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Clean up interactive text, bugfix

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efischer
2022-02-19 22:21:09 -06:00
parent 0026d8cdfe
commit 5b2ed165d0
3 changed files with 20 additions and 8 deletions
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16
src/main/java/UserInterface.java
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@@ -351,7 +351,7 @@ public class UserInterface {
// writer.writePlateFile();
// }
//method to output a CSV of sample plate
//Output a CSV of sample plate
private static void makePlate() {
String cellFile = null;
String filename = null;
@@ -454,6 +454,7 @@ public class UserInterface {
}
}
//Output serialized binary of GraphAndMapData object
private static void makeCDR3Graph() {
String filename = null;
String cellFile = null;
@@ -462,7 +463,7 @@ public class UserInterface {
Integer highThreshold = Integer.MAX_VALUE;
try {
String str = "\nGenerating bipartite weighted graph encoding occupancy data requires ";
str.concat("a cell sample file and a sample plate file.");
str = str.concat("a cell sample file and a sample plate file.");
System.out.println(str);
System.out.print("Please enter name of an existing cell sample file: ");
cellFile = sc.next();
@@ -500,10 +501,13 @@ public class UserInterface {
List<Integer[]> cells = cellReader.getCells();
GraphWithMapData data = Simulator.makeGraph(cells, plate, lowThreshold, highThreshold, true);
GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
System.out.println("Writing graph and occupancy data to file. This may take some time.");
System.out.println("Time to write file is not included in simulation time data.");
dataWriter.writeDataToFile();
}
}
//Simulate matching and output CSV file of results
private static void matchCDR3s() throws IOException {
String filename = null;
String dataFile = null;
@@ -516,6 +520,13 @@ public class UserInterface {
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();
System.out.println("What is the maximum difference in alpha/beta occupancy to attempt matching?");
maxOccupancyDiff = sc.nextInt();
System.out.println("What is the minimum overlap percentage to attempt matching? (0 - 100)");
minOverlapPercent = sc.nextInt();
if (minOverlapPercent < 0 || minOverlapPercent > 100) {
throw new InputMismatchException("Value outside range. Minimum percent set to 0");
}
} catch (InputMismatchException ex) {
System.out.println(ex);
sc.next();
@@ -529,6 +540,7 @@ public class UserInterface {
MatchingResult results = Simulator.matchCDR3s(data, maxOccupancyDiff, minOverlapPercent, true);
//write results to file
MatchingFileWriter writer = new MatchingFileWriter(filename, results);
System.out.println("Writing results to file");
writer.writeResultsToFile();
}