76 lines
2.5 KiB
Java
76 lines
2.5 KiB
Java
import org.apache.commons.csv.CSVFormat;
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import org.apache.commons.csv.CSVParser;
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import org.apache.commons.csv.CSVRecord;
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import java.io.BufferedReader;
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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.util.ArrayList;
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import java.util.List;
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public class CellFileReader {
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private String filename;
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private List<Integer[]> distinctCells = new ArrayList<>();
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private Integer cdr1Freq;
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public CellFileReader(String filename) {
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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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CSVFormat cellFileFormat = CSVFormat.Builder.create()
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.setHeader("Alpha CDR3", "Beta CDR3", "Alpha CDR1", "Beta CDR1")
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.setSkipHeaderRecord(true)
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.setCommentMarker('#')
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.build();
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try(//don't need to close reader bc of try-with-resources auto-closing
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BufferedReader reader = Files.newBufferedReader(Path.of(filename));
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CSVParser parser = new CSVParser(reader, cellFileFormat);
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){
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for(CSVRecord record: parser.getRecords()) {
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Integer[] cell = new Integer[4];
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cell[0] = Integer.valueOf(record.get("Alpha CDR3"));
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cell[1] = Integer.valueOf(record.get("Beta CDR3"));
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cell[2] = Integer.valueOf(record.get("Alpha CDR1"));
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cell[3] = Integer.valueOf(record.get("Beta CDR1"));
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distinctCells.add(cell);
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}
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} catch(IOException ex){
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System.out.println("cell file " + filename + " not found.");
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System.err.println(ex);
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}
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//get CDR1 frequency
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ArrayList<Integer> cdr1Alphas = new ArrayList<>();
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for (Integer[] cell : distinctCells) {
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cdr1Alphas.add(cell[3]);
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}
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double count = cdr1Alphas.stream().distinct().count();
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count = Math.ceil(distinctCells.size() / count);
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cdr1Freq = (int) count;
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}
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public CellSample getCellSample() {
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return new CellSample(distinctCells, cdr1Freq);
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}
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public String getFilename() { return filename;}
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//Refactor everything that uses this to have access to a Cell Sample and get the cells there instead.
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public List<Integer[]> getListOfDistinctCellsDEPRECATED(){
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return distinctCells;
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}
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public Integer getCellCountDEPRECATED() {
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//Refactor everything that uses this to have access to a Cell Sample and get the count there instead.
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return distinctCells.size();
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}
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}
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