this example was using the wrong Parameter class. fixed

andreasprlic · andreasprlic · commit 161c567fa0c2 · 2016-02-29T23:56:50.000-08:00
diff --git a/biojava-structure-gui/src/main/java/demo/DemoSW3DAligner.java b/biojava-structure-gui/src/main/java/demo/DemoSW3DAligner.java
@@ -30,67 +30,64 @@
 import org.biojava.nbio.structure.align.ce.CeParameters;
 import org.biojava.nbio.structure.align.gui.StructureAlignmentDisplay;
 import org.biojava.nbio.structure.align.model.AFPChain;
+import org.biojava.nbio.structure.align.seq.SmithWaterman3DParameters;
 import org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner;
 import org.biojava.nbio.structure.align.util.AtomCache;
 
 public class DemoSW3DAligner {
 
 
 
-	   public static void main(String[] args){
-	       
-	       //String name1 = "4hhb.A";
-	       //String name2 = "4hhb.B";
-	       
-	       String name1 = "1cdg.A";
-	       String name2 = "1tim.B";
-	      
-	       AtomCache cache = new AtomCache();
-	               
-	       Structure structure1 = null;
-	       Structure structure2 = null;
-
-	       try {
-
-	          StructureAlignment algorithm  = StructureAlignmentFactory.getAlgorithm(SmithWaterman3Daligner.algorithmName);
-	          
-	           structure1 = cache.getStructure(name1);
-	           structure2 = cache.getStructure(name2);
-	           
-	           Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
-	           Atom[] ca2 = StructureTools.getAtomCAArray(structure2);
-	           
-	           // get default parameters
-	           CeParameters params = new CeParameters();
-	           
-	           // add more print
-	           params.setShowAFPRanges(true);
-	           
-	           // set the maximum gap size to unlimited 
-	           params.setMaxGapSize(-1);
-	           
-	           AFPChain afpChain = algorithm.align(ca1,ca2,params);            
-
-	           afpChain.setName1(name1);
-	           afpChain.setName2(name2);
-
-	           // flexible original results:
-	           System.out.println(afpChain.toFatcat(ca1,ca2));
-	           
-	           // print rotation matrices
-	           System.out.println(afpChain.toRotMat());
-	           //System.out.println(afpChain.toCE(ca1, ca2));
-	           
-	           // print XML representation
-	           //System.out.println(AFPChainXMLConverter.toXML(afpChain,ca1,ca2));
-	                        
-	           StructureAlignmentDisplay.display(afpChain, ca1, ca2);
-	           
-	       } catch (Exception e) {
-	           e.printStackTrace();
-	           return;
-	       }
-	   }
+	public static void main(String[] args){
+
+		String name1 = "1MBN.A";
+		String name2 = "4ODC.A";
+
+		AtomCache cache = new AtomCache();
+
+		Structure structure1 = null;
+		Structure structure2 = null;
+
+		try {
+
+			StructureAlignment algorithm  = StructureAlignmentFactory.getAlgorithm(SmithWaterman3Daligner.algorithmName);
+
+			System.out.println("using " + algorithm.getAlgorithmName());
+
+			SmithWaterman3DParameters params = new SmithWaterman3DParameters();
+
+			System.out.println("Gap open:" + params.getGapOpen());
+			System.out.println("Gap extension:" + params.getGapExtend());
+
+			structure1 = cache.getStructure(name1);
+			structure2 = cache.getStructure(name2);
+
+			Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
+			Atom[] ca2 = StructureTools.getAtomCAArray(structure2);
+
+
+			AFPChain afpChain = algorithm.align(ca1,ca2,params);            
+
+			afpChain.setName1(name1);
+			afpChain.setName2(name2);
+
+			// flexible original results:
+			System.out.println(afpChain.toFatcat(ca1,ca2));
+
+			// print rotation matrices
+			System.out.println(afpChain.toRotMat());
+			//System.out.println(afpChain.toCE(ca1, ca2));
+
+			// print XML representation
+			//System.out.println(AFPChainXMLConverter.toXML(afpChain,ca1,ca2));
+
+			StructureAlignmentDisplay.display(afpChain, ca1, ca2);
+
+		} catch (Exception e) {
+			e.printStackTrace();
+			return;
+		}
+	}
 
 
 }
