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[Cdk-commits] SF.net SVN: cdk:[14743] jchempaint/trunk/src
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From: <sh...@us...> - 2009-08-19 13:20:03
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Revision: 14743
http://cdk.svn.sourceforge.net/cdk/?rev=14743&view=rev
Author: shk3
Date: 2009-08-19 12:25:09 +0000 (Wed, 19 Aug 2009)
Log Message:
-----------
working on the menus
Modified Paths:
--------------
jchempaint/trunk/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java
jchempaint/trunk/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java
jchempaint/trunk/src/main/org/openscience/jchempaint/JChemPaintPanel.java
jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java
jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintEditorApplet.java
jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties
jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPShort_Cuts.properties
jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JChemPaintResources.properties
jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletTest.java
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java 2009-08-18 16:58:02 UTC (rev 14742)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java 2009-08-19 12:25:09 UTC (rev 14743)
@@ -28,10 +28,14 @@
*/
package org.openscience.jchempaint;
+import java.io.IOException;
+
import javax.swing.JPanel;
import org.openscience.cdk.controller.ControllerHub;
+import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IChemModel;
+import org.openscience.jchempaint.action.CreateSmilesAction;
/**
* An abstract superclass for the viewer and editor panel.
@@ -76,4 +80,8 @@
public void setChemModel(IChemModel model){
renderPanel.setChemModel(model);
}
+
+ public String getSmiles() throws CDKException, ClassNotFoundException, IOException, CloneNotSupportedException{
+ return CreateSmilesAction.getSmiles(getChemModel());
+ }
}
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java 2009-08-18 16:58:02 UTC (rev 14742)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java 2009-08-19 12:25:09 UTC (rev 14743)
@@ -66,6 +66,8 @@
entries.put("redo", GT._("Redo"));
entries.put("selectAll", GT._("Select All"));
entries.put("copy", GT._("Copy"));
+ entries.put("copyAsSmiles", GT._("Copy as SMILES"));
+ entries.put("delete", GT._("Delete"));
entries.put("paste", GT._("Paste"));
entries.put("cutSelected", GT._("Cut"));
entries.put("cut", GT._("Cut"));
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/JChemPaintPanel.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/JChemPaintPanel.java 2009-08-18 16:58:02 UTC (rev 14742)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/JChemPaintPanel.java 2009-08-19 12:25:09 UTC (rev 14743)
@@ -640,16 +640,7 @@
public void keyReleased(KeyEvent arg0) {
RendererModel model = renderPanel.getRenderer().getRenderer2DModel();
ControllerHub relay = renderPanel.getHub();
- if (arg0.getKeyCode() == KeyEvent.VK_DELETE) {
- IChemObjectSelection selection = model.getSelection();
- if (selection.isFilled()) {
- IAtomContainer selected = selection.getConnectedAtomContainer();
- relay.deleteFragment(selected);
- model.setSelection(new LogicalSelection(
- LogicalSelection.Type.NONE));
- relay.updateView();
- }
- } else if (model.getHighlightedAtom() != null) {
+ if (model.getHighlightedAtom() != null) {
try {
IAtom closestAtom = model.getHighlightedAtom();
char x = arg0.getKeyChar();
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java 2009-08-18 16:58:02 UTC (rev 14742)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java 2009-08-19 12:25:09 UTC (rev 14743)
@@ -40,21 +40,16 @@
import java.io.StringWriter;
import java.io.Writer;
import java.lang.reflect.Constructor;
-import java.util.Iterator;
+import java.util.List;
import javax.swing.JOptionPane;
-import net.sf.jniinchi.INCHI_RET;
-
import org.openscience.cdk.ChemFile;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.controller.ControllerHub;
import org.openscience.cdk.controller.MoveModule;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.geometry.GeometryTools;
-import org.openscience.cdk.inchi.InChIGeneratorFactory;
-import org.openscience.cdk.inchi.InChIToStructure;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
@@ -73,7 +68,6 @@
import org.openscience.cdk.layout.TemplateHandler;
import org.openscience.cdk.renderer.RendererModel;
import org.openscience.cdk.renderer.selection.IChemObjectSelection;
-import org.openscience.cdk.renderer.selection.IncrementalSelection;
import org.openscience.cdk.renderer.selection.LogicalSelection;
import org.openscience.cdk.renderer.selection.RectangleSelection;
import org.openscience.cdk.renderer.selection.ShapeSelection;
@@ -86,8 +80,6 @@
import org.openscience.jchempaint.GT;
import org.openscience.jchempaint.InsertTextPanel;
-import sun.awt.AWTAutoShutdown;
-
/**
* Action to copy/paste structures.
