rewrite GraphML importer/exporter

src/main/java/GraphMLFileReader.java

@@ -1,3 +1,4 @@
+import org.jgrapht.graph.DefaultWeightedEdge;
 import org.jgrapht.graph.SimpleWeightedGraph;
 import org.jgrapht.nio.graphml.GraphMLImporter;
 
@@ -21,7 +22,12 @@ public class GraphMLFileReader {
         try(//don't need to close reader bc of try-with-resources auto-closing
             BufferedReader reader = Files.newBufferedReader(Path.of(filename));
         ){
-            GraphMLImporter<SimpleWeightedGraph, BufferedReader> importer = new GraphMLImporter<>();
+            GraphMLImporter<Vertex, DefaultWeightedEdge> importer = new GraphMLImporter<>();
+            importer.addVertexWithAttributesConsumer((vertex, attributes) -> {
+                vertex.setType(attributes.get("type").getValue());
+                vertex.setSequence(attributes.get("sequence").getValue());
+                vertex.setOccupancy((attributes.get("occupancy").getValue()));
+            });
             importer.importGraph(graph, reader);
         }
         catch (IOException ex) {

src/main/java/GraphMLFileWriter.java

@@ -1,12 +1,18 @@
+import org.jgrapht.graph.DefaultWeightedEdge;
 import org.jgrapht.graph.SimpleWeightedGraph;
-import org.jgrapht.nio.dot.DOTExporter;
+import org.jgrapht.nio.Attribute;
+import org.jgrapht.nio.AttributeType;
+import org.jgrapht.nio.DefaultAttribute;
 import org.jgrapht.nio.graphml.GraphMLExporter;
+import org.jgrapht.nio.graphml.GraphMLExporter.AttributeCategory;
 
 import java.io.BufferedWriter;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
+import java.util.HashMap;
+import java.util.Map;
 
 public class GraphMLFileWriter {
 
@@ -14,7 +20,7 @@ public class GraphMLFileWriter {
     SimpleWeightedGraph graph;
 
 
-    public GraphMLFileWriter(String filename, SimpleWeightedGraph graph) {
+    public GraphMLFileWriter(String filename, SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph) {
         if(!filename.matches(".*\\.graphml")){
             filename = filename + ".graphml";
         }
@@ -25,7 +31,23 @@ public class GraphMLFileWriter {
     public void writeGraphToFile() {
         try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
         ){
-            GraphMLExporter<SimpleWeightedGraph, BufferedWriter> exporter = new GraphMLExporter<>();
+            //create exporter. Let the vertex labels be the unique ids for the vertices
+            GraphMLExporter<Vertex, SimpleWeightedGraph<Vertex, DefaultWeightedEdge>> exporter = new GraphMLExporter<>(Vertex::getVertexLabel);
+            //set to export weights
+            exporter.setExportEdgeWeights(true);
+            //set type, sequnce, and occupancy attributes for each vertex
+            exporter.setVertexAttributeProvider( v -> {
+                Map<String, Attribute> attributes = new HashMap<>();
+                attributes.put("type", DefaultAttribute.createAttribute(v.getType()));
+                attributes.put("sequence", DefaultAttribute.createAttribute(v.getSequence()));
+                attributes.put("occupancy", DefaultAttribute.createAttribute(v.getOccupancy()));
+                return attributes;
+            });
+            //register the attributes
+            exporter.registerAttribute("type", AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("sequence", AttributeCategory.NODE, AttributeType.STRING);
+            exporter.registerAttribute("occupancy", AttributeCategory.NODE, AttributeType.STRING);
+            //export the graph
             exporter.exportGraph(graph, writer);
         } catch(IOException ex){
             System.out.println("Could not make new file named "+filename);

src/main/java/Vertex.java

@@ -1,10 +1,14 @@
 
 
 public class Vertex {
-    private final SequenceType type;
-    private final Integer vertexLabel;
-    private final Integer sequence;
-    private final Integer occupancy;
+    private  SequenceType type;
+    private  Integer vertexLabel;
+    private  Integer sequence;
+    private  Integer occupancy;
+
+    public Vertex(String vertexLabel) {
+        this.vertexLabel = Integer.parseInt((vertexLabel));
+    }
 
     public Vertex(SequenceType type, Integer sequence, Integer occupancy, Integer vertexLabel) {
         this.type = type;
@@ -13,15 +17,73 @@ public class Vertex {
         this.occupancy = occupancy;
     }
 
-    public SequenceType getType() { return type; }
 
-    public Integer getVertexLabel() { return vertexLabel; }
-
-    public Integer getSequence() {
-        return sequence;
+    public String getType() {
+        return type.name();
     }
 
-    public Integer getOccupancy() {
-        return occupancy;
+    public void setType(String type) {
+        this.type = SequenceType.valueOf(type);
     }
+
+    public String getVertexLabel() {
+        return vertexLabel.toString();
+    }
+
+    public void setVertexLabel(String label) {
+        this.vertexLabel = Integer.parseInt(label);
+    }
+
+    public String getSequence() {
+
+        return sequence.toString();
+    }
+
+    public void setSequence(String sequence) {
+        this.sequence = Integer.parseInt(sequence);
+    }
+
+    public String getOccupancy() {
+        return occupancy.toString();
+    }
+
+    public void setOccupancy(String occupancy) {
+        this.occupancy = Integer.parseInt(occupancy);
+    }
+
+    @Override //adapted from JGraphT example code
+    public int hashCode()
+    {
+        return (sequence == null) ? 0 : sequence.hashCode();
+    }
+
+    @Override //adapted from JGraphT example code
+    public boolean equals(Object obj)
+    {
+        if (this == obj)
+            return true;
+        if (obj == null)
+            return false;
+        if (getClass() != obj.getClass())
+            return false;
+        Vertex other = (Vertex) obj;
+        if (sequence == null) {
+            return other.sequence == null;
+        } else {
+            return sequence.equals(other.sequence);
+        }
+    }
+
+
+    @Override //adapted from JGraphT example code
+    public String toString()
+    {
+        StringBuilder sb = new StringBuilder();
+        sb.append("(").append(vertexLabel)
+                .append(", Type: ").append(type.name())
+                .append(", Sequence: ").append(sequence)
+                .append(", Occupancy: ").append(occupancy).append(")");
+        return sb.toString();
+    }
+
 }