Merge branch 'tasks/JAL-3035_remove_dasobert_dependency' into develop

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

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index 7fcb713..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
 {
@@ -32,7 +34,7 @@ public class SequencePoint
   private final SequenceI sequence;
 
   /*
-   * x, y, z position in 3-D space
+   * x, y, z values
    */
   public Point coord;
 
@@ -67,30 +69,21 @@ public class SequencePoint
   }
 
   /**
-   * Applies a negative translation of the 'shift' (x, y, z) coordinates
+   * Applies a translation to the (x, y, z) coordinates
    * 
    * @param centre
    */
-  public void translateBack(Point shift)
+  public void translate(float x, float y, float z)
   {
-    float x = coord.x - shift.x;
-    float y = coord.y - shift.y;
-    float z = coord.z - shift.z;
-
-    coord = new Point(x, y, z);
+    coord = new Point(coord.x + x, coord.y + y, coord.z + z);
   }
 
   /**
-   * Applies a positive translation of the 'shift' (x, y, z) coordinates
-   * 
-   * @param centre
+   * string representation for ease of inspection in debugging or logging only
    */
-  public void translate(Point shift)
+  @Override
+  public String toString()
   {
-    float x = coord.x + shift.x;
-    float y = coord.y + shift.y;
-    float z = coord.z + shift.z;
-
-    coord = new Point(x, y, z);
+    return sequence.getName() + " " + coord.toString();
   }
 }