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Implemented storing graphs in memory for multiple pairing experiments

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efischer
2022-02-22 21:30:00 -06:00
parent fd2ec76b71
commit 68ee9e4bb6
6 changed files with 208 additions and 99 deletions
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31
src/main/java/InteractiveInterface.java
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@@ -243,7 +243,7 @@ public class InteractiveInterface {
//Simulate matching and output CSV file of results
private static void matchCDR3s() throws IOException {
String filename = null;
String dataFilename = null;
String graphFilename = null;
Integer lowThreshold = 0;
Integer highThreshold = Integer.MAX_VALUE;
Integer maxOccupancyDiff = Integer.MAX_VALUE;
@@ -251,7 +251,7 @@ public class InteractiveInterface {
try {
System.out.println("\nBiGpairSEQ simulation requires an occupancy data and overlap graph file");
System.out.println("Please enter name of an existing graph and occupancy data file: ");
dataFilename = sc.next();
graphFilename = sc.next();
System.out.println("The matching results will be written to a file.");
System.out.print("Please enter a name for the output file: ");
filename = sc.next();
@@ -274,16 +274,25 @@ public class InteractiveInterface {
System.out.println(ex);
sc.next();
}
//read object data from file
System.out.println("Reading graph data from file. This may take some time");
System.out.println("File I/O time is not included in results");
assert dataFilename != null;
GraphDataObjectReader dataReader = new GraphDataObjectReader(dataFilename);
GraphWithMapData data = dataReader.getData();
//set source file name
data.setSourceFilename(dataFilename);
assert graphFilename != null;
//check if this is the same graph we already have in memory.
GraphWithMapData data;
if(!(graphFilename.equals(BiGpairSEQ.getGraphFilename()) || BiGpairSEQ.getGraph() == null)) {
BiGpairSEQ.clearGraph();
//read object data from file
System.out.println("Reading graph data from file. This may take some time");
System.out.println("File I/O time is not included in results");
GraphDataObjectReader dataReader = new GraphDataObjectReader(graphFilename);
data = dataReader.getData();
//set new graph in memory and new filename
BiGpairSEQ.setGraph(data);
BiGpairSEQ.setGraphFilename(graphFilename);
}
else {
data = BiGpairSEQ.getGraph();
}
//simulate matching
MatchingResult results = Simulator.matchCDR3s(data, dataFilename, lowThreshold, highThreshold, maxOccupancyDiff,
MatchingResult results = Simulator.matchCDR3s(data, graphFilename, lowThreshold, highThreshold, maxOccupancyDiff,
minOverlapPercent, true);
//write results to file
assert filename != null;