Implemented the converter factories for Cells --> POJO and POJO --> C…

…ell for CDKCell3

TODO: It would be worth creating a CDKCellFactory to handle creation of CDK cells.

git-svn-id: https://community.knime.org/svn/nodes4knime/trunk@9238 cd80d6f6-f959-11df-8f91-f7e70cbaf77b

org.openscience/org.openscience.cdk.knime/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: KNIME CDK Integration
 Bundle-SymbolicName: org.openscience.cdk.knime;singleton:=true
-Bundle-Version: 1.5.600.qualifier
+Bundle-Version: 1.5.700.qualifier
 Bundle-Vendor: KNIME GmbH, Konstanz and EMBL-EBI, Cambridge
 Bundle-ClassPath: knime-cdk.jar,
  lib/cdk-bundle-1.5.13.jar,

org.openscience/org.openscience.cdk.knime/plugin.xml

@@ -66,4 +66,16 @@
          </serializer>
       </DataType>
    </extension>
+<extension
+      point="org.knime.core.DataCellToJavaConverter">
+   <DataCellToJavaConverter
+         factoryClass="org.openscience.cdk.knime.type.snippets.java.CdkCellToJavaFactory">
+   </DataCellToJavaConverter>
+</extension>
+<extension
+      point="org.knime.core.JavaToDataCellConverter">
+   <JavaToDataCellConverter
+         factoryClass="org.openscience.cdk.knime.type.snippets.java.JavaToCdkCellFactory">
+   </JavaToDataCellConverter>
+</extension>
 </plugin>

org.openscience/org.openscience.cdk.knime/src/org/openscience/cdk/knime/type/snippets/java/CdkCellToJavaFactory.java

@@ -0,0 +1,29 @@
+package org.openscience.cdk.knime.type.snippets.java;
+
+import org.knime.core.data.convert.java.DataCellToJavaConverter;
+import org.knime.core.data.convert.java.SimpleDataCellToJavaConverterFactory;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.knime.type.CDKAdapterCell;
+import org.openscience.cdk.knime.type.CDKCell3;
+import org.openscience.cdk.knime.type.CDKValue;
+
+/**
+ * Allows access to a CDK Value in Java Snippets. As there is no CDKCellFactory this will
+ * create a {@link CDKAdapterCell} with a {@link CDKCell3}. 
+ * <br></br>
+ * TODO: Create a cell factory!
+ * 
+ * @author Samuel Webb, Lhasa Limited
+ * @since 1.5.700, 13/03/2017
+ *
+ */
+public class CdkCellToJavaFactory extends SimpleDataCellToJavaConverterFactory<CDKValue, IAtomContainer> {
+	public CdkCellToJavaFactory() {
+		super(CDKValue.class, IAtomContainer.class, new DataCellToJavaConverter<CDKValue, IAtomContainer>() {
+			@Override
+			public IAtomContainer convert(CDKValue structure) throws Exception {
+				return structure.getAtomContainer();
+			}
+		}, "IAtomContainer");
+	}
+}

org.openscience/org.openscience.cdk.knime/src/org/openscience/cdk/knime/type/snippets/java/JavaToCdkCellFactory.java

@@ -0,0 +1,29 @@
+package org.openscience.cdk.knime.type.snippets.java;
+
+import org.knime.core.data.DataCell;
+import org.knime.core.data.convert.datacell.JavaToDataCellConverter;
+import org.knime.core.data.convert.datacell.SimpleJavaToDataCellConverterFactory;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.knime.type.CDKAdapterCell;
+import org.openscience.cdk.knime.type.CDKCell3;
+
+/**
+ * Converts an IAtomContainer to a CDK Cell. The implementation is not safe to
+ * updates to CDK Cells as the choice in CDK Cell is currently hard coded. This
+ * should be replaced with a CDK Cell Factory.
+ * 
+ * @author Samuel Webb, Lhasa Limited
+ * @since 1.5.700, 13/03/2017
+ */
+public class JavaToCdkCellFactory extends SimpleJavaToDataCellConverterFactory<IAtomContainer> {
+	// Constructor
+	public JavaToCdkCellFactory() {
+		super(IAtomContainer.class, CDKAdapterCell.RAW_TYPE, new JavaToDataCellConverter<IAtomContainer>() {
+			@Override
+			public DataCell convert(IAtomContainer structure) throws Exception {
+				return new CDKAdapterCell(new CDKCell3(structure));
+			}
+		}, "IAtomContainer");
+
+	}
+}