All working, able to be built to .jar

2021-11-12 10:41:44 -06:00
parent d39fdbee3b
commit e15cbc6672
21 changed files with 1003 additions and 12 deletions
--- a/src/main/java/PlateFileWriter.java
+++ b/src/main/java/PlateFileWriter.java
@@ -0,0 +1,93 @@
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVPrinter;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
+import java.util.*;
+import java.util.regex.Pattern;
+
+public class PlateFileWriter {
+    private int size;
+    private List<List<Integer[]>> wells;
+    private double stdDev;
+    private Double error;
+    private String filename;
+    private String[] headers;
+    private List<Integer> concentrations;
+
+    public PlateFileWriter(String filename, Plate plate) {
+        if(!filename.matches(".*\\.csv")){
+            filename = filename + ".csv";
+        }
+        this.filename = filename;
+        this.size = plate.getSize();
+        this.stdDev = plate.getStdDev();
+        this.error = plate.getError();
+        this.wells = plate.getWells();
+        this.concentrations = Arrays.asList(plate.getConcentrations());
+        concentrations.sort(Comparator.reverseOrder());
+    }
+
+    public void writePlateFile(){
+        //works as is, but too many columns in csv, need to make them all rows.
+
+        //will now redo it so that every column is a well, with well names as headers
+        //need to give plate error, sample pop size, stdDev, num sections, concentration per section as comments
+        Comparator<List<Integer[]>> listLengthDescending = Comparator.comparingInt(List::size);
+        wells.sort(listLengthDescending.reversed());
+        int maxLength = wells.get(0).size();
+        List<List<String>> wellsAsStrings = new ArrayList<>();
+        for (List<Integer[]> w: wells){
+            List<String> tmp = new ArrayList<>();
+            for(Integer[] c: w) {
+                tmp.add(Arrays.toString(c));
+            }
+            wellsAsStrings.add(tmp);
+        }
+        for(List<String> w: wellsAsStrings){
+            while(w.size() < maxLength){
+                w.add("");
+            }
+        }
+
+        //this took forever
+        List<List<String>> rows = new ArrayList<>();
+        List<String> tmp = new ArrayList<>();
+        for(int i = 0; i < wellsAsStrings.size(); i++){//List<Integer[]> w: wells){
+            tmp.add("well " + (i+1));
+        }
+        rows.add(tmp);
+        for(int row = 0; row < maxLength; row++){
+            tmp = new ArrayList<>();
+            for(List<String> c: wellsAsStrings){
+                tmp.add(c.get(row));
+            }
+            rows.add(tmp);
+        }
+        StringBuilder concen = new StringBuilder();
+        for(Integer i: concentrations){
+            concen.append(i.toString());
+            concen.append(" ");
+        }
+        String concenString = concen.toString();
+
+        CSVFormat plateFileFormat = CSVFormat.Builder.create().setCommentMarker('#').build();
+
+        try(BufferedWriter writer = Files.newBufferedWriter(Path.of(filename), StandardOpenOption.CREATE_NEW);
+            CSVPrinter printer = new CSVPrinter(writer, plateFileFormat);
+        ){
+            printer.printComment("Each row represents one well on the plate.");
+            printer.printComment("Plate size: " + size);
+            printer.printComment("Error rate: " + error);
+            printer.printComment("Concentrations: " + concenString);
+            printer.printComment("Std. dev.: " + stdDev);
+            printer.printRecords(wellsAsStrings);
+        } catch(IOException ex){
+            System.out.println("Could not make new file named "+filename);
+            System.err.println(ex);
+        }
+    }
+}