X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequencePoint.java;h=b22229b47c4da7178c50c8159f49d14024c72ec9;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=2c5d2a350d965bcafcee3df8acceb5e88bbbf7d8;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index 2c5d2a3..b22229b 100755
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,43 +1,50 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.datamodel;
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class SequencePoint
-{
-    // SMJS PUBLIC
-
-    /** DOCUMENT ME!! */
-    public SequenceI sequence;
-
-    /** DOCUMENT ME!! */
-    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 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+package jalview.datamodel;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequencePoint
+{
+  // SMJS PUBLIC
+  /**
+   * for points with no real physical association with an alignment sequence
+   */
+  public boolean isPlaceholder = false;
+
+  /**
+   * Associated alignment sequence, or dummy sequence object.
+   */
+  public SequenceI sequence;
+
+  /**
+   * array of coordinates in embedded sequence space.
+   */
+  public float[] coord;
+
+  // SMJS ENDPUBLIC
+  public SequencePoint(SequenceI sequence, float[] coord)
+  {
+    this.sequence = sequence;
+    this.coord = coord;
+  }
+}