Adapt for latest cdk update + cleanup of warnings.

bioclipse · Jul 17, 2012 · d3cd997 · d3cd997
1 parent 85d3923
commit d3cd997
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Showing 6 changed files with 16 additions and 14 deletions.
diff --git a/plugins/net.bioclipse.ds/META-INF/MANIFEST.MF b/plugins/net.bioclipse.ds/META-INF/MANIFEST.MF
@@ -13,9 +13,11 @@ Require-Bundle: org.eclipse.ui,
  net.bioclipse.cdk.business,
  net.bioclipse.cdk.jchempaint,
  org.openscience.cdk.interfaces,
- org.openscience.cdk.nonotify,
- org.openscience.cdk.render;bundle-version="1.3.5",
- org.openscience.cdk.renderbasic;bundle-version="1.3.5"
+ org.openscience.cdk.render,
+ org.openscience.cdk.renderbasic,
+ org.openscience.cdk.standard,
+ org.openscience.cdk.silent,
+ org.openscience.cdk.valencycheck
 Bundle-ActivationPolicy: lazy
 Import-Package: javax.vecmath,
  nu.xom;version="1.1.0",

diff --git a/plugins/net.bioclipse.ds/src/net/bioclipse/ds/model/AbstractDSTest.java b/plugins/net.bioclipse.ds/src/net/bioclipse/ds/model/AbstractDSTest.java
@@ -10,7 +10,6 @@
  ******************************************************************************/
 package net.bioclipse.ds.model;
 
-import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -38,7 +37,7 @@
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 import org.openscience.cdk.tools.CDKHydrogenAdder;
 import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
 
@@ -235,7 +234,7 @@ protected List<ITestResult> returnError(String name, String errorMessage) {
 
 
     public IAtomContainer getAtomContainer() {
-        return NoNotificationChemObjectBuilder.getInstance().
+        return SilentChemObjectBuilder.getInstance().
         newInstance(IAtomContainer.class);
     }
 

diff --git a/plugins/net.bioclipse.ds/src/net/bioclipse/ds/model/ITestResult.java b/plugins/net.bioclipse.ds/src/net/bioclipse/ds/model/ITestResult.java
@@ -14,11 +14,8 @@
 
 import org.eclipse.core.runtime.IAdaptable;
 import org.eclipse.swt.graphics.Image;
-import org.openscience.cdk.renderer.generators.IGenerator;
 import org.openscience.cdk.renderer.generators.IGeneratorParameter;
 
-import net.bioclipse.cdk.domain.ISubStructure;
-
 
 /**
  * A base interface for all test results. Extends ISubStructure since even if 

diff --git a/plugins/net.bioclipse.ds/src/net/bioclipse/ds/model/ModelPropertySource.java b/plugins/net.bioclipse.ds/src/net/bioclipse/ds/model/ModelPropertySource.java
@@ -51,7 +51,8 @@ public class ModelPropertySource extends BasicPropertySource
 
 
 
-    private Object ModelPropertiesTable[][] =
+    @SuppressWarnings("unused")
+	private Object ModelPropertiesTable[][] =
     {
             { MODEL_NAME, new TextPropertyDescriptor(MODEL_NAME,MODEL_NAME)},
             { MODEL_TYPE, new TextPropertyDescriptor(MODEL_TYPE,MODEL_TYPE)},
@@ -62,6 +63,7 @@ public class ModelPropertySource extends BasicPropertySource
             { LEARNING_PARAMETERS, new TextPropertyDescriptor(LEARNING_PARAMETERS,LEARNING_PARAMETERS)}
     };
 
+    @SuppressWarnings("unused")
     private Object DatasetPropertiesTable[][] =
     {
             { DATASET_NAME, new TextPropertyDescriptor(DATASET_NAME,DATASET_NAME)},

diff --git a/plugins/net.bioclipse.ds/src/net/bioclipse/ds/model/TestRun.java b/plugins/net.bioclipse.ds/src/net/bioclipse/ds/model/TestRun.java
@@ -28,7 +28,7 @@
 import org.eclipse.ui.views.properties.IPropertySource;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
 
 /**
  * Class to associate an editor with a test
@@ -129,7 +129,7 @@ public Object getAdapter( Class adapter ) {
     }
 
     public IAtomContainer getAtomContainer() {
-        return NoNotificationChemObjectBuilder.getInstance().
+        return SilentChemObjectBuilder.getInstance().
         newInstance(IAtomContainer.class);
     }
 

diff --git a/plugins/net.bioclipse.ds/src/net/bioclipse/ds/model/TestRunPropertySource.java b/plugins/net.bioclipse.ds/src/net/bioclipse/ds/model/TestRunPropertySource.java
@@ -51,7 +51,8 @@ public class TestRunPropertySource extends BasicPropertySource
 
 
 
-    private Object ModelPropertiesTable[][] =
+    @SuppressWarnings("unused")
+	private Object ModelPropertiesTable[][] =
     {
             { MODEL_NAME, new TextPropertyDescriptor(MODEL_NAME,MODEL_NAME)},
             { MODEL_TYPE, new TextPropertyDescriptor(MODEL_TYPE,MODEL_TYPE)},
@@ -62,7 +63,8 @@ public class TestRunPropertySource extends BasicPropertySource
             { LEARNING_PARAMETERS, new TextPropertyDescriptor(LEARNING_PARAMETERS,LEARNING_PARAMETERS)}
     };
 
-    private Object DatasetPropertiesTable[][] =
+    @SuppressWarnings("unused")
+	private Object DatasetPropertiesTable[][] =
     {
             { DATASET_NAME, new TextPropertyDescriptor(DATASET_NAME,DATASET_NAME)},
             { DATASET_URL, new TextPropertyDescriptor(DATASET_URL,DATASET_URL)},