version 2.1
! * of the License, or (at your option) any later version.
! *
! * This program is distributed in the hope that it will be useful,
! * but WITHOUT ANY WARRANTY; without even the implied warranty of
! * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
! * GNU Lesser General Public License for more details.
! *
! * You should have received a copy of the GNU Lesser General Public License
! * along with this program; if not, write to the Free Software
! * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
package org.openscience.cdk.renderer;
import org.openscience.cdk.*;
import org.openscience.cdk.renderer.*;
***************
*** 38,60 ****
!
! /**
! * A Swing-based implementation of Renderer2D for viewing molecules
*/
public class MoleculeViewer2D extends JPanel implements CDKChangeListener
{
public AtomContainer atomContainer;
public Renderer2DModel r2dm;
public Renderer2D renderer;
public String title = "Molecule Viewer";
/**
! * Constructs a MoleculeViewer with a molecule to display
! * and a Renderer2DModel containing the information on how to display it.
*
! * @param molecule The molecule to be displayed
! * @param r2dm The rendere settings determining how the molecule is displayed
*/
! public MoleculeViewer2D(AtomContainer atomContainer,Renderer2DModel r2dm)
{
this.atomContainer = atomContainer;
--- 37,75 ----
! /**
! * A Swing-based implementation of Renderer2D for viewing molecules
! *
! * @author steinbeck
! * @created May 30, 2002
*/
public class MoleculeViewer2D extends JPanel implements CDKChangeListener
{
+ /**
+ * Description of the Field
+ */
public AtomContainer atomContainer;
+ /**
+ * Description of the Field
+ */
public Renderer2DModel r2dm;
+ /**
+ * Description of the Field
+ */
public Renderer2D renderer;
+ /**
+ * Description of the Field
+ */
public String title = "Molecule Viewer";
+ private JFrame frame = null;
+
+
/**
! * Constructs a MoleculeViewer with a molecule to display and a Renderer2DModel containing the information on how to display it.
*
! * @param r2dm The rendere settings determining how the molecule is displayed
! * @param atomContainer Description of Parameter
*/
! public MoleculeViewer2D(AtomContainer atomContainer, Renderer2DModel r2dm)
{
this.atomContainer = atomContainer;
***************
*** 62,167 ****
r2dm.addCDKChangeListener(this);
renderer = new Renderer2D(r2dm);
}
!
/**
! * Constructs a MoleculeViewer with a molecule to display
*
! * @param molecule The molecule to be displayed
*/
public MoleculeViewer2D(AtomContainer atomContainer)
{
! setAtomContainer(atomContainer);
! r2dm = new Renderer2DModel();
! r2dm.addCDKChangeListener(this);
! renderer = new Renderer2D(r2dm);
}
!
/**
! * Constructs a MoleculeViewer with a molecule to display
! *
*/
public MoleculeViewer2D()
{
! r2dm = new Renderer2DModel();
! r2dm.addCDKChangeListener(this);
! renderer = new Renderer2D(r2dm);
}
/**
! * Contructs a JFrame into which this JPanel is
! * put and displays the frame with the molecule
*/
! public void display()
{
! setPreferredSize(new Dimension(600, 400));
! JFrame frame = new JFrame();
! frame.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE);
! frame.getContentPane().add(this);
! frame.setTitle(title);
! frame.pack();
! frame.setVisible(true);
!
}
!
/**
! * Paints the molecule onto the JPanel
*
! * @param g The graphics used to paint with.
*/
! public void paint(Graphics g)
{
! super.paint(g);
! if (atomContainer != null)
! {
! setBackground(r2dm.getBackColor());
! GeometryTools.translateAllPositive(atomContainer);
! GeometryTools.scaleMolecule(atomContainer, getSize(), 0.8);
! GeometryTools.center(atomContainer, getSize());
! renderer.paintMolecule(atomContainer, g);
! }
}
/**
! * The main method.
*
! * @param args An MDL molfile
! */
!
! public static void main(String[] args)
! {
! AtomContainer ac = null;
! try
! {
! FileInputStream fis = new FileInputStream(args[0]);
! MDLReader mr = new MDLReader(fis);
! ac = ((ChemFile)mr.read(new ChemFile())).getChemSequence(0).getChemModel(0).getSetOfMolecules().getMolecule(0);
! fis.close();
! }
! catch(Exception exc)
! {
! exc.printStackTrace();
! }
!
