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Fix GraphML writer

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efischer
2022-02-26 10:36:00 -06:00
parent e4d094d796
commit 9fcc20343d
2 changed files with 54 additions and 5 deletions
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57
src/main/java/GraphMLFileWriter.java
View File

@@ -1,4 +1,8 @@
import org.jgrapht.graph.DefaultWeightedEdge;
import org.jgrapht.graph.SimpleWeightedGraph; 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.dot.DOTExporter;
import org.jgrapht.nio.graphml.GraphMLExporter; import org.jgrapht.nio.graphml.GraphMLExporter;
@@ -7,25 +11,69 @@ import java.io.IOException;
import java.nio.file.Files; import java.nio.file.Files;
import java.nio.file.Path; import java.nio.file.Path;
import java.nio.file.StandardOpenOption; import java.nio.file.StandardOpenOption;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;
public class GraphMLFileWriter { public class GraphMLFileWriter {
String filename; String filename;
SimpleWeightedGraph graph; GraphWithMapData data;
public GraphMLFileWriter(String filename, SimpleWeightedGraph graph) { public GraphMLFileWriter(String filename, GraphWithMapData data) {
if(!filename.matches(".*\\.graphml")){ if(!filename.matches(".*\\.graphml")){
filename = filename + ".graphml"; filename = filename + ".graphml";
} }
this.filename = filename; this.filename = filename;
this.graph = graph; this.data = data;
} }
// public void writeGraphToFile() {
// try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
// ){
// GraphMLExporter<SimpleWeightedGraph, BufferedWriter> exporter = new GraphMLExporter<>();
// exporter.exportGraph(graph, writer);
// } catch(IOException ex){
// System.out.println("Could not make new file named "+filename);
// System.err.println(ex);
// }
// }
public void writeGraphToFile() { 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); 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<Integer, SimpleWeightedGraph<Vertex, DefaultWeightedEdge>> exporter = new GraphMLExporter<>(v -> v.toString());
//set to export weights
exporter.setExportEdgeWeights(true);
//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("CDR3 Alpha"));
attributes.put("sequence", DefaultAttribute.createAttribute(vertexToAlphaMap.get(v)));
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);
exporter.registerAttribute("sequence", GraphMLExporter.AttributeCategory.NODE, AttributeType.STRING);
exporter.registerAttribute("occupancy", GraphMLExporter.AttributeCategory.NODE, AttributeType.STRING);
//export the graph
exporter.exportGraph(graph, writer); exporter.exportGraph(graph, writer);
} catch(IOException ex){ } catch(IOException ex){
System.out.println("Could not make new file named "+filename); System.out.println("Could not make new file named "+filename);
@@ -33,3 +81,4 @@ public class GraphMLFileWriter {
} }
} }
} }

2
src/main/java/InteractiveInterface.java
View File

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