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[Cdk-commits] SF.net SVN: cdk:[15503] jchempaint/trunk/src
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From: <mar...@us...> - 2010-04-07 14:04:26
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Revision: 15503
http://cdk.svn.sourceforge.net/cdk/?rev=15503&view=rev
Author: mark_rynbeek
Date: 2010-04-07 14:04:20 +0000 (Wed, 07 Apr 2010)
Log Message:
-----------
Fixed some tests. Updated getMol/setMol and copy paste to work with RG file format
Modified Paths:
--------------
jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java
jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java
jchempaint/trunk/src/main/org/openscience/jchempaint/controller/AddBondDragModule.java
jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletBugsTest.java
jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletMenuTest.java
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java 2010-04-07 11:58:46 UTC (rev 15502)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java 2010-04-07 14:04:20 UTC (rev 15503)
@@ -35,7 +35,7 @@
import java.awt.datatransfer.UnsupportedFlavorException;
import java.awt.event.ActionEvent;
import java.io.ByteArrayInputStream;
-import java.io.StringBufferInputStream;
+import java.io.IOException;
import java.io.StringReader;
import java.io.StringWriter;
import java.io.Writer;
@@ -45,6 +45,7 @@
import javax.vecmath.Point2d;
import org.openscience.cdk.ChemFile;
+import org.openscience.cdk.ChemModel;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
@@ -64,7 +65,10 @@
import org.openscience.cdk.io.ISimpleChemObjectReader;
import org.openscience.cdk.io.MDLReader;
import org.openscience.cdk.io.MDLWriter;
+import org.openscience.cdk.io.RGroupQueryReader;
import org.openscience.cdk.io.ReaderFactory;
+import org.openscience.cdk.isomorphism.matchers.IRGroupQuery;
+import org.openscience.cdk.isomorphism.matchers.RGroupQuery;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.layout.TemplateHandler;
import org.openscience.cdk.smiles.SmilesGenerator;
@@ -90,11 +94,10 @@
import org.openscience.jchempaint.renderer.selection.RectangleSelection;
import org.openscience.jchempaint.renderer.selection.ShapeSelection;
import org.openscience.jchempaint.renderer.selection.SingleSelection;
+import org.openscience.jchempaint.rgroups.RGroupHandler;
/**
* Action to copy/paste structures.
- *
- * @cdk.bug 1288449
*/
public class CopyPasteAction extends JCPAction{
@@ -182,7 +185,6 @@
sysClip.setContents(new SmilesSelection(CreateSmilesAction.getSmiles(chemModel)),null);
}
} catch (Exception e1) {
- // TODO Auto-generated catch block
e1.printStackTrace();
}
} else if ("eraser".equals(type)) {
@@ -235,21 +237,33 @@
String content=null;
if (supported(transfer, molFlavor) ) {
- try {
- StringBufferInputStream sbis = (StringBufferInputStream) transfer.getTransferData(molFlavor);
- int x;
- StringBuffer sb = new StringBuffer();
+ StringBuffer sb = new StringBuffer();
+ try {
+ //StringBufferInputStream sbis=null;
+ //sbis = (StringBufferInputStream) transfer.getTransferData(molFlavor);
+
+ StringReader sbis=null;
+ sbis = (StringReader) transfer.getTransferData(molFlavor);
+
+
+ int x;
while((x=sbis.read())!=-1){
sb.append((char)x);
}
reader = new MDLReader(new StringReader(sb.toString()));
- } catch (Exception e1) {
- e1.printStackTrace();
+ } catch (UnsupportedFlavorException e1) {
+ e1.printStackTrace();
+ } catch (IOException e1) {
+ e1.printStackTrace();
+ } catch (Exception e1) {
+ reader = new RGroupQueryReader(new StringReader(sb.toString()));
}
+
} else if (supported(transfer, DataFlavor.stringFlavor) ) {
try {
content = (String) transfer.getTransferData(DataFlavor.stringFlavor);
reader = new ReaderFactory().createReader(new StringReader(content));
+ System.out.println(reader.getClass());
} catch (Exception e1) {
e1.printStackTrace();
}
@@ -261,6 +275,7 @@
}
IMolecule toPaste = null;
+ boolean rgrpQuery=false;
if (reader != null) {
IMolecule readMolecule =
chemModel.getBuilder().newMolecule();
@@ -275,14 +290,24 @@
toPaste.add(ac);
}
- }
+ } else if (reader.accepts(RGroupQuery.class)) {
+ rgrpQuery=true;
+ IRGroupQuery rgroupQuery = (RGroupQuery) reader.read(new RGroupQuery());
+ chemModel = new ChemModel();
+ RGroupHandler rgHandler = new RGroupHandler(rgroupQuery);
+ this.jcpPanel.get2DHub().setRGroupHandler(rgHandler);
+ chemModel.setMoleculeSet(rgHandler.getMoleculeSet(chemModel));
+ rgHandler.layoutRgroup();
+
+ }
+
} catch (CDKException e1) {
e1.printStackTrace();
}
}
//Attempt SMILES or InChI if no reader is found for content.
