X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequencePoint.java;h=a21209a6b7c4b0fef8b34fc4373bcecdef493819;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=fa91e59502ce117f8c6014f13ec1df377d152de0;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index fa91e59..a21209a 100755
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,36 +1,53 @@
-/*
-* 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;
-
-import java.awt.*;
-
-import java.util.*;
-
-
-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 2.9.0b1)
+ * Copyright (C) 2015 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;
+
+/**
+ * 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;
+  }
+}