Refactor cdr3 matching to use new Vertex class

src/main/java/Vertex.java

@@ -6,6 +6,9 @@ public class Vertex implements Serializable {
     private  Integer sequence;
     private  Integer occupancy;
 
+    public Vertex(Integer vertexLabel) {
+        this.vertexLabel = vertexLabel;
+    }
     public Vertex(String vertexLabel) {
         this.vertexLabel = Integer.parseInt((vertexLabel));
     }
@@ -18,33 +21,33 @@ public class Vertex implements Serializable {
     }
 
 
-    public String getType() {
-        return type.name();
+    public SequenceType getType() {
+        return type;
     }
 
     public void setType(String type) {
         this.type = SequenceType.valueOf(type);
     }
 
-    public String getVertexLabel() {
-        return vertexLabel.toString();
+    public Integer getVertexLabel() {
+        return vertexLabel;
     }
 
     public void setVertexLabel(String label) {
         this.vertexLabel = Integer.parseInt(label);
     }
 
-    public String getSequence() {
+    public Integer getSequence() {
 
-        return sequence.toString();
+        return sequence;
     }
 
     public void setSequence(String sequence) {
         this.sequence = Integer.parseInt(sequence);
     }
 
-    public String getOccupancy() {
-        return occupancy.toString();
+    public Integer getOccupancy() {
+        return occupancy;
     }
 
     public void setOccupancy(String occupancy) {