coverageqc.data.DoNotCall.java Source code

Introduction

Here is the source code for coverageqc.data.DoNotCall.java

Source

/*
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package coverageqc.data;

import java.util.HashMap;
import java.util.Iterator;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlRootElement;
import org.apache.poi.ss.usermodel.Cell;
import org.apache.poi.ss.usermodel.Row;

/**
 *
 * @author Tom
 * DoNotCall is a like a subtype OF VARIANT ///in future should make it an offical subclass by using "extends" feature
 */
@XmlRootElement
public class DoNotCall {
    //key inheritance
    //public String hgvscComplete;
    @XmlAttribute
    public String ensp;
    @XmlAttribute
    public String hgvsc;
    // @XmlAttribute
    // public String hgvsp;
    @XmlAttribute
    public String callType;
    @XmlAttribute
    public String transcript;
    @XmlAttribute
    public Long coordinate;

    // @XmlAttribute
    public static DoNotCall populate(Row xslxHeadingRow, Row xslxDataRow, Integer calltype) {
        DoNotCall donotcall = new DoNotCall();
        int columnNumber;
        int cellIndex;
        String[] headerArray;
        HashMap<String, Integer> headings = new HashMap<String, Integer>();

        columnNumber = xslxHeadingRow.getLastCellNum();
        headerArray = new String[columnNumber];

        Iterator<Cell> cellIterator = xslxHeadingRow.cellIterator();
        while (cellIterator.hasNext()) {
            Cell cell = cellIterator.next();
            cellIndex = cell.getColumnIndex();
            switch (cell.getCellType()) {
            case Cell.CELL_TYPE_BOOLEAN:
                headerArray[cellIndex] = Boolean.toString(cell.getBooleanCellValue());
                break;
            case Cell.CELL_TYPE_NUMERIC:
                headerArray[cellIndex] = Double.toString(cell.getNumericCellValue());
                break;
            case Cell.CELL_TYPE_STRING:
                headerArray[cellIndex] = cell.getStringCellValue();
                break;
            default:
                headerArray[cellIndex] = "";
            }

        } //end while celliterator

        for (int x = 0; x < headerArray.length; x++) {
            headings.put(headerArray[x].substring(0, headerArray[x].indexOf("_")), x);
        }

        //String[] dataArray = xslxDataLine.split("\t");
        if (xslxDataRow.getCell(headings.get("HGVSc")) != null) {
            donotcall.hgvsc = xslxDataRow.getCell(headings.get("HGVSc").intValue()).getStringCellValue();

        }
        //donotcall.hgvsp = xslxDataRow.getCell(headings.get("HGVSp").intValue()).getStringCellValue();
        if (xslxDataRow.getCell(headings.get("ENSP")) != null) {
            donotcall.ensp = xslxDataRow.getCell(headings.get("ENSP").intValue()).getStringCellValue();
        }
        if (xslxDataRow.getCell(headings.get("Transcript")) != null) {
            donotcall.transcript = xslxDataRow.getCell(headings.get("Transcript").intValue()).getStringCellValue();
        } else {
            System.out.println(
                    "Transcript_27 column entry is negative!  This is essential to do not call! Do not call list needs to be fixed!  Crashing to prevent abnormal behavior!");
            System.exit(1);
        }
        donotcall.coordinate = (long) xslxDataRow.getCell(headings.get("Coordinate").intValue())
                .getNumericCellValue();

        // CallType is the page of the xlsx :
        // 1 => Always_Not_Real
        // 2 => Not_Real_When_Percentage_Low
        // 3 => Undetermined_Importance
        if (calltype == 1) {
            donotcall.callType = "Don't call, always";
        } else if (calltype == 2) {
            donotcall.callType = "If percentage low, don't call";

        } else {
            donotcall.callType = "On lab list, Unknown significance";
        }

        return donotcall;
    }

}