JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index 2c5d2a3..a6b967e 100755 (executable)
--- a/src/jalview/datamodel/SequencePoint.java
+++ b/src/jalview/datamodel/SequencePoint.java
@@ -1,43 +1,53 @@
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class SequencePoint\r
-{\r
-    // SMJS PUBLIC\r
-\r
-    /** DOCUMENT ME!! */\r
-    public SequenceI sequence;\r
-\r
-    /** DOCUMENT ME!! */\r
-    public float[] coord;\r
-\r
-    // SMJS ENDPUBLIC\r
-    public SequencePoint(SequenceI sequence, float[] coord)\r
-    {\r
-        this.sequence = sequence;\r
-        this.coord = coord;\r
-    }\r
-}\r
+/*
+ * 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;
+
+/**
+ * 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;
+  }
+}