Create Test templates for MultipleAlignment

Author: lafita

biojava-structure-gui/src/main/java/demo/DemoCEMC.java

@@ -38,7 +38,7 @@ public static void main(String[] args) throws IOException, StructureException, I
 		//Calcium Binding (MUSTA paper)
 		//List<String> names = Arrays.asList("4cpv", "2scp.A", "2sas", "1top", "1scm.B", "3icb");
 		//Serine Rich Proteins SERP (MUSTA paper)
-		List<String> names = Arrays.asList("7api.A", "8api.A", "1hle.A", "1ova.A", "2ach.A", "9api.A", "1psi", "1atu", "1kct", "1ath.A", "1att.A");
+		//List<String> names = Arrays.asList("7api.A", "8api.A", "1hle.A", "1ova.A", "2ach.A", "9api.A", "1psi", "1atu", "1kct", "1ath.A", "1att.A");
 		//Serine Proteases (MUSTA paper)
 		//List<String> names = Arrays.asList("1cse.E", "1sbn.E", "1pek.E", "3prk", "3tec.E");
 		//GPCRs
@@ -48,11 +48,13 @@ public static void main(String[] args) throws IOException, StructureException, I
 		//Globins (MAMMOTH and MUSTA papers)
 		//List<String> names = Arrays.asList("1mbc", "1hlb", "1thb.A", "1ith.A", "1idr.A", "1dlw", "1kr7.A", "1ew6.A", "1it2.A", "1eco", "3sdh.A", "1cg5.B", "1fhj.B", "1ird.A", "1mba", "2gdm", "1b0b", "1h97.A", "1ash.A", "1jl7.A");
 		//Rossman-Fold (POSA paper)
-		//List<String> names = Arrays.asList("d1heta2", "d1ek6a_", "d1obfo1", "2cmd", "d1np3a2", "d1bgva1", "d1id1a_", "d1id1a_", "d1oi7a1");
+		List<String> names = Arrays.asList("d1heta2", "d1ek6a_", "d1obfo1", "2cmd", "d1np3a2", "d1bgva1", "d1id1a_", "d1id1a_", "d1oi7a1");
 		//Circular Permutations (Bliven CECP paper) - dynamin GTP-ase with CP G-domain
 		//List<String> names = Arrays.asList("d1u0la2", "d1jwyb_");
 		//Circular Permutations: SAND and MFPT domains
 		//List<String> names = Arrays.asList("d2bjqa1", "d1h5pa_", "d1ufna_");  //"d1oqja"
+		//Flexible domain family of proteins (FatCat paper?)
+		
 		//Ankyrin Repeats
 		//List<String> names = Arrays.asList("d1n0ra_", "3ehq.A", "1awc.B");  //ankyrin
 

biojava-structure/src/main/java/org/biojava/nbio/structure/align/cemc/CeMcOptimizer.java

@@ -1,5 +1,6 @@
 package org.biojava.nbio.structure.align.cemc;
 
+import java.io.FileNotFoundException;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -36,10 +37,10 @@ public class CeMcOptimizer implements Callable<MultipleAlignment> {
 
 	private static final boolean debug = true;  //Prints the optimization moves and saves a file of the history
 	private Random rnd;
-	private MultipleSuperimposer imposer;;
+	private MultipleSuperimposer imposer;
 
 	//Optimization parameters
-	private static int Rmin = 2;   //Minimum number of aligned structures without a gap (33% of initial)
+	private int Rmin = 2;   //Minimum number of aligned structures without a gap (33% of initial)
 	private static final int Lmin = 15;   //Minimum alignment length of a Block
 	private static final int iterFactor = 100; //Factor to control the max number of iterations of optimization
 	private static final double C = 20; //Probability function constant (probability of acceptance for bad moves)
@@ -82,7 +83,10 @@ public CeMcOptimizer(MultipleAlignment seedAln, long randomSeed, int reference)
 	public MultipleAlignment call() throws Exception {
 		//The maximum number of iterations depends on the maximum possible alignment length and the number of structures
 		optimizeMC(iterFactor*Collections.min(structureLengths)*size);
-		if (debug) saveHistory("/scratch/cemc/CeMcOptimizationHistory.csv");
+		try {
+			if (debug) saveHistory("/scratch/cemc/CeMcOptimizationHistory.csv");
+		} catch(FileNotFoundException e) {}
+		
 		return msa;
 	}
 

biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentScorerTest.java

@@ -18,11 +18,12 @@
 import static org.junit.Assert.*;
 
 /**
- * Test the correctness of various Scores calculation for {@link MultipleAlignment}s.
+ * Test the correctness of various Score calculations for {@link MultipleAlignment}s.
  * <p>
  * Currently tested:
  * <ul><li>Reference-RMSD
  * <li>Reference-TMscore
+ * <li>CEMC-Score TODO
  * </ul>
  * 
  * @author Aleix Lafita

biojava-structure/src/test/java/org/biojava/nbio/structure/align/multiple/MultipleAlignmentWriterTest.java

@@ -0,0 +1,47 @@
+package org.biojava.nbio.structure.align.multiple;
+
+import java.util.List;
+
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.structure.Structure;
+import org.biojava.nbio.structure.align.util.AtomCache;
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+/**
+ * Test the correctness of various Text outputs for {@link MultipleAlignment}s.
+ * <p>
+ * Currently tested:
+ * <ul><li>FASTA
+ * <li>FatCat format
+ * <li>Aligned Pairs
+ * </ul>
+ * 
+ * @author Aleix Lafita
+ *
+ */
+public class MultipleAlignmentWriterTest {
+	
+	@Test
+	public void testFASTA(){
+		
+	}
+	
+	@Test
+	public void testFatCat(){
+		
+	}
+	
+	@Test
+	public void testAlignedPairs(){
+		
+	}
+	
+	private List<String> generateTestMSA(){
+		
+		//TODO load a file structure and generate a multiple alignment with multiple blocks
+	
+		return null;
+	}
+}