efischer/BiGpairSEQ
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add graph attributes to graphml writer

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efischer
2022-02-26 08:15:48 -06:00
parent fb8d8d8785
commit b3dc10f287
1 changed files with 30 additions and 0 deletions
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30
src/main/java/GraphMLFileWriter.java
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@@ -18,7 +18,18 @@ public class GraphMLFileWriter {
String filename;
SimpleWeightedGraph graph;
GraphWithMapData data;
Map<String, Attribute> graphAttributes = new HashMap<>();
public GraphMLFileWriter(String filename, GraphWithMapData data) {
if(!filename.matches(".*\\.graphml")){
filename = filename + ".graphml";
}
this.filename = filename;
this.data = data;
this.graph = data.getGraph();
createGraphAttributes();
}
public GraphMLFileWriter(String filename, SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph) {
if(!filename.matches(".*\\.graphml")){
@@ -28,6 +39,23 @@ public class GraphMLFileWriter {
this.graph = graph;
}
private void createGraphAttributes(){
//Sample plate filename
graphAttributes.put("sample plate filename", DefaultAttribute.createAttribute(data.getSourceFilename()));
// Number of wells
graphAttributes.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();
graphAttributes.put("well populations", DefaultAttribute.createAttribute(wellPopulationsString));
}
public void writeGraphToFile() {
try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
){
@@ -35,6 +63,8 @@ public class GraphMLFileWriter {
GraphMLExporter<Vertex, SimpleWeightedGraph<Vertex, DefaultWeightedEdge>> exporter = new GraphMLExporter<>(Vertex::getVertexLabel);
//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<>();