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Adding GraphML output to options menu

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This commit is contained in:
efischer
2022-02-24 17:22:07 -06:00
parent f385ebc31f
commit e4d094d796
3 changed files with 27 additions and 8 deletions
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22
src/main/java/InteractiveInterface.java
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@@ -252,7 +252,6 @@ public class InteractiveInterface {
String filename = null;
String cellFile = null;
String plateFile = null;
try {
String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data ";
str = str.concat("\nrequires a cell sample file and a sample plate file.");
@@ -310,9 +309,16 @@ public class InteractiveInterface {
List<Integer[]> cells = cellSample.getCells();
GraphWithMapData data = Simulator.makeGraph(cells, plate, true);
assert filename != null;
GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
dataWriter.writeDataToFile();
System.out.println("Graph and Data file written to: " + filename);
if(BiGpairSEQ.outputBinary()) {
GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
dataWriter.writeDataToFile();
System.out.println("Serialized binary graph/data file written to: " + filename);
}
if(BiGpairSEQ.outputGraphML()) {
GraphMLFileWriter graphMLWriter = new GraphMLFileWriter(filename, data.getGraph());
graphMLWriter.writeGraphToFile();
System.out.println("GraphML file written to: " + filename);
}
if(BiGpairSEQ.cacheGraph()) {
BiGpairSEQ.setGraphInMemory(data, filename);
@@ -500,7 +506,9 @@ public class InteractiveInterface {
System.out.println("1) Turn " + getOnOff(!BiGpairSEQ.cacheCells()) + " cell sample file caching");
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) Maximum weight matching algorithm options");
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("6) Maximum weight matching algorithm options");
System.out.println("0) Return to main menu");
try {
input = sc.nextInt();
@@ -508,7 +516,9 @@ public class InteractiveInterface {
case 1 -> BiGpairSEQ.setCacheCells(!BiGpairSEQ.cacheCells());
case 2 -> BiGpairSEQ.setCachePlate(!BiGpairSEQ.cachePlate());
case 3 -> BiGpairSEQ.setCacheGraph(!BiGpairSEQ.cacheGraph());
case 4 -> algorithmOptions();
case 4 -> BiGpairSEQ.setOutputBinary(!BiGpairSEQ.outputBinary());
case 5 -> BiGpairSEQ.setOutputGraphML(!BiGpairSEQ.outputGraphML());
case 6 -> algorithmOptions();
case 0 -> backToMain = true;
default -> System.out.println("Invalid input");
}