- if (toPaste == null &&
+ if(rgrpQuery!=true && toPaste == null &&
supported(transfer, DataFlavor.stringFlavor)) {
try{
if (content.toLowerCase().indexOf("inchi")>-1 ) {
@@ -316,16 +341,22 @@
ex.printStackTrace();
}
}
- if (toPaste != null) {
+
+ if (toPaste != null || rgrpQuery==true) {
jcpPanel.getRenderPanel().setZoomWide(true);
jcpPanel.get2DHub().getRenderer().getRenderer2DModel().setZoomFactor(1);
-
- scaleStructure(toPaste);
- insertStructure(toPaste, renderModel);
-
- }else{
+ if ( rgrpQuery==true) {
+ this.jcpPanel.setChemModel(chemModel);
+ }
+ else {
+ scaleStructure(toPaste);
+ insertStructure(toPaste, renderModel);
+ }
+ }
+ else{
JOptionPane.showMessageDialog(jcpPanel, GT._("The content you tried to copy could not be read to any known format"), GT._("Could not process content"), JOptionPane.WARNING_MESSAGE);
}
+
} else if (type.equals("cut")) {
handleSystemClipboard(sysClip);
IAtom atomInRange = null;
@@ -373,9 +404,11 @@
MoveModule newActiveModule = new MoveModule(hub, succusorModule);
newActiveModule.setID("move");
hub.setActiveDrawModule(newActiveModule);
+
} else if (type.equals("selectFromChemObject")) {
- // FIXME: implement for others than Reaction, Atom, Bond
- IChemObject object = getSource(e);
+
+ // FIXME: implement for others than Reaction, Atom, Bond
+ IChemObject object = getSource(e);
if (object instanceof IAtom) {
SingleSelection<IAtom> container = new SingleSelection<IAtom>((IAtom)object);
renderModel.setSelection(container);
@@ -585,15 +618,15 @@
public synchronized Object getTransferData (DataFlavor parFlavor) throws UnsupportedFlavorException {
if (parFlavor.equals (molFlavor)) {
- return new StringBufferInputStream(mol);
+ return new StringReader(mol);
} else if (parFlavor.equals (smilesFlavor)) {
- return new StringBufferInputStream(smiles);
+ return new StringReader(smiles);
} else if(parFlavor.equals(DataFlavor.stringFlavor)) {
return mol;
} else if(parFlavor.equals(cmlFlavor)) {
- return new StringBufferInputStream(cml);
+ return new StringReader(cml);
} else if(parFlavor.equals(svgFlavor)) {
- return new StringBufferInputStream(svg);
+ return new StringReader(svg);
} else {
throw new UnsupportedFlavorException (parFlavor);
}
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java 2010-04-07 11:58:46 UTC (rev 15502)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java 2010-04-07 14:04:20 UTC (rev 15503)
@@ -37,6 +37,7 @@
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.io.IOException;
+import java.io.InputStream;
import java.io.StringReader;
import java.io.StringWriter;
import java.net.URL;
@@ -62,7 +63,10 @@
import org.openscience.cdk.io.ISimpleChemObjectReader;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.io.MDLWriter;
+import org.openscience.cdk.io.RGroupQueryReader;
+import org.openscience.cdk.io.RGroupQueryWriter;
import org.openscience.cdk.io.IChemObjectReader.Mode;
+import org.openscience.cdk.isomorphism.matchers.RGroupQuery;
import org.openscience.cdk.layout.StructureDiagramGenerator;
import org.openscience.cdk.layout.TemplateHandler;
import org.openscience.cdk.smiles.SmilesParser;
@@ -355,21 +359,29 @@
}
/**
- * Gives a mol file of the current molecules in the editor (not reactions)
+ * Gives a mol file of the current molecules in the editor (not reactions).
