testing graph attributes

src/main/java/BiGpairSEQ.java

@@ -14,8 +14,8 @@ public class BiGpairSEQ {
     private static boolean cachePlate = false;
     private static boolean cacheGraph = false;
     private static HeapType priorityQueueHeapType = HeapType.FIBONACCI;
-    private static boolean outputBinary = false;
+    private static boolean outputBinary = true;
-    private static boolean outputGraphML = true;
+    private static boolean outputGraphML = false;
 
     public static void main(String[] args) {
         if (args.length == 0) {

src/main/java/GraphMLFileReader.java

@@ -6,11 +6,14 @@ import java.io.BufferedReader;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.HashMap;
+import java.util.Map;
 
 public class GraphMLFileReader {
 
-    private String filename;
+    private final String filename;
-    private SimpleWeightedGraph graph;
+    private final SimpleWeightedGraph graph;
+    private final Map<String, String> graphAttributes = new HashMap<>();
 
     public GraphMLFileReader(String filename, SimpleWeightedGraph graph) {
         if(!filename.matches(".*\\.graphml")){
@@ -23,6 +26,9 @@ public class GraphMLFileReader {
             BufferedReader reader = Files.newBufferedReader(Path.of(filename));
         ){
             GraphMLImporter<Vertex, DefaultWeightedEdge> importer = new GraphMLImporter<>();
+            importer.addGraphAttributeConsumer((str, attribute) -> {
+                graphAttributes.put(str, attribute.getValue());
+            });
             importer.addVertexWithAttributesConsumer((vertex, attributes) -> {
                 vertex.setType(attributes.get("type").getValue());
                 vertex.setSequence(attributes.get("sequence").getValue());
@@ -38,4 +44,8 @@ public class GraphMLFileReader {
 
     public SimpleWeightedGraph getGraph() { return graph; }
 
+    public Map<String, String> getGraphAttributes() { return graphAttributes; }
+
+    public String getFilename() {return filename;}
+
 }

src/main/java/GraphMLFileWriter.java

@@ -5,6 +5,7 @@ import org.jgrapht.nio.AttributeType;
 import org.jgrapht.nio.DefaultAttribute;
 import org.jgrapht.nio.graphml.GraphMLExporter;
 import org.jgrapht.nio.graphml.GraphMLExporter.AttributeCategory;
+import org.w3c.dom.Attr;
 
 import java.io.BufferedWriter;
 import java.io.IOException;
@@ -19,7 +20,7 @@ public class GraphMLFileWriter {
     String filename;
     SimpleWeightedGraph graph;
     GraphWithMapData data;
-    Map<String, Attribute> graphAttributes = new HashMap<>();
+    Map<String, Attribute> graphAttributes;
 
     public GraphMLFileWriter(String filename, GraphWithMapData data) {
         if(!filename.matches(".*\\.graphml")){
@@ -28,7 +29,7 @@ public class GraphMLFileWriter {
         this.filename = filename;
         this.data = data;
         this.graph = data.getGraph();
-        createGraphAttributes();
+        graphAttributes = createGraphAttributes();
     }
 
     public GraphMLFileWriter(String filename, SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph) {
@@ -39,11 +40,12 @@ public class GraphMLFileWriter {
         this.graph = graph;
     }
 
-    private void createGraphAttributes(){
+    private Map<String, Attribute> createGraphAttributes(){
+        Map<String, Attribute> ga = new HashMap<>();
         //Sample plate filename
-        graphAttributes.put("sample plate filename", DefaultAttribute.createAttribute(data.getSourceFilename()));
+        ga.put("sample plate filename", DefaultAttribute.createAttribute(data.getSourceFilename()));
         // Number of wells
-        graphAttributes.put("well count", DefaultAttribute.createAttribute(data.getNumWells().toString()));
+        ga.put("well count", DefaultAttribute.createAttribute(data.getNumWells().toString()));
         //Well populations
         Integer[] wellPopulations = data.getWellPopulations();
         StringBuilder populationsStringBuilder = new StringBuilder();
@@ -53,7 +55,8 @@ public class GraphMLFileWriter {
             populationsStringBuilder.append(wellPopulations[i].toString());
         }
         String wellPopulationsString = populationsStringBuilder.toString();
-        graphAttributes.put("well populations", DefaultAttribute.createAttribute(wellPopulationsString));
+        ga.put("well populations", DefaultAttribute.createAttribute(wellPopulationsString));
+        return ga;
     }
 
     public void writeGraphToFile() {
@@ -74,6 +77,9 @@ public class GraphMLFileWriter {
                 return attributes;
             });
             //register the attributes
+            for(String s : graphAttributes.keySet()) {
+                exporter.registerAttribute(s, AttributeCategory.GRAPH, AttributeType.STRING);
+            }
             exporter.registerAttribute("type", AttributeCategory.NODE, AttributeType.STRING);
             exporter.registerAttribute("sequence", AttributeCategory.NODE, AttributeType.STRING);
             exporter.registerAttribute("occupancy", AttributeCategory.NODE, AttributeType.STRING);

src/main/java/InteractiveInterface.java

@@ -315,7 +315,7 @@ public class InteractiveInterface {
                 System.out.println("Serialized binary graph/data file written to: " + filename);
             }
             if(BiGpairSEQ.outputGraphML()) {
-                GraphMLFileWriter graphMLWriter = new GraphMLFileWriter(filename, data.getGraph());
+                GraphMLFileWriter graphMLWriter = new GraphMLFileWriter(filename, data);
                 graphMLWriter.writeGraphToFile();
                 System.out.println("GraphML file written to: " + filename);
             }