biojava#383 updating of demo scripts to new StructureIdentifier convention

andreasprlic · andreasprlic · commit aea237a99324 · 2016-01-25T16:07:59.000-08:00
diff --git a/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java b/biojava-structure-gui/src/main/java/demo/DemoMultipleMC.java
@@ -28,6 +28,8 @@
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureIdentifier;
+import org.biojava.nbio.structure.SubstructureIdentifier;
 import org.biojava.nbio.structure.align.StructureAlignment;
 import org.biojava.nbio.structure.align.ce.CeMain;
 import org.biojava.nbio.structure.align.gui.MultipleAlignmentDisplay;
@@ -94,9 +96,13 @@ public static void main(String[] args) throws IOException, StructureException, I
 		
 		//Load the CA atoms of the structures
 		AtomCache cache = new AtomCache();
+
+		List<StructureIdentifier> identifiers = new ArrayList<StructureIdentifier>();
+
 		List<Atom[]> atomArrays = new ArrayList<Atom[]>();
 		for (String name:names)	{
 			atomArrays.add(cache.getAtoms(name));
+			identifiers.add(new SubstructureIdentifier(name));
 		}
 		
 		//Here the multiple structural alignment algorithm comes in place to generate the alignment object
@@ -108,7 +114,7 @@ public static void main(String[] args) throws IOException, StructureException, I
 		params.setGapExtension(20.0);
 		
 		MultipleAlignment result = algorithm.align(atomArrays);
-		result.getEnsemble().setStructureNames(names);
+		result.getEnsemble().setStructureIdentifiers(identifiers);
 		
 		//Information about the alignment
 		result.getEnsemble().setAlgorithmName(algorithm.getAlgorithmName());
diff --git a/biojava-structure/src/main/java/demo/DemoMultipleMC.java b/biojava-structure/src/main/java/demo/DemoMultipleMC.java
@@ -28,6 +28,8 @@
 
 import org.biojava.nbio.structure.Atom;
 import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureIdentifier;
+import org.biojava.nbio.structure.SubstructureIdentifier;
 import org.biojava.nbio.structure.align.ce.CeMain;
 import org.biojava.nbio.structure.align.multiple.MultipleAlignment;
 import org.biojava.nbio.structure.align.multiple.mc.MultipleMcMain;
@@ -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> identifiers = new ArrayList<StructureIdentifier>();
 		for (String name:names)	{
 			atomArrays.add(cache.getAtoms(name));
+			identifiers.add(new SubstructureIdentifier(name));
 		}
 
 		//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(identifiers);
 
 		//Information about the alignment
 		result.getEnsemble().setAlgorithmName(algorithm.getAlgorithmName());
