X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequencePoint.java;h=7fcb713bac79a2fa14aa491170b0cfb592730ec7;hb=2cc3a62e1ae63428db854af668e963f1b23af553;hp=093c45a952c4a36857e0f78bdf5849d180078a68;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index 093c45a..7fcb713 100755
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,36 +1,96 @@
-/* Jalview - a java multiple alignment editor
- * Copyright (C) 1998  Michele Clamp
- *
- * 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 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.
- *
- * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
- */
-
-package jalview.datamodel;
-import java.util.*;
-import java.awt.*;
-
-
-public class SequencePoint {
-
-  // SMJS PUBLIC
-  public SequenceI sequence;
-  public float[] coord;
-  // SMJS ENDPUBLIC
-
-  public SequencePoint(SequenceI sequence, float[] coord) {
-    this.sequence = sequence;
-    this.coord = coord;
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+/**
+ * A bean that models a point with (x, y, z) coordinates and a reference to a
+ * sequence
+ */
+public class SequencePoint
+{
+  /*
+   * Associated alignment sequence, or dummy sequence object
+   */
+  private final SequenceI sequence;
+
+  /*
+   * x, y, z position in 3-D space
+   */
+  public Point coord;
+
+  /**
+   * Constructor
+   * 
+   * @param sequence
+   * @param coord
+   */
+  public SequencePoint(SequenceI sequence, Point pt)
+  {
+    this.sequence = sequence;
+    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 negative translation of the 'shift' (x, y, z) coordinates
+   * 
+   * @param centre
+   */
+  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);
+  }
+
+  /**
+   * Applies a positive translation of the 'shift' (x, y, z) coordinates
+   * 
+   * @param centre
+   */
+  public void translate(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);
+  }
+}