JAL-2962 code tidying/documentation (non-functional) changes

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

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index e229af7..28db278 100755 (executable)
--- 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 +21,35 @@
 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
-  /**
-   * for points with no real physical association with an alignment sequence
+  /*
+   * Associated alignment sequence, or dummy sequence object
    */
-  public boolean isPlaceholder = false;
+  private final SequenceI sequence;
 
-  /**
-   * Associated alignment sequence, or dummy sequence object.
+  /*
+   * array of coordinates in embedded sequence space
    */
-  public SequenceI sequence;
+  public float[] coord;
 
   /**
-   * array of coordinates in embedded sequence space.
+   * Constructor
+   * 
+   * @param sequence
+   * @param coord
    */
-  public float[] coord;
-
-  // SMJS ENDPUBLIC
   public SequencePoint(SequenceI sequence, float[] coord)
   {
     this.sequence = sequence;
     this.coord = coord;
   }
+
+  public SequenceI getSequence()
+  {
+    return sequence;
+  }
 }