Some exception handling fixes (biojava#111)

josemduarte · josemduarte · commit 4e271f5eb552 · 2015-02-20T10:53:02.000+01:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -76,8 +76,10 @@ public class StructureTools {
 	 */
 	public static final String CB_ATOM_NAME = "CB";
 
-
-	public static final Character UNKNOWN_GROUP_LABEL = new Character('x');
+	/**
+	 * The character to use for unknown compounds in sequence strings
+	 */
+	public static final char UNKNOWN_GROUP_LABEL = 'X';
 
 	/**
 	 * Below this ratio of aminoacid/nucleotide residues to the sequence total,
@@ -665,8 +667,9 @@ public static final Character convert_3code_1code(String code3)
 	}
 
 	/** 
-	 * Convert a three letter code into single character.
-	 * catches for unusual characters
+	 * Convert a three letter aminoacid code into a single character code.
+	 * If the code corresponds to a nucleotide null is returned, in all other cases 
+	 * {@value #UNKNOWN_GROUP_LABEL} is returned
 	 *
 	 * @param groupCode3 three letter representation
 	 * @return null if group is a nucleotide code
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/BioJavaStructureAlignment.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/BioJavaStructureAlignment.java
@@ -199,11 +199,11 @@ private void copyResults(AFPChain afpChain, AlternativeAlignment altAlig, Atom[]
 	}
 	
 	private static char getOneLetter(Group g){
-        try {
-	        return StructureTools.get1LetterCode(g.getPDBName());
-        } catch (Exception e) {
-           return 'X';
-        }
-     }
+
+		if (g==null) return StructureTools.UNKNOWN_GROUP_LABEL;
+		
+		return StructureTools.get1LetterCode(g.getPDBName());
+
+	}
 
 }
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
@@ -1320,12 +1320,9 @@ private void checkPrintRmsdNew(int traceMaxSize, int winSize, Atom[] ca1, Atom[]
 
 	private static char getOneLetter(Group g){
 
-		try {
-			Character c = StructureTools.get1LetterCode(g.getPDBName());
-			return c;
-		} catch (Exception e){
-			return 'X';
-		}
+		if (g==null) return StructureTools.UNKNOWN_GROUP_LABEL;
+		
+		return StructureTools.get1LetterCode(g.getPDBName());
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/CeCalculatorEnhanced.java
@@ -1324,12 +1324,9 @@ private void checkPrintRmsdNew(int traceMaxSize, int winSize, Atom[] ca1, Atom[]
 
 	private static char getOneLetter(Group g){
 
-		try {
-			Character c = StructureTools.get1LetterCode(g.getPDBName());
-			return c;
-		} catch (Exception e){
-			return 'X';
-		}
+		if (g==null) return StructureTools.UNKNOWN_GROUP_LABEL;
+		
+		return StructureTools.get1LetterCode(g.getPDBName());
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AfpChainWriter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/model/AfpChainWriter.java
@@ -1048,12 +1048,13 @@ private static CharSequence getPDBPos(Atom atom)
 
 	private static char getOneLetter(Group g){
 
-		try {
-			Character c = StructureTools.get1LetterCode(g.getPDBName());
-			return c;
-		} catch (Exception e){
-			return 'X';
-		}
+		
+		if (g==null) return StructureTools.UNKNOWN_GROUP_LABEL;
+		
+		
+		return StructureTools.get1LetterCode(g.getPDBName());
+		
+		
 	}
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/seq/SmithWaterman3Daligner.java
@@ -47,6 +47,8 @@
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
 import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
 import org.biojava.nbio.core.sequence.template.Compound;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 
 /** provides a 3D superimposition based on the sequence alignment
@@ -57,6 +59,8 @@
 public class SmithWaterman3Daligner extends AbstractStructureAlignment implements StructureAlignment {
 
 	public static final String algorithmName = "Smith-Waterman superposition";
+	
+	private static final Logger logger = LoggerFactory.getLogger(SmithWaterman3Daligner.class);
 
 	/**
 	 *  version history:
@@ -117,10 +121,12 @@ public AFPChain align(Atom[] ca1, Atom[] ca2, Object parameters)
 
 			SequencePair<ProteinSequence, AminoAcidCompound> pair = smithWaterman.getPair();
 
-			// Print the alignment to the screen
-			// System.out.println(aligner.getAlignmentString());
+			logger.debug("Smith-Waterman alignment is: "+pair.toString(100));
+			
 			// convert to a 3D alignment...
 			afpChain = convert(ca1,ca2,pair, smithWaterman);
+			
+
 
 		} catch (CompoundNotFoundException e){
 
@@ -291,11 +297,10 @@ private AFPChain convert(Atom[] ca1, Atom[] ca2,  SequencePair<ProteinSequence,
 
 	private static char getOneLetter(Group g){
 
-		try {
-			return StructureTools.get1LetterCode(g.getPDBName());
-		} catch (Exception e){
-			return 'X';
-		}
+		if (g==null) return StructureTools.UNKNOWN_GROUP_LABEL;
+		
+		return StructureTools.get1LetterCode(g.getPDBName());
+		
 	}
 
 	@Override
@@ -305,7 +310,6 @@ public String getAlgorithmName() {
 
 	@Override
 	public ConfigStrucAligParams getParameters() {
-		// TODO Auto-generated method stub
 		return params;
 	}
 
