Some biojava#111

josemduarte · josemduarte · commit d4d3d5bcc19b · 2015-03-11T12:16:38.000+01:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java
@@ -364,4 +364,22 @@ private static void printOptAln(AFPChain cpAlignment) {
 			System.out.println();
 		}
 	}
+	
+	public static void main(String[] args) throws Exception {
+		// this is to test this issue:
+		// https://github.com/rcsb/symmetry/issues/46
+		// 
+		
+		OptimalCECPMainTest t = new OptimalCECPMainTest();
+		System.out.println("Test 1");
+		t.testPermuteOptAlnUnpermuted();
+		System.out.println("Test 2");
+		t.testOptimalAlignmentConsistency();
+		//System.out.println("Test 3");
+		//t.testUnpermuted();
+		//System.out.println("Test 4");
+		//t.testPermuteArray();
+		//System.out.println("Test 5");
+		//t.testPermuteOptAln();
+	}
 }
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignmentFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/StructureAlignmentFactory.java
@@ -100,7 +100,6 @@ public static void clearAlgorithms() {
 		algorithms.clear();
 	}
 
-	@SuppressWarnings("unchecked")
 	public static StructureAlignment getAlgorithm(String name) throws StructureException{
 		for ( StructureAlignment algo : algorithms){
 			if (algo.getAlgorithmName().equalsIgnoreCase(name)) {
@@ -109,12 +108,21 @@ public static StructureAlignment getAlgorithm(String name) throws StructureExcep
 				// avoid issues with this in multi-threaded environments bu
 				// creating a new StructureAlignment every time this is called
 				try {
+					@SuppressWarnings("unchecked")
 					Class<StructureAlignment> c = (Class<StructureAlignment>) Class.forName(algo.getClass().getName());
 					return c.newInstance();
-				} catch (Exception e){
+				} catch (ClassNotFoundException e){
+					logger.error("Exception: ", e);
+					return null;
+				} catch (IllegalAccessException e){
+					logger.error("Exception: ", e);
+					return null;
+				} catch (InstantiationException e){
 					logger.error("Exception: ", e);
 					return null;
 				}
+
+
 			}
 		}
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CECalculator.java
@@ -26,7 +26,12 @@
 
 import org.biojava.nbio.alignment.aaindex.ScaledSubstitutionMatrix;
 import org.biojava.nbio.alignment.template.SubstitutionMatrix;
-import org.biojava.nbio.structure.*;
+import org.biojava.nbio.structure.Atom;
+import org.biojava.nbio.structure.Calc;
+import org.biojava.nbio.structure.Group;
+import org.biojava.nbio.structure.SVDSuperimposer;
+import org.biojava.nbio.structure.StructureException;
+import org.biojava.nbio.structure.StructureTools;
 import org.biojava.nbio.structure.align.model.AFP;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AFPAlignmentDisplay;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeMain.java
@@ -114,12 +114,12 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object param) throws StructureExce
 		afpChain.setVersion(version);
 		
 		// Try to guess names
-		try {
+
+		if (ca1.length!=0 && ca1[0].getGroup().getChain()!=null && ca1[0].getGroup().getChain().getParent()!=null)
 			afpChain.setName1(ca1[0].getGroup().getChain().getParent().getName());
-		} catch( Exception e) {}
-		try {
+
+		if (ca2.length!=0 && ca2[0].getGroup().getChain()!=null && ca2[0].getGroup().getChain().getParent()!=null)
 			afpChain.setName2(ca2[0].getGroup().getChain().getParent().getName());
-		} catch( Exception e) {}
 		
 		if ( afpChain.getNrEQR() == 0)
 		   return afpChain;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/OptimalCECPMain.java
@@ -53,7 +53,7 @@
  *
  */
 public class OptimalCECPMain extends CeMain {
-	private static boolean debug = true;
+	private static final boolean debug = true;
 
 
 	public static final String algorithmName = "jCE Optimal Circular Permutation";
@@ -507,11 +507,11 @@ public AFPChain alignOptimal(Atom[] ca1, Atom[] ca2, Object param, AFPChain[] al
 			if(debug) System.out.print(".");
 			
 			// fix up names, since cloning ca2 wipes it
-			try {
+			
+			if (ca2.length!=0 && ca2[0].getGroup().getChain()!=null && ca2[0].getGroup().getChain().getParent()!=null) {
 				currentAlignment.setName2(ca2[0].getGroup().getChain().getParent().getName()+" CP="+cp);
-			} catch( Exception e) {
-				//null pointers, empty arrays, etc.
 			}
+			
 			double currentScore = currentAlignment.getAlignScore();
 			
 			if(alignments != null) {
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDNAAlignment.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestDNAAlignment.java
@@ -24,7 +24,10 @@
 
 package org.biojava.nbio.structure;
 
+import java.io.IOException;
+
 import junit.framework.TestCase;
+
 import org.biojava.nbio.structure.align.ce.CeMain;
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.util.AtomCache;
@@ -37,7 +40,7 @@
 public class TestDNAAlignment extends TestCase
 {
 
-   public void test1(){
+   public void test1() throws IOException {
       String name1="1l3s.A";
       String name2="1t7p.P";
 
@@ -53,7 +56,7 @@ public void test1(){
         
         assertNotNull(txt);
         
-      } catch (Exception e){
+      } catch (StructureException e){
          e.printStackTrace();
          fail(e.getMessage());
       }
