package jalview.datamodel;
/**
- * A bean that models a point with (x, y, z) coordinates and a reference to a
- * sequence
+ * A bean that models a set of (x, y, z) values and a reference to a sequence.
+ * As used in Principal Component Analysis, the (x, y, z) values are the
+ * sequence's score for the currently selected first, second and third
+ * dimensions of the PCA.
*/
public class SequencePoint
{
private final SequenceI sequence;
/*
- * array of coordinates in embedded sequence space
+ * x, y, z values
*/
- public float[] coord;
+ public Point coord;
/**
* Constructor
* @param sequence
* @param coord
*/
- public SequencePoint(SequenceI sequence, float[] coord)
+ public SequencePoint(SequenceI sequence, Point pt)
{
this.sequence = sequence;
- this.coord = coord;
+ this.coord = pt;
+ }
+
+ /**
+ * Constructor given a sequence and an array of x, y, z coordinate positions
+ *
+ * @param sequence
+ * @param coords
+ * @throws ArrayIndexOutOfBoundsException
+ * if array length is less than 3
+ */
+ public SequencePoint(SequenceI sequence, float[] coords)
+ {
+ this(sequence, new Point(coords[0], coords[1], coords[2]));
}
public SequenceI getSequence()
{
return sequence;
}
+
+ /**
+ * Applies a translation to the (x, y, z) coordinates
+ *
+ * @param centre
+ */
+ public void translate(float x, float y, float z)
+ {
+ coord = new Point(coord.x + x, coord.y + y, coord.z + z);
+ }
+
+ /**
+ * string representation for ease of inspection in debugging or logging only
+ */
+ @Override
+ public String toString()
+ {
+ return sequence.getName() + " " + coord.toString();
+ }
}