X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequencePoint.java;h=7fcb713bac79a2fa14aa491170b0cfb592730ec7;hb=2cc3a62e1ae63428db854af668e963f1b23af553;hp=e229af7993eb197d325a27682eb5488e14be4489;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index e229af7..7fcb713 100755
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,6 +1,6 @@
 /*
- * 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.
  * 
@@ -21,33 +21,76 @@
 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);
   }
 }