Hand-merge of some things from Dev_Vertex branch that didn't make it in for some reason

readme.md

@@ -347,9 +347,9 @@ roughly as though it had a constant well population equal to the plate's average
   * ~~Apache Commons CSV library writes entries a row at a time~~ 
     * _Got this working, but at the cost of a profoundly strange bug in graph occupancy filtering. Have reverted the repo until I can figure out what caused that. Given how easily Thingiverse transposes CSV matrices in R, might not even be worth fixing.
 * ~~Enable GraphML output in addition to serialized object binaries, for data portability~~ DONE
-  * ~~Custom vertex type with attribute for sequence occupancy?~~ ABANDONED
+  * ~~Custom vertex type with attribute for sequence occupancy?~~ DONE
     * Advantage: would eliminate the need to use maps to associate vertices with sequences, which would make the code easier to understand.
-    * Have a branch where this is implemented, but there's a bug that broke matching. Don't currently have time to fix.
+    * ~~Have a branch where this is implemented, but there's a bug that broke matching. Don't currently have time to fix.~~
 * ~~Re-implement command line arguments, to enable scripting and statistical simulation studies~~ DONE
 * ~~Implement custom Vertex class to simplify code and make it easier to implement different MWM algorithms~~ DONE
   * This also seems to be faster when using the same algorithm than the version with lots of maps, which is a nice bonus!

src/main/java/BiGpairSEQ.java

@@ -16,7 +16,7 @@ public class BiGpairSEQ {
     private static HeapType priorityQueueHeapType = HeapType.FIBONACCI;
     private static boolean outputBinary = true;
     private static boolean outputGraphML = false;
-    private static final String version = "version 2.0";
+    private static final String version = "version 3.0";
 
     public static void main(String[] args) {
         if (args.length == 0) {

src/main/java/GraphMLFileWriter.java

@@ -3,8 +3,9 @@ import org.jgrapht.graph.SimpleWeightedGraph;
 import org.jgrapht.nio.Attribute;
 import org.jgrapht.nio.AttributeType;
 import org.jgrapht.nio.DefaultAttribute;
-import org.jgrapht.nio.dot.DOTExporter;
 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;
@@ -12,14 +13,14 @@ import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
 import java.util.HashMap;
-import java.util.LinkedHashMap;
 import java.util.Map;
 
 public class GraphMLFileWriter {
 
     String filename;
+    SimpleWeightedGraph graph;
     GraphWithMapData data;
-
+    Map<String, Attribute> graphAttributes;
 
     public GraphMLFileWriter(String filename, GraphWithMapData data) {
         if(!filename.matches(".*\\.graphml")){
@@ -27,52 +28,61 @@ public class GraphMLFileWriter {
         }
         this.filename = filename;
         this.data = data;
+        this.graph = data.getGraph();
+        graphAttributes = createGraphAttributes();
     }
 
-//    public void writeGraphToFile() {
+    public GraphMLFileWriter(String filename, SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph) {
-//        try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
+        if(!filename.matches(".*\\.graphml")){
-//        ){
+            filename = filename + ".graphml";
-//            GraphMLExporter<SimpleWeightedGraph, BufferedWriter> exporter = new GraphMLExporter<>();
+        }
-//            exporter.exportGraph(graph, writer);
+        this.filename = filename;
-//        } catch(IOException ex){
+        this.graph = graph;
-//            System.out.println("Could not make new file named "+filename);
+    }
-//            System.err.println(ex);
+
-//        }
+    private Map<String, Attribute> createGraphAttributes(){
-//    }
+        Map<String, Attribute> ga = new HashMap<>();
+        //Sample plate filename
+        ga.put("sample plate filename", DefaultAttribute.createAttribute(data.getSourceFilename()));
+        // Number of wells
+        ga.put("well count", DefaultAttribute.createAttribute(data.getNumWells().toString()));
+        //Well populations
+        Integer[] wellPopulations = data.getWellPopulations();
+        StringBuilder populationsStringBuilder = new StringBuilder();
+        populationsStringBuilder.append(wellPopulations[0].toString());
+        for(int i = 1; i < wellPopulations.length; i++){
+            populationsStringBuilder.append(", ");
+            populationsStringBuilder.append(wellPopulations[i].toString());
+        }
+        String wellPopulationsString = populationsStringBuilder.toString();
+        ga.put("well populations", DefaultAttribute.createAttribute(wellPopulationsString));
+        return ga;
+    }
 