*
@@ -129,9 +121,38 @@
IChemModel chemModel = jcpPanel.getChemModel();
if ("copy".equals(type)) {
- if(renderModel.getSelection().getConnectedAtomContainer()!=null)
+ if(renderModel.getSelection().getConnectedAtomContainer()!=null){
addToClipboard(sysClip,
renderModel.getSelection().getConnectedAtomContainer());
+ }else{
+ List<IAtomContainer> acs=ChemModelManipulator.getAllAtomContainers(chemModel);
+ IAtomContainer allinone=chemModel.getBuilder().newAtomContainer();
+ for(int i=0;i<acs.size();i++){
+ allinone.add(acs.get(i));
+ }
+ addToClipboard(sysClip,allinone);
+ }
+ } else if ("copyAsSmiles".equals(type)) {
+ try {
+ if(renderModel.getSelection().getConnectedAtomContainer()!=null){
+ SmilesGenerator sg=new SmilesGenerator();
+ sysClip.setContents(new SmilesSelection(sg.createSMILES(renderModel.getSelection().getConnectedAtomContainer().getBuilder().newMolecule(renderModel.getSelection().getConnectedAtomContainer()))),null);
+ }else{
+ sysClip.setContents(new SmilesSelection(CreateSmilesAction.getSmiles(chemModel)),null);
+ }
+ } catch (Exception e1) {
+ // TODO Auto-generated catch block
+ e1.printStackTrace();
+ }
+ } else if ("delete".equals(type)) {
+ IChemObjectSelection selection = renderModel.getSelection();
+ if (selection.isFilled()) {
+ IAtomContainer selected = selection.getConnectedAtomContainer();
+ jcpPanel.get2DHub().deleteFragment(selected);
+ renderModel.setSelection(new LogicalSelection(
+ LogicalSelection.Type.NONE));
+ jcpPanel.get2DHub().updateView();
+ }
} else if ("paste".equals(type)) {
Transferable transfer = sysClip.getContents( null );
ISimpleChemObjectReader reader = null;
@@ -485,5 +506,41 @@
System.out.println ("Lost ownership");
}
}
+
+ class SmilesSelection implements Transferable, ClipboardOwner {
+ private DataFlavor [] supportedFlavors = {
+ DataFlavor.stringFlavor
+ };
+
+ String smiles;
+
+ public SmilesSelection(String smiles) throws Exception {
+ this.smiles = smiles;
+ }
+
+ public synchronized DataFlavor [] getTransferDataFlavors () {
+ return (supportedFlavors);
+ }
+
+ public boolean isDataFlavorSupported (DataFlavor parFlavor) {
+ for(int i=0;i<supportedFlavors.length;i++){
+ if(supportedFlavors[i].equals(parFlavor))
+ return true;
+ }
+ return false;
+ }
+
+ public synchronized Object getTransferData (DataFlavor parFlavor) throws UnsupportedFlavorException {
+ if(parFlavor.equals(DataFlavor.stringFlavor)) {
+ return smiles;
+ } else {
+ throw new UnsupportedFlavorException (parFlavor);
+ }
+ }
+
+ public void lostOwnership (Clipboard parClipboard, Transferable parTransferable) {
+ System.out.println ("Lost ownership");
+ }
+ }
}
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintEditorApplet.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintEditorApplet.java 2009-08-18 16:58:02 UTC (rev 14742)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintEditorApplet.java 2009-08-19 12:25:09 UTC (rev 14743)
@@ -39,6 +39,7 @@
chemModel.setMoleculeSet(chemModel.getBuilder().newMoleculeSet());
chemModel.getMoleculeSet().addAtomContainer(chemModel.getBuilder().newMolecule());
JChemPaintPanel p = new JChemPaintPanel(chemModel,GUI_APPLET,debug);
+ p.setName("appletframe");
p.setShowInsertTextField(false);
p.setShowStatusBar(false);
setTheJcpp(p);
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties 2009-08-18 16:58:02 UTC (rev 14742)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties 2009-08-19 12:25:09 UTC (rev 14743)
@@ -51,20 +51,22 @@
#######################################################
# menubar definition #
#######################################################
-menubar=file edit view report
+menubar=file edit view atom bond tools
file=new open save saveAs - export print - close - exit
-edit=undo redo - selectAll copy paste cutSelected - @hydrogen \
- adjustBondOrders resetBondOrders - @flip cleanup - \
- @preferences
-view=toolbar++ statusbar++ menubar++ insertstructure++ - zoomin zoomout zoomoriginal - renderOptions
-report=@validate - createSMILES createInChI
+edit=undo redo - cutSelected copy copyAsSmiles paste - delete selectAll - @preferences renderOptions
+view=zoomin zoomout zoomoriginal - cleanup @flip @hydrogen