+ * RGroup queries are also saved as .mol files by convention.
*
* @return The mol file
* @throws CDKException
*/
public String getMolFile() throws CDKException {
+
StringWriter sw = new StringWriter();
- MDLWriter mdlwriter = new MDLWriter(sw);
- // mdlwriter.dontWriteAromatic();
- org.openscience.cdk.interfaces.IChemModel som = theJcpp
- .getChemModel();
- mdlwriter.write(som);
+ org.openscience.cdk.interfaces.IChemModel som = theJcpp.getChemModel();
+
+ if (theJcpp.get2DHub().getRGroupHandler()!=null) {
+ RGroupQueryWriter rgw = new RGroupQueryWriter (sw);
+ rgw.write(theJcpp.get2DHub().getRGroupHandler().getrGroupQuery());
+ }
+ else {
+ MDLWriter mdlwriter = new MDLWriter(sw);
+ mdlwriter.write(som);
+ }
return (sw.toString());
}
+
/**
* Gives a smiles of the current editor content
*
@@ -461,18 +473,29 @@
* @throws Exception
*/
public void setMolFile(String mol) throws CDKException {
-
- ISimpleChemObjectReader cor = new MDLV2000Reader(new StringReader(mol), Mode.RELAXED); //TODO assess R-group?
- IChemModel chemModel = JChemPaint.getChemModelFromReader(cor, theJcpp);
- JChemPaint.cleanUpChemModel(chemModel,true);
- theJcpp.setChemModel(chemModel);
+
+ ISimpleChemObjectReader cor=null;
+ IChemModel chemModel = null;
+
+ if (mol.contains("$RGP")) {
+ cor= new RGroupQueryReader(new StringReader(mol));
+ chemModel=JChemPaint.getChemModelFromReader(cor, theJcpp);
+ }
+ else {
+ cor= new MDLV2000Reader(new StringReader(mol), Mode.RELAXED);
+ chemModel=JChemPaint.getChemModelFromReader(cor, theJcpp);
+ JChemPaint.cleanUpChemModel(chemModel,true);
+ }
+
+ theJcpp.setChemModel(chemModel);
theJcpp.get2DHub().updateView();
+
// the newly opened file should nicely fit the screen
theJcpp.getRenderPanel().setFitToScreen(true);
- theJcpp.getRenderPanel().update(
- theJcpp.getRenderPanel().getGraphics());
- // enable zooming by removing constraint
+ theJcpp.getRenderPanel().update(theJcpp.getRenderPanel().getGraphics());
+ // ..enable zooming by removing constraint again
theJcpp.getRenderPanel().setFitToScreen(false);
+
}
/**
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/controller/AddBondDragModule.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/controller/AddBondDragModule.java 2010-04-07 11:58:46 UTC (rev 15502)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/controller/AddBondDragModule.java 2010-04-07 14:04:20 UTC (rev 15503)
@@ -196,7 +196,6 @@
@Override
public void mouseClickedUp( Point2d worldCoord ) {
- System.out.println("mouseClickedUp addbonddragmod");
chemModelRelay.clearPhantoms();
if(isBond) return;
Modified: jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletBugsTest.java
===================================================================
--- jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletBugsTest.java 2010-04-07 11:58:46 UTC (rev 15502)
+++ jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletBugsTest.java 2010-04-07 14:04:20 UTC (rev 15503)
@@ -30,6 +30,8 @@
public class JCPEditorAppletBugsTest extends AbstractAppletTest {
+ private static int SAVE_AS_MOL_COMBOBOX_POS=6;
+
@Test
public void testSquareSelectSingleAtom() {
JPanelFixture jcppanel = applet.panel("appletframe");
@@ -433,7 +435,7 @@
Assert.assertEquals(12, panel.getChemModel().getMoleculeSet().getAtomContainer(0).getAtomCount() );
}
-
+
@Test public void testBug70() throws FileNotFoundException, CDKException{
JPanelFixture jcppanel=applet.panel("appletframe");
JChemPaintPanel panel = (JChemPaintPanel)jcppanel.target;
@@ -441,7 +443,7 @@
applet.click();
Point2d point = getAtomPoint(panel,0);
applet.panel("renderpanel").robot.click(applet.panel("renderpanel").component(), new Point((int)point.x, (int)point.y), MouseButton.RIGHT_BUTTON,1);
- applet.menuItem("showACProperties2").click();
