Refactor Vertex class to use SequenceRecords

src/main/java/Simulator.java

@@ -105,8 +105,7 @@ public class Simulator implements GraphModificationFunctions {
         //the list of alpha vertices
         List<Vertex> alphaVertices = new ArrayList<>();
         for (String seq : plateAtoVMap.keySet()) {
-            Vertex alphaVertex = new Vertex(SequenceType.CDR3_ALPHA, seq, alphaSequences.get(seq).getOccupancy(),
+            Vertex alphaVertex = new Vertex(alphaSequences.get(seq), plateAtoVMap.get(seq));
-                    plateAtoVMap.get(seq), alphaSequences.get(seq).getReadCount());
             alphaVertices.add(alphaVertex);
         }
         //Sort to make sure the order of vertices in list matches the order of the adjacency matrix
@@ -116,8 +115,7 @@ public class Simulator implements GraphModificationFunctions {
         //the list of beta vertices
         List<Vertex> betaVertices = new ArrayList<>();
         for (String seq : plateBtoVMap.keySet()) {
-            Vertex betaVertex = new Vertex(SequenceType.CDR3_BETA, seq, betaSequences.get(seq).getOccupancy(),
+            Vertex betaVertex = new Vertex(betaSequences.get(seq), plateBtoVMap.get(seq));
-                    plateBtoVMap.get(seq), betaSequences.get(seq).getReadCount());
             betaVertices.add(betaVertex);
         }
         //Sort to make sure the order of vertices in list matches the order of the adjacency matrix

src/main/java/Vertex.java

@@ -1,76 +1,43 @@
 import org.jheaps.AddressableHeap;
 
 import java.io.Serializable;
+import java.util.Map;
 
 public class Vertex implements Serializable, Comparable<Vertex> {
-    private  SequenceType type;
+    private SequenceRecord record;
-    private  Integer vertexLabel;
+    private Integer vertexLabel;
-    private  String sequence;
+    private Double potential;
-    private  Integer occupancy;
-    private  Integer readCount;
-    private  Double potential;
     private AddressableHeap queue;
 
-    public Vertex(Integer vertexLabel) {
+    public Vertex(SequenceRecord record, Integer vertexLabel) {
+        this.record = record;
         this.vertexLabel = vertexLabel;
     }
-    public Vertex(String vertexLabel) {
-        this.vertexLabel = Integer.parseInt((vertexLabel));
-    }
 
-    public Vertex(SequenceType type, String sequence, Integer occupancy, Integer vertexLabel) {
+    public SequenceRecord getRecord() { return record; }
-        this.type = type;
-        this.vertexLabel = vertexLabel;
-        this.sequence = sequence;
-        this.occupancy = occupancy;
-        this.readCount = 1;
-    }
 
-    public Vertex(SequenceType type, String sequence, Integer occupancy, Integer vertexLabel, Integer readCount) {
+    public SequenceType getType() { return record.getSequenceType(); }
-        this.type = type;
-        this.vertexLabel = vertexLabel;
-        this.sequence = sequence;
-        this.occupancy = occupancy;
-        this.readCount = readCount;
-    }
-
-
-    public SequenceType getType() {
-        return type;
-    }
-
-    public void setType(String type) {
-        this.type = SequenceType.valueOf(type);
-    }
 
     public Integer getVertexLabel() {
         return vertexLabel;
     }
 
-    public void setVertexLabel(String label) {
-        this.vertexLabel = Integer.parseInt(label);
-    }
-
     public String getSequence() {
-        return sequence;
+        return record.getSequence();
-    }
-
-    public void setSequence(String sequence) {
-        this.sequence = sequence;
     }
 
     public Integer getOccupancy() {
-        return occupancy;
+        return record.getOccupancy();
     }
 
-    public void setOccupancy(String occupancy) {
+    public Integer getReadCount() { return record.getReadCount(); }
-        this.occupancy = Integer.parseInt(occupancy);
+
-    }
+    public Map<Integer, Integer> getWellOccupancies() { return record.getWellOccupancies(); }
 
     @Override //adapted from JGraphT example code
     public int hashCode()
     {
-        return (sequence == null) ? 0 : sequence.hashCode();
+        return (this.getSequence() == null) ? 0 : this.getSequence().hashCode();
     }
 
     @Override //adapted from JGraphT example code
@@ -83,22 +50,21 @@ public class Vertex implements Serializable, Comparable<Vertex> {
         if (getClass() != obj.getClass())
             return false;
         Vertex other = (Vertex) obj;
-        if (sequence == null) {
+        if (this.getSequence() == null) {
-            return other.sequence == null;
+            return other.getSequence() == null;
         } else {
-            return sequence.equals(other.sequence);
+            return this.getSequence().equals(other.getSequence());
         }
     }
 
-
     @Override //adapted from JGraphT example code
     public String toString()
     {
         StringBuilder sb = new StringBuilder();
         sb.append("(").append(vertexLabel)
-                .append(", Type: ").append(type.name())
+                .append(", Type: ").append(this.getType().name())
-                .append(", Sequence: ").append(sequence)
+                .append(", Sequence: ").append(this.getSequence())
-                .append(", Occupancy: ").append(occupancy).append(")");
+                .append(", Occupancy: ").append(this.getOccupancy()).append(")");
         return sb.toString();
     }
 
@@ -106,12 +72,4 @@ public class Vertex implements Serializable, Comparable<Vertex> {
     public int compareTo(Vertex other) {
         return this.vertexLabel - other.getVertexLabel();
     }
-
-    public Integer getReadCount() {
-        return readCount;
-    }
-
-    public void setReadCount(Integer readCount) {
-        this.readCount = readCount;
-    }
 }