+atom=@formalCharge @isotopeChange convertToRadical @pseudoSymbols @valence - @symbolChange
+bond=singleBond stereoDownBond stereoUpBond undefinedStereoBond undefinedEZBond
+tools=@validate - createSMILES createInChI
help=help tutorial - about license
-hydrogen=addImplHydrogen++ makeHydrogenExplicit makeHydrogenImplicit updateHydrogenImplicit
+hydrogen=hydroon hydrooff
preferences=editPreferences reloadPreferences savePreferences
validate=runValidate clearValidate
flip=flipHorizontal flipVertical
+formalCharge=chargePlus2 chargePlus1 chargeZero chargeMinus1 chargeMinus2
+valence= valencyOff valency1 valency2 valency3 valency4 valency5 valency6 valency7 valency8
#######################################################
# popup menu definitions #
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPShort_Cuts.properties
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPShort_Cuts.properties 2009-08-18 16:58:02 UTC (rev 14742)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPShort_Cuts.properties 2009-08-19 12:25:09 UTC (rev 14743)
@@ -41,6 +41,7 @@
close=alt C
cutSelected=control X
copy=control X
+delete=pressed DELETE
paste=control V
selectAll=control A
modelProps=control M
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JChemPaintResources.properties
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JChemPaintResources.properties 2009-08-18 16:58:02 UTC (rev 14742)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JChemPaintResources.properties 2009-08-19 12:25:09 UTC (rev 14743)
@@ -104,6 +104,8 @@
selectAllAction=org.openscience.jchempaint.action.CopyPasteAction@selectAll
selectMoleculeAction=org.openscience.jchempaint.action.CopyPasteAction@selectMolecule
copyAction=org.openscience.jchempaint.action.CopyPasteAction@copy
+copyAsSmilesAction=org.openscience.jchempaint.action.CopyPasteAction@copyAsSmiles
+deleteAction=org.openscience.jchempaint.action.CopyPasteAction@delete
pasteAction=org.openscience.jchempaint.action.CopyPasteAction@paste
addImplHydrogenAction=org.openscience.jchempaint.action.AddHydrogenAction@trackimplicit
makeHydrogenExplicitAction=org.openscience.jchempaint.action.AddHydrogenAction@allexplicit
Modified: jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletTest.java
===================================================================
--- jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletTest.java 2009-08-18 16:58:02 UTC (rev 14742)
+++ jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletTest.java 2009-08-19 12:25:09 UTC (rev 14743)
@@ -1,20 +1,25 @@
package org.openscience.jchempaint;
+import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import org.fest.swing.applet.AppletViewer;
import org.fest.swing.fixture.FrameFixture;
+import org.fest.swing.fixture.JPanelFixture;
import org.fest.swing.launcher.AppletLauncher;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.jchempaint.applet.JChemPaintEditorApplet;
public class JCPEditorAppletTest {
private static AppletViewer viewer;
private static FrameFixture applet;
+ private static IChemModel originalModel;
@BeforeClass public static void setUp() {
@@ -25,6 +30,9 @@
.start();
applet = new FrameFixture(viewer);
applet.show();
+ JPanelFixture jcppanel=applet.panel("appletframe");
+ JChemPaintPanel panel = (JChemPaintPanel)jcppanel.target;
+ originalModel=panel.getChemModel();
}
@Test public void testReportSmiles() {
@@ -34,6 +42,21 @@
Assert.assertTrue(text.indexOf("[H]C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]")>-1);
applet.dialog("smilestextdialog").close();
}
+
+ @Test public void testMenuNew() throws CDKException, ClassNotFoundException, IOException, CloneNotSupportedException {
+ applet.menuItem("new").click();
+ JPanelFixture jcppanel=applet.panel("appletframe");
+ JChemPaintPanel panel = (JChemPaintPanel)jcppanel.target;
+ Assert.assertEquals("",panel.getSmiles());
+ restoreModel();
+ }
+
+ private void restoreModel(){
+ JPanelFixture jcppanel=applet.panel("appletframe");
+ JChemPaintPanel panel = (JChemPaintPanel)jcppanel.target;
+ panel.setChemModel(originalModel);
+ }
+
@AfterClass public static void tearDown() {
viewer.unloadApplet();
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