Extracting coordinates file that are inside a bounding box
First of all, note that you can always use Point2D.Double for representing points in a plane.

Next, I would split your program into two methods: the first one for pruning points that are not within a specified bounding box, and the second one for reading the points from the standard input, and putting them into the first one.

What comes to coding conventions, I would have a blank line before the if statement. Also, you should surround the condition of an if statement with a single space. So, instead of 

String[] values = data.split(",", 3);
if(Double.parseDouble(values[0])){ ...


you should write 

String[] values = data.split(",", 3);

if (Double.parseDouble(values[0])) { ...


All in all, I had this in mind:

import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import java.util.Scanner;

public class CoordinateUtilities {

    public static List&lt;Point2D.Double&gt; 
        getPointsWithinBoundingBox(final List&lt;Point2D.Double&gt; pointList,
                                   final double lowX,
                                   final double highX,
                                   final double lowY,
                                   final double highY) {
        Objects.requireNonNull(pointList, "The list of points is null.");
        checkXBounds(lowX, highX);
        checkYBounds(lowY, highY);
        final List&lt;Point2D.Double&gt; ret = new ArrayList&lt;&gt;(pointList.size());

        for (final Point2D.Double point : pointList) {
            final double x = point.x;
            final double y = point.y;

            if (lowX &lt;= x &amp;&amp; x &lt;= highX &amp;&amp; lowY &lt;= y &amp;&amp; y &lt;= highY) {
                ret.add(point);
            }
        }

        return ret;
    }

    public static void main(final String... args) {
        final Scanner scanner = new Scanner(System.in);
        final double lowX  = 50.0; 
        final double highX = 100.0;
        final double lowY  = 30.0;
        final double highY = 60.0;

        final List&lt;Point2D.Double&gt; allPoints = new ArrayList&lt;&gt;();

        while (scanner.hasNextLine()) {
            final String line = scanner.nextLine();

            if (line.trim().equals("quit")) {
                break;
            }

            final Point2D.Double point = parsePoint(line);

            if (point != null) {
                allPoints.add(point);
            }
        }

        final List&lt;Point2D.Double&gt; boundedPoints = 
                getPointsWithinBoundingBox(allPoints, lowX, highX, lowY, highY);

        boundedPoints.forEach(System.out::println);
    }

    private static Point2D.Double parsePoint(final String line) {
        final String[] tokens = line.trim().split("\\s*,\\s*");

        if (tokens.length &lt; 2) {
            return null;
        }

        try {
            final double x = Double.parseDouble(tokens[0]);
            final double y = Double.parseDouble(tokens[1]);
            return new Point2D.Double(x, y);
        } catch (final NumberFormatException ex) {
            return null;
        }
    }

    private static void checkXBounds(final double lowX, final double highX) {
        if (Double.isNaN(lowX)) {
            throw new IllegalArgumentException(
                    "The lower bound of the x-coordinate is NaN.");
        }

        if (Double.isNaN(highX)) {
            throw new IllegalArgumentException(
                    "The upper bound of the x-coordinate is NaN.");
        }

        if (lowX &gt; highX) {
            throw new IllegalArgumentException(
                    "The lower bound of the x-coordinate (" + lowX + "is " +
                    "larger than the upper bound of the x-coordinate (" +
                    highX + ").");
        }
    }

    private static void checkYBounds(final double lowY, final double highY) {
        if (Double.isNaN(lowY)) {
            throw new IllegalArgumentException(
                    "The lower bound of the y-coordinate is NaN.");
        }

        if (Double.isNaN(highY)) {
            throw new IllegalArgumentException(
                    "The upper bound of the y-coordinate is NaN.");
        }

        if (lowY &gt; highY) {
            throw new IllegalArgumentException(
                    "The lower bound of the y-coordinate (" + lowY + "is " +
                    "larger than the upper bound of the y-coordinate (" +
                    highY + ").");
        }
    }
}


Hope that helps.