+ applet.menuItem("showACProperties").click();
DialogFixture dialog = applet.dialog();
JTextComponent textfield = dialog.robot.finder().find(JTextComponentMatcher.withName("Title"));
textfield.setText("aaa");
@@ -450,7 +452,7 @@
applet.menuItem("save").click();
dialog = applet.dialog();
JComboBox combobox = dialog.robot.finder().find(new ComboBoxTextComponentMatcher("org.openscience.jchempaint.io.JCPFileFilter"));
- combobox.setSelectedItem(combobox.getItemAt(5));
+ combobox.setSelectedItem(combobox.getItemAt(SAVE_AS_MOL_COMBOBOX_POS));
JTextComponentFixture text = dialog.textBox();
File file=new File(System.getProperty("java.io.tmpdir")+File.separator+"test.mol");
if(file.exists())
@@ -472,7 +474,7 @@
applet.menuItem("saveAs").click();
DialogFixture dialog = applet.dialog();
JComboBox combobox = dialog.robot.finder().find(new ComboBoxTextComponentMatcher("org.openscience.jchempaint.io.JCPFileFilter"));
- combobox.setSelectedItem(combobox.getItemAt(5));
+ combobox.setSelectedItem(combobox.getItemAt(SAVE_AS_MOL_COMBOBOX_POS));
JTextComponentFixture text = dialog.textBox();
File file=new File(System.getProperty("java.io.tmpdir")+File.separator+"test1.mol");
if(file.exists())
@@ -488,13 +490,13 @@
applet.menuItem("new").click();
applet.button("hexagon").click();
applet.click();
- applet.button("bond").click();
+ applet.button("bondTool").click();
Point2d moveto=getAtomPoint(panel,0);
applet.panel("renderpanel").robot.click(applet.panel("renderpanel").component(), new Point((int)moveto.x,(int)moveto.y), MouseButton.LEFT_BUTTON,1);
applet.menuItem("saveAs").click();
dialog = applet.dialog();
combobox = dialog.robot.finder().find(new ComboBoxTextComponentMatcher("org.openscience.jchempaint.io.JCPFileFilter"));
- combobox.setSelectedItem(combobox.getItemAt(5));
+ combobox.setSelectedItem(combobox.getItemAt(SAVE_AS_MOL_COMBOBOX_POS));
text = dialog.textBox();
file=new File(System.getProperty("java.io.tmpdir")+File.separator+"test2.mol");
if(file.exists())
@@ -520,7 +522,7 @@
applet.menuItem("saveAs").click();
dialog = applet.dialog();
combobox = dialog.robot.finder().find(new ComboBoxTextComponentMatcher("org.openscience.jchempaint.io.JCPFileFilter"));
- combobox.setSelectedItem(combobox.getItemAt(5));
+ combobox.setSelectedItem(combobox.getItemAt(SAVE_AS_MOL_COMBOBOX_POS));
text = dialog.textBox();
text.setText(file.toString());
okbutton = new JButtonFixture(dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Save")));
@@ -556,8 +558,14 @@
applet.panel("renderpanel").robot.click(applet.panel("renderpanel").component(), new Point((int)point.x, (int)point.y), MouseButton.LEFT_BUTTON,1);
point = getBondPoint(panel,2);
applet.panel("renderpanel").robot.click(applet.panel("renderpanel").component(), new Point((int)point.x, (int)point.y), MouseButton.LEFT_BUTTON,1);
- Assert.assertEquals(6, panel.getChemModel().getMoleculeSet().getMolecule(0).getAtomCount());
- Assert.assertEquals(4, panel.getChemModel().getMoleculeSet().getMolecule(0).getBondCount());
+
+ int atomCount=0, bondCount=0;
+ for(IAtomContainer atc : panel.getChemModel().getMoleculeSet().atomContainers()) {
+ atomCount+=atc.getAtomCount();
+ bondCount+=atc.getBondCount();
+ }
+ Assert.assertEquals(6, atomCount);
+ Assert.assertEquals(4, bondCount);
restoreModelToEmpty();
}
Modified: jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletMenuTest.java
===================================================================
--- jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletMenuTest.java 2010-04-07 11:58:46 UTC (rev 15502)
+++ jchempaint/trunk/src/test/org/openscience/jchempaint/JCPEditorAppletMenuTest.java 2010-04-07 14:04:20 UTC (rev 15503)
@@ -547,20 +547,10 @@
Assert.assertEquals(1,panel.getChemModel().getMoleculeSet().getAtomContainer(1).getAtomCount());
