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[Cdk-commits] SF.net SVN: cdk:[13461] jchempaint/trunk/src/main/org/openscience/ jchempaint/applet/JChemPaintAbstractApplet.java
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From: <sh...@us...> - 2008-12-04 11:54:56
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Revision: 13461
http://cdk.svn.sourceforge.net/cdk/?rev=13461&view=rev
Author: shk3
Date: 2008-12-04 11:54:51 +0000 (Thu, 04 Dec 2008)
Log Message:
-----------
most of the applet parameters are handled properly
Modified Paths:
--------------
jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java 2008-12-04 11:14:33 UTC (rev 13460)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java 2008-12-04 11:54:51 UTC (rev 13461)
@@ -35,13 +35,19 @@
import java.io.StringReader;
import java.io.StringWriter;
import java.net.URL;
+import java.util.Iterator;
+import java.util.List;
+import java.util.StringTokenizer;
import javax.swing.JApplet;
import javax.vecmath.Vector2d;
import org.openscience.cdk.ChemModel;
import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.controller.IControllerModel;
import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.io.ISimpleChemObjectReader;
@@ -49,7 +55,10 @@
import org.openscience.cdk.io.MDLWriter;
import org.openscience.cdk.io.ReaderFactory;
import org.openscience.cdk.layout.StructureDiagramGenerator;
+import org.openscience.cdk.renderer.Renderer2DModel;
import org.openscience.cdk.smiles.SmilesParser;
+import org.openscience.cdk.tools.CDKHydrogenAdder;
+import org.openscience.cdk.tools.manipulator.ChemModelManipulator;
import org.openscience.jchempaint.AbstractJChemPaintPanel;
import org.openscience.jchempaint.InsertTextPanel;
import org.openscience.jchempaint.action.CreateSmilesAction;
@@ -71,13 +80,13 @@
{ "atomNumbersVisible", "true or false", "should atom numbers be shown"},
{ "load", "url", "URL of the chemical data" },
{ "compact", "true or false", "compact means elements shown as dots, no figures etc. (default false)"},
- { "tooltips", "string like 'atomumber|test|atomnumber|text", "the texts will be used as tooltips for the respective atoms (leave out if none required"},
+ { "tooltips", "string like 'atomumber|test|atomnumber|text'", "the texts will be used as tooltips for the respective atoms (leave out if none required"},
{ "impliciths", "true or false", "the implicit hs will be added from start (default false)"},
- { "spectrumRenderer", "string", "name of a spectrum applet (see subproject in NMRShiftDB) where peaks should be highlighted when hovering over atom"},
- { "hightlightTable", "true or false", "if true peaks in a table will be highlighted when hovering over atom, ids are assumed to be tableid$atomnumber (default false)"},
+ { "spectrumRenderer", "string", "TODO name of a spectrum applet (see subproject in NMRShiftDB) where peaks should be highlighted when hovering over atom"},
+ { "hightlightTable", "true or false", "TODO if true peaks in a table will be highlighted when hovering over atom, ids are assumed to be tableid$atomnumber (default false)"},
{ "smiles", "string", "a structure to load as smiles"},
{ "scrollbars", "true or false", "if the molecule is too big to be displayed in normal size, shall scrollbars be used (default) or the molecule be resized - only for viewer applet"},
- { "detachable", "true or false", "should the applet be detacheable by a double click (default false)"}
+ { "detachable", "true or false", "TODO should the applet be detacheable by a double click (default false)"}
};
@Override
@@ -109,94 +118,7 @@
// jcpp.registerModel(theModel);
// if(detacheable)
// jcpp.addFilePopUpMenu();
