JAL-1767 refactorings to enable faithful restore of PCA from project

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

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index 9a881bc..3db7cee 100755 (executable)
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,51 +1,89 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * 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
 {
-  // SMJS PUBLIC
+  /*
+   * Associated alignment sequence, or dummy sequence object
+   */
+  private final SequenceI sequence;
+
+  /*
+   * x, y, z values
+   */
+  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 translation to the (x, y, z) coordinates
+   * 
+   * @param centre
    */
-  public float[] coord;
+  public void translate(float x, float y, float z)
+  {
+    coord = new Point(coord.x + x, coord.y + y, coord.z + z);
+  }
 
-  // SMJS ENDPUBLIC
-  public SequencePoint(SequenceI sequence, float[] coord)
+  /**
+   * string representation for ease of inspection in debugging or logging only
+   */
+  @Override
+  public String toString()
   {
-    this.sequence = sequence;
-    this.coord = coord;
+    return sequence.getName() + " " + coord.toString();
   }
 }