Merge remote-tracking branch 'origin/bug/JAL-3049colourCellTooltip' into

[jalview.git] / src / jalview / datamodel / SequencePoint.java

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index 28db278..3db7cee 100755 (executable)
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -21,8 +21,10 @@
 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
 {
@@ -32,9 +34,9 @@ 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
@@ -42,14 +44,46 @@ public class SequencePoint
    * @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();
+  }
 }