From b46843eaeaa468ca849df40167f859475bb04319 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 13 Jul 2007 15:03:57 +0000
Subject: [PATCH] preliminary states for pca distribution io

---
 src/jalview/datamodel/SequencePoint.java |   93 ++++++++++++++++--------------
 1 file changed, 50 insertions(+), 43 deletions(-)

diff --git a/src/jalview/datamodel/SequencePoint.java b/src/jalview/datamodel/SequencePoint.java
index 9c28672..f105cc8 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) 2007 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
+ * Copyright (C) 2007 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
+  /**
+   * 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;
+  }
+}
-- 
1.7.10.2