Updates to make serializable for Spark

abradle · abradle · commit d85e3315df9d · 2016-03-07T09:59:23.000-08:00
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleGapPenalty.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/SimpleGapPenalty.java
@@ -23,16 +23,22 @@
 
 package org.biojava.nbio.alignment;
 
+import java.io.Serializable;
+
 import org.biojava.nbio.alignment.template.GapPenalty;
 
 /**
  * Implements a data structure for the gap penalties used during a sequence alignment routine.
  *
  * @author Mark Chapman
  */
-public class SimpleGapPenalty implements GapPenalty {
+public class SimpleGapPenalty implements GapPenalty, Serializable {
 
-    private static int dgop = 10, dgep = 1;
+    /**
+	 * 
+	 */
+	private static final long serialVersionUID = 3945671344135815456L;
+	private static int dgop = 10, dgep = 1;
 
     /**
      * Sets the default gap extension penalty.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixHelper.java
@@ -30,6 +30,7 @@
 import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
 
 import java.io.InputStreamReader;
+import java.io.Serializable;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -40,9 +41,14 @@
  * @author Mark Chapman
  * @author Paolo Pavan
  */
-public class SubstitutionMatrixHelper {
+public class SubstitutionMatrixHelper implements Serializable {
 
-    private static Map<String, SubstitutionMatrix<AminoAcidCompound>> aminoAcidMatrices =
+    /**
+	 * 
+	 */
+	private static final long serialVersionUID = 148491724604653225L;
+	
+	private static Map<String, SubstitutionMatrix<AminoAcidCompound>> aminoAcidMatrices =
             new HashMap<String, SubstitutionMatrix<AminoAcidCompound>>();
     private static Map<String, SubstitutionMatrix<NucleotideCompound>> nucleotideMatrices =
             new HashMap<String, SubstitutionMatrix<NucleotideCompound>>();
