Fixed compile issues

bioclipse · Sep 17, 2011 · 579dba6 · 579dba6
1 parent 46c9894
commit 579dba6
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Showing 2 changed files with 20 additions and 7 deletions.
diff --git a/plugins/net.bioclipse.medea.case/META-INF/MANIFEST.MF b/plugins/net.bioclipse.medea.case/META-INF/MANIFEST.MF
@@ -8,13 +8,11 @@ Bundle-Vendor: Miguel Rojas
 Require-Bundle: org.eclipse.ui,
  org.eclipse.core.runtime,
  org.eclipse.core.resources,
- net.bioclipse.logger,
  net.bioclipse.ui,
  net.bioclipse.cml,
  net.bioclipse.spectrum,
  net.bioclipse.cdk.jchempaint,
  net.bioclipse.specmol,
- org.xmlcml.cmlxom,
  org.openscience.cdk.core,
  org.openscience.cdk.interfaces,
  org.openscience.cdk.standard,
@@ -24,6 +22,9 @@ Require-Bundle: org.eclipse.ui,
  org.eclipse.ui.views,
  net.bioclipse.seneca,
  net.bioclipse.medea,
- net.bioclipse.core;bundle-version="2.0.0"
+ net.bioclipse.core
 Eclipse-LazyStart: true
-Import-Package: nu.xom
+Import-Package: nu.xom,
+ org.xmlcml.cml.base,
+ org.xmlcml.cml.element,
+ org.apache.log4j
diff --git a/plugins/net.bioclipse.medea.case/src/net/bioclipse/plugins/extensions/WCCMedeaJudge.java b/plugins/net.bioclipse.medea.case/src/net/bioclipse/plugins/extensions/WCCMedeaJudge.java
@@ -6,8 +6,8 @@
 
 import net.bioclipse.core.util.LogUtils;
 import net.bioclipse.medea.core.Medea;
+import net.bioclipse.seneca.judge.AbstractJudge;
 import net.bioclipse.seneca.judge.IJudge;
-import net.bioclipse.seneca.judge.Judge;
 import net.bioclipse.seneca.judge.JudgeResult;
 import net.bioclipse.seneca.judge.MissingInformationException;
 import net.bioclipse.seneca.judge.WCCNMRShiftDBJudge;
@@ -48,7 +48,7 @@
 
 import spok.utils.SpectrumUtils;
 
-public class WCCMedeaJudge extends Judge implements IJudge, Serializable, Cloneable {
+public class WCCMedeaJudge extends AbstractJudge implements IJudge, Serializable, Cloneable {
 
   private static Logger logger = Logger.getLogger(WCCNMRShiftDBJudge.class);
 
@@ -107,7 +107,7 @@ public void configure(CMLElement input) throws MissingInformationException {
 	}
 
 	public JudgeResult evaluate(IAtomContainer ac) throws Exception {
-		IMolecule mol = ac.getBuilder().newMolecule(ac);
+		IMolecule mol = ac.getBuilder().newInstance(IMolecule.class,ac);
 		System.out.print(count+" smi: " + new SmilesGenerator().createSMILES(mol));
 		count++;
 		// FIXME: need to do atom type perception first.
@@ -250,4 +250,16 @@ public IFile setData( ISelection selection, IFile sjsFile ) {
             }
         }
     }
+
+	@Override
+	public boolean isLabelling() {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+	@Override
+	public void labelStartStructure(IAtomContainer startStructure) {
+		// TODO Auto-generated method stub
+
+	}
 }