     public void writeGraphToFile() {
-        SimpleWeightedGraph graph = data.getGraph();
-        Map<Integer, Integer> vertexToAlphaMap = data.getPlateVtoAMap();
-        Map<Integer, Integer> vertexToBetaMap = data.getPlateVtoBMap();
-        Map<Integer, Integer> alphaOccs = data.getAlphaWellCounts();
-        Map<Integer, Integer> betaOccs = data.getBetaWellCounts();
         try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
         ){
             //create exporter. Let the vertex labels be the unique ids for the vertices
-            GraphMLExporter<Integer, SimpleWeightedGraph<Vertex, DefaultWeightedEdge>> exporter = new GraphMLExporter<>(v -> v.toString());
+            GraphMLExporter<Vertex, SimpleWeightedGraph<Vertex, DefaultWeightedEdge>> exporter = new GraphMLExporter<>(v -> v.getVertexLabel().toString());
             //set to export weights
             exporter.setExportEdgeWeights(true);
+            //Set graph attributes
+            exporter.setGraphAttributeProvider( () -> graphAttributes);
             //set type, sequence, and occupancy attributes for each vertex
             exporter.setVertexAttributeProvider( v -> {
                 Map<String, Attribute> attributes = new HashMap<>();
-                if(vertexToAlphaMap.containsKey(v)) {
+                attributes.put("type", DefaultAttribute.createAttribute(v.getType().name()));
-                    attributes.put("type", DefaultAttribute.createAttribute("CDR3 Alpha"));
+                attributes.put("sequence", DefaultAttribute.createAttribute(v.getSequence()));
-                    attributes.put("sequence", DefaultAttribute.createAttribute(vertexToAlphaMap.get(v)));
+                attributes.put("occupancy", DefaultAttribute.createAttribute(v.getOccupancy()));
-                    attributes.put("occupancy", DefaultAttribute.createAttribute(
-                            alphaOccs.get(vertexToAlphaMap.get(v))));
-                }
-                else if(vertexToBetaMap.containsKey(v)) {
-                    attributes.put("type", DefaultAttribute.createAttribute("CDR3 Beta"));
-                    attributes.put("sequence", DefaultAttribute.createAttribute(vertexToBetaMap.get(v)));
-                    attributes.put("occupancy", DefaultAttribute.createAttribute(
-                            betaOccs.get(vertexToBetaMap.get(v))));
-                }
                 return attributes;
             });
             //register the attributes
-            exporter.registerAttribute("type", GraphMLExporter.AttributeCategory.NODE, AttributeType.STRING);
+            for(String s : graphAttributes.keySet()) {
-            exporter.registerAttribute("sequence", GraphMLExporter.AttributeCategory.NODE, AttributeType.STRING);
+                exporter.registerAttribute(s, AttributeCategory.GRAPH, AttributeType.STRING);
-            exporter.registerAttribute("occupancy", GraphMLExporter.AttributeCategory.NODE, AttributeType.STRING);
+            }
+            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){
@@ -81,4 +91,3 @@ public class GraphMLFileWriter {
         }
     }
 }
-

src/main/java/InteractiveInterface.java

@@ -258,7 +258,7 @@ public class InteractiveInterface {
             cellFile = sc.next();
             System.out.print("\nPlease enter name of an existing sample plate file: ");
             plateFile = sc.next();
-            System.out.println("\nThe graph and occupancy data will be written to a serialized binary file.");
+            System.out.println("\nThe graph and occupancy data will be written to a file.");
             System.out.print("Please enter a name for the output file: ");
             filename = sc.next();
         } catch (InputMismatchException ex) {
@@ -504,7 +504,7 @@ public class InteractiveInterface {
             System.out.println("2) Turn " + getOnOff(!BiGpairSEQ.cachePlate()) + " plate file caching");
             System.out.println("3) Turn " + getOnOff(!BiGpairSEQ.cacheGraph()) + " graph/data file caching");
             System.out.println("4) Turn " + getOnOff(!BiGpairSEQ.outputBinary()) + " serialized binary graph output");
-            System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output");
+            System.out.println("5) Turn " + getOnOff(!BiGpairSEQ.outputGraphML()) + " GraphML graph output (for data portability to other programs)");
             System.out.println("6) Maximum weight matching algorithm options");
             System.out.println("0) Return to main menu");
             try {

src/main/java/SequenceType.java

@@ -0,0 +1,8 @@
+//enum for tagging types of sequences
+//Listed in order that they appear in a cell array, so ordinal() method will return correct index
+public enum SequenceType {
+    CDR3_ALPHA,
+    CDR3_BETA,
+    CDR1_ALPHA,
+    CDR1_BETA
+}