-// if(getParameter("compact")!=null && getParameter("compact").equals("true")){
-// theModel.getRendererModel().setIsCompact(true);
// }
-// if(getParameter("impliciths")!=null && getParameter("impliciths").equals("false")){
-// theModel.getControllerModel().setAutoUpdateImplicitHydrogens(false);
-// theModel.getRendererModel().setShowImplicitHydrogens(false);
-// theModel.getRendererModel().setShowEndCarbons(false);
-// }else{
-// theModel.getControllerModel().setAutoUpdateImplicitHydrogens(true);
-// theModel.getRendererModel().setShowImplicitHydrogens(true);
-// theModel.getRendererModel().setShowEndCarbons(true);
-//
-// HydrogenAdder hydrogenAdder = new HydrogenAdder("org.openscience.cdk.tools.ValencyChecker");
-// if(theModel.getChemModel()!=null && theModel.getChemModel().getMoleculeSet()!=null){
-// java.util.Iterator mols = theModel.getChemModel().getMoleculeSet().molecules();
-// while (mols.hasNext())
-// {
-// org.openscience.cdk.interfaces.IMolecule molecule = (IMolecule)mols.next();
-// if (molecule != null)
-//
-// {
-// try{
-// hydrogenAdder.addImplicitHydrogensToSatisfyValency(molecule);
-// }catch(Exception ex){
-// //do nothing
-// }
-// }
-// }
-// }
-//
-// }
-// if(getParameter("tooltips")!=null){
-// StringTokenizer st=new StringTokenizer(getParameter("tooltips"),"|");
-// IAtomContainer container = theModel.getChemModel().getBuilder().newAtomContainer();
-// Iterator containers = ChemModelManipulator.getAllAtomContainers(theModel.getChemModel()).iterator();
-// while (containers.hasNext()) {
-// container.add((IAtomContainer)containers.next());
-// }
-// while(st.hasMoreTokens()){
-// IAtom atom = container.getAtom(Integer.parseInt(st.nextToken())-1);
-// theModel.getRendererModel().getToolTipTextMap().put(atom,st.nextToken());
-// }
-// theModel.getRendererModel().setShowTooltip(true);
-// }
-// if(theJcpp.getJChemPaintModel()!=null){
-// jcpp.scaleAndCenterMolecule(theModel.getChemModel(),new Dimension((int)this.getSize().getWidth()-100,(int)this.getSize().getHeight()-100));
-// if(theModel.getChemModel().getMoleculeSet()!=null){
-// int smallestX=Integer.MAX_VALUE;
-// int largestX=Integer.MIN_VALUE;
-// int smallestY=Integer.MAX_VALUE;
-// int largestY=Integer.MIN_VALUE;
-// for(int i=0;i<theModel.getChemModel().getMoleculeSet().getMoleculeCount();i++){
-// for(int k=0;k<theModel.getChemModel().getMoleculeSet().getMolecule(i).getAtomCount();k++){
-// if(((Point2d)theModel.getRendererModel().getRenderingCoordinate(theModel.getChemModel().getMoleculeSet().getMolecule(i).getAtom(k))).x<smallestX)
-// smallestX=(int)((Point2d)theModel.getRendererModel().getRenderingCoordinate(theModel.getChemModel().getMoleculeSet().getMolecule(i).getAtom(k))).x;
-// if(((Point2d)theModel.getRendererModel().getRenderingCoordinate(theModel.getChemModel().getMoleculeSet().getMolecule(i).getAtom(k))).x>largestX)
-// largestX=(int)((Point2d)theModel.getRendererModel().getRenderingCoordinate(theModel.getChemModel().getMoleculeSet().getMolecule(i).getAtom(k))).x;
-// if(((Point2d)theModel.getRendererModel().getRenderingCoordinate(theModel.getChemModel().getMoleculeSet().getMolecule(i).getAtom(k))).y<smallestY)
-// smallestY=(int)((Point2d)theModel.getRendererModel().getRenderingCoordinate(theModel.getChemModel().getMoleculeSet().getMolecule(i).getAtom(k))).y;
-// if(((Point2d)theModel.getRendererModel().getRenderingCoordinate(theModel.getChemModel().getMoleculeSet().getMolecule(i).getAtom(k))).y>largestY)
-// largestY=(int)((Point2d)theModel.getRendererModel().getRenderingCoordinate(theModel.getChemModel().getMoleculeSet().getMolecule(i).getAtom(k))).y;
-// }
-// }
