Fixed error from changes in API

Solves bug 3051
bioclipse · Jun 12, 2012 · 5fb8318 · 5fb8318
1 parent f44b469
commit 5fb8318
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Showing 3 changed files with 7 additions and 15 deletions.
diff --git a/plugins/net.bioclipse.cdk.ui.tests/src/net/bioclipse/cdk/ui/tests/HandlerTests.java b/plugins/net.bioclipse.cdk.ui.tests/src/net/bioclipse/cdk/ui/tests/HandlerTests.java
@@ -10,30 +10,23 @@
  ******************************************************************************/
 package net.bioclipse.cdk.ui.tests;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 
 import java.io.IOException;
-import java.io.InputStream;
-import java.lang.reflect.InvocationTargetException;
 import java.net.MalformedURLException;
-import java.net.URI;
 import java.net.URISyntaxException;
-import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
 
 import net.bioclipse.cdk.business.Activator;
 import net.bioclipse.cdk.business.ICDKManager;
 import net.bioclipse.cdk.domain.ICDKMolecule;
 import net.bioclipse.cdk.ui.filters.FilterOutSalts;
-import net.bioclipse.cdk.ui.handlers.ConvertSMILEStoSDF;
-import net.bioclipse.core.MockIFile;
 import net.bioclipse.core.business.BioclipseException;
 
 import org.eclipse.core.runtime.CoreException;
-import org.eclipse.core.runtime.FileLocator;
 import org.eclipse.core.runtime.NullProgressMonitor;
-import org.junit.Assert;
 import org.junit.Test;
 
 /**
@@ -62,8 +55,7 @@ public void testFilterOutSalts() throws MalformedURLException, IOException, Bioc
 
 		//Remove salts
 		//FIXME The next line does not compile
-//		FilterOutSalts.filterOutSalts(mols, new NullProgressMonitor());
-		Assert.fail();
+        new FilterOutSalts().applyFilter( mols, new NullProgressMonitor() );
 		//Assert we have NO salts in all mols
 		for (ICDKMolecule mol : mols){
 			assertTrue(cdk.isConnected(mol));

diff --git a/plugins/net.bioclipse.cdk.ui/src/net/bioclipse/cdk/ui/filters/BaseFilter.java b/plugins/net.bioclipse.cdk.ui/src/net/bioclipse/cdk/ui/filters/BaseFilter.java
@@ -99,7 +99,7 @@ protected IStatus run(IProgressMonitor monitor) {
 	protected abstract String getFilterName();
 
 	protected abstract List<ICDKMolecule> applyFilter(List<ICDKMolecule> mols,
-			SubProgressMonitor subProgressMonitor);
+                                                       IProgressMonitor subProgressMonitor );
 
 
 }

diff --git a/plugins/net.bioclipse.cdk.ui/src/net/bioclipse/cdk/ui/filters/FilterOutSalts.java b/plugins/net.bioclipse.cdk.ui/src/net/bioclipse/cdk/ui/filters/FilterOutSalts.java
@@ -9,7 +9,7 @@
 import net.bioclipse.core.business.BioclipseException;
 
 import org.apache.log4j.Logger;
-import org.eclipse.core.runtime.SubProgressMonitor;
+import org.eclipse.core.runtime.IProgressMonitor;
 import org.openscience.cdk.interfaces.IAtomContainer;
 
 /**
@@ -28,8 +28,8 @@ protected String getFilterName() {
 	}
 
 	@Override
-	protected List<ICDKMolecule> applyFilter(List<ICDKMolecule> mols,
-			SubProgressMonitor monitor) {
+    public List<ICDKMolecule> applyFilter( List<ICDKMolecule> mols,
+                                              IProgressMonitor monitor ) {
 
 		ICDKManager cdk = Activator.getDefault().getJavaCDKManager();