X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequencePoint.java;h=3db7ceee9924dced6a1acaddaa69040c3e62b7c5;hb=bc18effe68ba80213a6d03ca7e6175adc6be71d6;hp=3690b439351540f6ed0f85ada7dd1e44dd2c7e54;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index 3690b43..3db7cee 100755
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,51 +1,89 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 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.
*
* 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* 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();
}
}