-// if(!theModel.getRendererModel().getIsCompact()){
-// if(jcpp.isShowscrollbars()){
-// int x=largestX-smallestX+30;
-// int y=largestY - smallestY+30;
-// if(x<300)
-// x=300;
-// if(y<300)
-// y=300;
-// //the -60 is to prevent the vertical scrollbar to display even if not needed
-// theModel.getRendererModel().setBackgroundDimension(new Dimension(x,y-60));
-// }
-// jcpp.scaleAndCenterMolecule(theModel.getChemModel(),theModel.getRendererModel().getBackgroundDimension());
-// }else{
-// theModel.getRendererModel().setBackgroundDimension(new Dimension((int)(.9*this.getSize().getWidth()),(int)(.9*this.getSize().getHeight())));
-// IAtomContainer atomContainer = theModel.getChemModel().getBuilder().newAtomContainer();
-// Iterator containers = ChemModelManipulator.getAllAtomContainers(theModel.getChemModel()).iterator();
-// while (containers.hasNext()) {
-// atomContainer.add((IAtomContainer)containers.next());
-// }
-// GeometryTools.translateAllPositive(atomContainer,theModel.getRendererModel().getRenderingCoordinates());
-// GeometryTools.scaleMolecule(atomContainer, theModel.getRendererModel().getBackgroundDimension(), 0.8,theModel.getRendererModel().getRenderingCoordinates());
-// GeometryTools.center(atomContainer, theModel.getRendererModel().getBackgroundDimension(),theModel.getRendererModel().getRenderingCoordinates());
-//
-// }
-// }
// }
// //embedded means that additional instances can't be created, which is
// // needed for applet as well
@@ -285,6 +207,9 @@
@Override
public void start() {
+ Renderer2DModel rendererModel = theJcpp.get2DHub().getIJava2DRenderer().getRenderer2DModel();
+ IChemModel chemModel = theJcpp.getChemModel();
+ IControllerModel controllerModel = theJcpp.get2DHub().getController2DModel();
//Parameter parsing goes here
loadModelFromParam();
String atomNumbers=getParameter("atomNumbersVisible");
@@ -299,6 +224,42 @@
else
theJcpp.get2DHub().getIJava2DRenderer().getRenderer2DModel().setBackColor(new Color(Integer.parseInt(background)));
}
+ if(getParameter("compact")!=null && getParameter("compact").equals("true")){
+ theJcpp.get2DHub().getIJava2DRenderer().getRenderer2DModel().setIsCompact(true);
+ }
+ if(getParameter("tooltips")!=null){
+ StringTokenizer st=new StringTokenizer(getParameter("tooltips"),"|");
+ IAtomContainer container = theJcpp.getChemModel().getBuilder().newAtomContainer();
+ Iterator containers = ChemModelManipulator.getAllAtomContainers(theJcpp.getChemModel()).iterator();
+ while (containers.hasNext()) {
+ container.add((IAtomContainer)containers.next());
+ }
+ while(st.hasMoreTokens()){
+ IAtom atom = container.getAtom(Integer.parseInt(st.nextToken())-1);
+ theJcpp.get2DHub().getIJava2DRenderer().getRenderer2DModel().getToolTipTextMap().put(atom,st.nextToken());
+ }
+ theJcpp.get2DHub().getIJava2DRenderer().getRenderer2DModel().setShowTooltip(true);
+ }
+ if(getParameter("impliciths")!=null && getParameter("impliciths").equals("false")){
+ controllerModel.setAutoUpdateImplicitHydrogens(false);
+ rendererModel.setShowImplicitHydrogens(false);
+ rendererModel.setShowEndCarbons(false);
+ }else{
+ controllerModel.setAutoUpdateImplicitHydrogens(true);
+ rendererModel.setShowImplicitHydrogens(true);
+ rendererModel.setShowEndCarbons(true);
+ if(chemModel!=null){
+ List<IAtomContainer> atomContainers = ChemModelManipulator.getAllAtomContainers(chemModel);
+ for(int i=0;i<atomContainers.size();i++)
+ {
+ try {
+ CDKHydrogenAdder.getInstance(atomContainers.get(i).getBuilder()).addImplicitHydrogens(atomContainers.get(i));
+ } catch (CDKException e) {
+ //do nothing
+ }
+ }
+ }
+ }
}
@Override
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