Point2d moveto=panel.getRenderPanel().getRenderer().toScreenCoordinates(panel.getChemModel().getMoleculeSet().getAtomContainer(0).getAtom(4).getPoint2d().x,panel.getChemModel().getMoleculeSet().getAtomContainer(0).getAtom(4).getPoint2d().y);
JPopupMenuFixture popup = applet.panel("renderpanel").showPopupMenuAt(new Point((int)moveto.x,(int)moveto.y));
- try {
- Thread.sleep(5000);
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- popup.menuItem("cut2").click();
+ //try {Thread.sleep(5000);} catch (InterruptedException e) {e.printStackTrace();}
+ popup.menuItem("cut").click();
Assert.assertEquals(3,panel.getChemModel().getMoleculeSet().getAtomContainerCount());
- try {
- Thread.sleep(5000);
- } catch (InterruptedException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
+ //try {Thread.sleep(5000);} catch (InterruptedException e) {e.printStackTrace();}
Assert.assertEquals(1,panel.getChemModel().getMoleculeSet().getAtomContainer(0).getAtomCount());
Assert.assertEquals(4,panel.getChemModel().getMoleculeSet().getAtomContainer(1).getAtomCount());
Assert.assertEquals(2,panel.getChemModel().getMoleculeSet().getAtomContainer(2).getAtomCount());
@@ -576,22 +566,6 @@
Assert.assertEquals(22,panel.getChemModel().getMoleculeSet().getAtomContainer(1).getAtomCount());
}
- @Test public void testMenuTemplatesAlkaloids() throws CDKException, ClassNotFoundException, IOException, CloneNotSupportedException {
- restoreModelWithBasicmol();
- applet.menuItem("alkaloids").click();
- DialogFixture dialog = applet.dialog("templates");
- JButtonFixture morphinebutton = new JButtonFixture(dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Morphine")));
- morphinebutton.click();
- Assert.assertEquals(2,panel.getChemModel().getMoleculeSet().getAtomContainerCount());
- Assert.assertEquals(22,panel.getChemModel().getMoleculeSet().getAtomContainer(1).getAtomCount());
- applet.menuItem("alkaloids").click();
- dialog = applet.dialog("templates");
- morphinebutton = new JButtonFixture(dialog.robot, dialog.robot.finder().find(new ButtonTextComponentMatcher("Morphine")));
- morphinebutton.click();
- Assert.assertEquals(3,panel.getChemModel().getMoleculeSet().getAtomContainerCount());
- Assert.assertEquals(22,panel.getChemModel().getMoleculeSet().getAtomContainer(2).getAtomCount());
- }
-
@Test public void testSwitchLanguage(){
applet.menuItem("options").click();
DialogFixture dialog = applet.dialog();
@@ -600,22 +574,29 @@
JComboBox combobox = (JComboBox)dialog.robot.finder().find(new NameMatcher("language"));
for(int i=0;i<combobox.getItemCount();i++){
if(((String)combobox.getItemAt(i)).equals("German")){
- combobox.setSelectedItem(combobox.getItemAt(i));
+ combobox.setSelectedIndex(i);
break;
}
}
JButtonFixture applybutton = new JButtonFixture(dialog.robot, (JButton)dialog.robot.finder().find(new NameMatcher("apply",true)));
applybutton.click();
Assert.assertEquals("Neu", applet.menuItem("new").component().getText());
+
for(int i=0;i<combobox.getItemCount();i++){
if(((String)combobox.getItemAt(i)).equals("American English")){
- combobox.setSelectedItem(combobox.getItemAt(i));
+ combobox.setSelectedIndex(i);
+ System.out.println("set USA");
break;
}
}
- JButtonFixture okbutton = new JButtonFixture(dialog.robot, (JButton)dialog.robot.finder().find(new NameMatcher("ok",true)));
+
+ JButtonFixture okbutton = new JButtonFixture(dialog.robot, (JButton)dialog.robot.finder().find(new NameMatcher("apply",true)));
okbutton.click();
+
Assert.assertFalse(dialog.component().isShowing());
- Assert.assertEquals("New", applet.menuItem("new").component().getText());
+ Assert.assertEquals("New", applet.menuItem("new").component().getText()); // fails in test only?
}
+
+
+
}
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