! new MoleculeViewer2D(ac, new Renderer2DModel());
}
/**
! * Sets a Renderer2DModel which determins the way a molecule is displayed
*
! * @param r2dm The Renderer2DModel
*/
! public void setRenderer2DModel(Renderer2DModel r2dm)
{
! this.r2dm = r2dm;
! r2dm.addCDKChangeListener(this);
! renderer = new Renderer2D(r2dm);
}
/**
! * Gets the Renderer2DModel which determins the way a molecule is displayed
*/
public Renderer2DModel getRenderer2DModel()
--- 77,154 ----
r2dm.addCDKChangeListener(this);
renderer = new Renderer2D(r2dm);
+ frame = new JFrame();
}
!
!
/**
! * Constructs a MoleculeViewer with a molecule to display
*
! * @param atomContainer Description of Parameter
*/
public MoleculeViewer2D(AtomContainer atomContainer)
{
! this(atomContainer, new Renderer2DModel());
}
!
/**
! * Constructs a MoleculeViewer with a molecule to display
*/
public MoleculeViewer2D()
{
! this(null, new Renderer2DModel());
}
/**
! * Sets the Frame attribute of the MoleculeViewer2D object
! *
! * @param frame The new Frame value
*/
! public void setFrame(JFrame frame)
{
! this.frame = frame;
}
!
/**
! * Sets a Renderer2DModel which determins the way a molecule is displayed
*
! * @param r2dm The Renderer2DModel
*/
! public void setRenderer2DModel(Renderer2DModel r2dm)
{
! this.r2dm = r2dm;
! r2dm.addCDKChangeListener(this);
! renderer = new Renderer2D(r2dm);
}
+
/**
! * Sets the AtomContainer to be displayed
*
! * @param atomContainer The AtomContainer to be displayed
! */
! public void setAtomContainer(AtomContainer atomContainer)
! {
! this.atomContainer = atomContainer;
}
/**
! * Gets the Frame attribute of the MoleculeViewer2D object
*
! * @return The Frame value
*/
! public JFrame getFrame()
{
! return frame;
}
+
/**
! * Gets the Renderer2DModel which determins the way a molecule is displayed
! *
! * @return The Renderer2DModel value
*/
public Renderer2DModel getRenderer2DModel()
***************
*** 170,204 ****
}
!
!
/**
! * Method to notify this CDKChangeListener if something
! * has changed in another object
*
! * @param e The EventObject containing information on the nature and source of the event
*/
! public void stateChanged(EventObject e)
{
! repaint();
}
/**
! * Returns the AtomContainer which is being displayed
*
! * @return The AtomContainer which is being displayed
*/
! public AtomContainer getAtomContainer()
{
! return this.atomContainer;
}
/**
! * Sets the AtomContainer to be displayed
*
! * @param atomContainer The AtomContainer to be displayed
*/
! public void setAtomContainer(AtomContainer atomContainer)
{
! this.atomContainer = atomContainer;
}
}
--- 157,240 ----
}
!
/**
! * Returns the AtomContainer which is being displayed
*
! * @return The AtomContainer which is being displayed
*/
! public AtomContainer getAtomContainer()
{
! return this.atomContainer;
! }
!
!
!
! /**
! * Contructs a JFrame into which this JPanel is put and displays the frame with the molecule
! */
! public void display()
! {
! setPreferredSize(new Dimension(600, 400));
! frame.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE);
! frame.getContentPane().add(this);
! frame.setTitle(title);
! frame.pack();
! frame.setVisible(true);
}
+
/**
! * Paints the molecule onto the JPanel
*
! * @param g The graphics used to paint with.
*/
! public void paint(Graphics g)
{
! super.paint(g);
! if (atomContainer != null)
! {
! setBackground(r2dm.getBackColor());
! GeometryTools.translateAllPositive(atomContainer);
! GeometryTools.scaleMolecule(atomContainer, getSize(), 0.8);
! GeometryTools.center(atomContainer, getSize());
! renderer.paintMolecule(atomContainer, g);
! }
}
+
+
/**
! * Method to notify this CDKChangeListener if something has changed in another object
*
! * @param e The EventObject containing information on the nature and source of the event
*/
! public void stateChanged(EventObject e)
{
! repaint();
! }
!
!
! /**
! * The main method.
! *
! * @param args An MDL molfile
! */
!
! public static void main(String[] args)
! {
! AtomContainer ac = null;
! try
! {
! FileInputStream fis = new FileInputStream(args[0]);
! MDLReader mr = new MDLReader(fis);
! ac = ((ChemFile) mr.read(new ChemFile())).getChemSequence(0).getChemModel(0).getSetOfMolecules().getMolecule(0);
! fis.close();
! }
! catch (Exception exc)
! {
! exc.printStackTrace();
! }
!
! new MoleculeViewer2D(ac, new Renderer2DModel());
}
}
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