/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
package jalview.datamodel;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * A bean that models a point with (x, y, z) coordinates and a reference to a
+ * sequence
*/
public class SequencePoint
{
- // SMJS PUBLIC
+ /*
+ * Associated alignment sequence, or dummy sequence object
+ */
+ private final SequenceI sequence;
+
+ /*
+ * x, y, z position in 3-D space
+ */
+ public Point coord;
+
/**
- * for points with no real physical association with an alignment sequence
+ * Constructor
+ *
+ * @param sequence
+ * @param coord
*/
- public boolean isPlaceholder = false;
+ public SequencePoint(SequenceI sequence, Point pt)
+ {
+ this.sequence = sequence;
+ this.coord = pt;
+ }
/**
- * Associated alignment sequence, or dummy sequence object.
+ * 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 SequenceI sequence;
+ public SequencePoint(SequenceI sequence, float[] coords)
+ {
+ this(sequence, new Point(coords[0], coords[1], coords[2]));
+ }
+
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
/**
- * array of coordinates in embedded sequence space.
+ * Applies a negative translation of the 'shift' (x, y, z) coordinates
+ *
+ * @param centre
*/
- public float[] coord;
+ public void translateBack(Point shift)
+ {
+ float x = coord.x - shift.x;
+ float y = coord.y - shift.y;
+ float z = coord.z - shift.z;
+
+ coord = new Point(x, y, z);
+ }
- // SMJS ENDPUBLIC
- public SequencePoint(SequenceI sequence, float[] coord)
+ /**
+ * Applies a positive translation of the 'shift' (x, y, z) coordinates
+ *
+ * @param centre
+ */
+ public void translate(Point shift)
{
- this.sequence = sequence;
- this.coord = coord;
+ float x = coord.x + shift.x;
+ float y = coord.y + shift.y;
+ float z = coord.z + shift.z;
+
+ coord = new Point(x, y, z);
}
}