113 lines
4.0 KiB
Java
113 lines
4.0 KiB
Java
import org.apache.commons.csv.CSVFormat;
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import org.apache.commons.csv.CSVPrinter;
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import java.io.BufferedWriter;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.StandardOpenOption;
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import java.util.*;
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public class PlateFileWriter {
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private int size;
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private List<List<Integer[]>> wells;
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private double stdDev;
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private double lambda;
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private Double error;
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private String filename;
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private String sourceFileName;
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private String[] headers;
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private Integer[] concentrations;
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private boolean isExponential = false;
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public PlateFileWriter(String filename, Plate plate) {
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if(!filename.matches(".*\\.csv")){
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filename = filename + ".csv";
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}
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this.filename = filename;
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this.sourceFileName = plate.getSourceFileName();
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this.size = plate.getSize();
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this.isExponential = plate.isExponential();
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if(isExponential) {
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this.lambda = plate.getLambda();
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}
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else{
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this.stdDev = plate.getStdDev();
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}
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this.error = plate.getError();
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this.wells = plate.getWells();
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this.concentrations = plate.getPopulations();
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Arrays.sort(concentrations);
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}
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public void writePlateFile(){
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Comparator<List<Integer[]>> listLengthDescending = Comparator.comparingInt(List::size);
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wells.sort(listLengthDescending.reversed());
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int maxLength = wells.get(0).size();
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List<List<String>> wellsAsStrings = new ArrayList<>();
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for (List<Integer[]> w: wells){
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List<String> tmp = new ArrayList<>();
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for(Integer[] c: w) {
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tmp.add(Arrays.toString(c));
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}
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wellsAsStrings.add(tmp);
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}
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for(List<String> w: wellsAsStrings){
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while(w.size() < maxLength){
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w.add("");
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}
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}
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//this took forever and I don't use it
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List<List<String>> rows = new ArrayList<>();
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List<String> tmp = new ArrayList<>();
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for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
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tmp.add("well " + (i+1));
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}
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rows.add(tmp);
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for(int row = 0; row < maxLength; row++){
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tmp = new ArrayList<>();
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for(List<String> c: wellsAsStrings){
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tmp.add(c.get(row));
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}
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rows.add(tmp);
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}
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//get list of well populations
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List<Integer> wellPopulations = Arrays.asList(concentrations);
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//make string out of populations list
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StringBuilder populationsStringBuilder = new StringBuilder();
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populationsStringBuilder.append(wellPopulations.remove(0).toString());
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for(Integer i: wellPopulations){
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populationsStringBuilder.append(", ");
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populationsStringBuilder.append(i.toString());
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}
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String wellPopulationsString = populationsStringBuilder.toString();
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//set CSV format
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CSVFormat plateFileFormat = CSVFormat.Builder.create()
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.setCommentMarker('#')
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.build();
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try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
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CSVPrinter printer = new CSVPrinter(writer, plateFileFormat);
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){
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printer.printComment("Cell source file name: " + sourceFileName);
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printer.printComment("Each row represents one well on the plate.");
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printer.printComment("Plate size: " + size);
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printer.printComment("Error rate: " + error);
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printer.printComment("Well populations: " + wellPopulationsString);
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if(isExponential){
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printer.printComment("Lambda: " + lambda);
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}
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else {
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printer.printComment("Std. dev.: " + stdDev);
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}
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printer.printRecords(wellsAsStrings);
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} catch(IOException ex){
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System.out.println("Could not make new file named "+filename);
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System.err.println(ex);
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}
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}
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}
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