efischer/BiGpairSEQ
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Recording source file names in output files, allowing output of intermediate results

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efischer
2021-11-18 15:38:29 -06:00
parent 09aa5961f3
commit 2ab93dd4b7
8 changed files with 73 additions and 29 deletions
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40
src/main/java/UserInterface.java
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@@ -1,6 +1,8 @@
import java.util.List;
import java.util.Scanner;
import java.util.InputMismatchException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
//
public class UserInterface {
@@ -142,7 +144,7 @@ public class UserInterface {
stdDev = Math.sqrt(cellReader.getCellCount()); //gaussian with square root of elements approximates poisson
}
Plate samplePlate = new Plate(numWells, dropOutRate, concentrations, stdDev);
samplePlate.fillWells(cellReader.getCells());
samplePlate.fillWells(cellReader.getFilename(), cellReader.getCells());
PlateFileWriter writer = new PlateFileWriter(filename, samplePlate);
writer.writePlateFile();
}
@@ -175,7 +177,7 @@ public class UserInterface {
}
CellFileReader cellReader = new CellFileReader(cellFile);
PlateFileReader plateReader = new PlateFileReader(plateFile);
Plate plate = new Plate(plateReader.getWells());
Plate plate = new Plate(plateReader.getFilename(), plateReader.getWells());
if (cellReader.getCells().size() == 0){
System.out.println("No cell sample found.");
System.out.println("Returning to main menu.");
@@ -192,8 +194,7 @@ public class UserInterface {
List<Integer[]> cells = cellReader.getCells();
MatchingResult results = Simulator.matchCDR3s(cells, plate, lowThreshold, highThreshold);
//result writer
MatchingFileWriter writer = new MatchingFileWriter(filename, results.getComments(),
results.getHeaders(), results.getAllResults());
MatchingFileWriter writer = new MatchingFileWriter(filename, results);
writer.writeResultsToFile();
}
}
@@ -205,12 +206,14 @@ public class UserInterface {
match
*/
String filename = null;
String preliminaryResultsFilename = null;
String cellFile = null;
String plateFile = null;
Integer lowThresholdCDR3 = 0;
Integer highThresholdCDR3 = Integer.MAX_VALUE;
Integer lowThresholdCDR1 = 0;
Integer highThresholdCDR1 = Integer.MAX_VALUE;
boolean outputCDR3Matches = false;
try {
System.out.println("\nSimulated experiment requires a cell sample file and a sample plate file.");
System.out.print("Please enter name of an existing cell sample file: ");
@@ -234,13 +237,28 @@ public class UserInterface {
}
System.out.println("What is the maximum number of CDR3/CDR1 overlap wells to attempt matching?");
highThresholdCDR1 = sc.nextInt();
System.out.println("Matching CDR3s to CDR1s requires first matching CDR3 alpha/betas.");
System.out.println("Output a file for CDR3 alpha/beta match results as well?");
System.out.print("Please enter y/n: ");
String ans = sc.next();
Pattern pattern = Pattern.compile("(?:yes|y)", Pattern.CASE_INSENSITIVE);
Matcher matcher = pattern.matcher(ans);
if(matcher.matches()){
outputCDR3Matches = true;
System.out.println("Please enter filename for CDR3 alpha/beta match results");
preliminaryResultsFilename = sc.next();
System.out.println("CDR3 alpha/beta matches will be output to file");
}
else{
System.out.println("CDR3 alpha/beta matches will not be output to file");
}
} catch (InputMismatchException ex) {
System.out.println(ex);
sc.next();
}
CellFileReader cellReader = new CellFileReader(cellFile);
PlateFileReader plateReader = new PlateFileReader(plateFile);
Plate plate = new Plate(plateReader.getWells());
Plate plate = new Plate(plateReader.getFilename(), plateReader.getWells());
if (cellReader.getCells().size() == 0){
System.out.println("No cell sample found.");
System.out.println("Returning to main menu.");
@@ -261,14 +279,14 @@ public class UserInterface {
MatchingResult preliminaryResults = Simulator.matchCDR3s(cells, plate, lowThresholdCDR3, highThresholdCDR3);
MatchingResult[] results = Simulator.matchCDR1s(cells, plate, lowThresholdCDR1,
highThresholdCDR1, preliminaryResults);
//result writer
MatchingFileWriter writer = new MatchingFileWriter(filename + "First", results[0].getComments(),
results[0].getHeaders(), results[0].getAllResults());
MatchingFileWriter writer = new MatchingFileWriter(filename + "_FirstPass", results[0]);
writer.writeResultsToFile();
writer = new MatchingFileWriter(filename + "Dual", results[1].getComments(),
results[1].getHeaders(), results[1].getAllResults());
writer = new MatchingFileWriter(filename + "_SecondPass", results[1]);
writer.writeResultsToFile();
if(outputCDR3Matches){
writer = new MatchingFileWriter(preliminaryResultsFilename, preliminaryResults);
writer.writeResultsToFile();
}
}
}