Update demo because of StructureIdentifier

lafita · lafita · commit 35102f58a9e2 · 2016-01-25T17:42:37.000+01:00
diff --git a/biojava-structure/src/main/java/demo/DemoMultipleMC.java b/biojava-structure/src/main/java/demo/DemoMultipleMC.java
@@ -28,7 +28,9 @@
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureIdentifier;
 import org.biojava.nbio.structure.align.ce.CeMain;
+import org.biojava.nbio.structure.align.client.StructureName;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 import org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain;
 import org.biojava.nbio.structure.align.multiple.mc.MultipleMcParameters;
@@ -91,8 +93,11 @@ public static void main(String[] args) throws IOException, StructureException, I
 		//Load the CA atoms of the structures
 		AtomCache cache = new AtomCache();
 		List<Atom[]> atomArrays = new ArrayList<Atom[]>();
+		List<StructureIdentifier> ids = new ArrayList<StructureIdentifier>();
 		for (String name:names)	{
-			atomArrays.add(cache.getAtoms(name));
+			StructureIdentifier id = new StructureName(name);
+			ids.add(id);
+			atomArrays.add(cache.getAtoms(id));
 		}
 
 		//Here the multiple structural alignment algorithm comes in place to generate the alignment object
@@ -102,7 +107,7 @@ public static void main(String[] args) throws IOException, StructureException, I
 		params.setMinAlignedStructures(10);
 
 		MultipleAlignment result = algorithm.align(atomArrays);
-		result.getEnsemble().setStructureNames(names);
+		result.getEnsemble().setStructureIdentifiers(ids);
 
 		//Information about the alignment
 		result.getEnsemble().setAlgorithmName(algorithm.getAlgorithmName());
