Merge branch 'improvement/JAL-4023_snotation_for_trees' into develop

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

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index ea3e515..0a694c2 100755 (executable)
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,24 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
-import java.awt.*;
+import java.awt.Color;
 
 /**
  * DOCUMENT ME!
@@ -29,13 +31,13 @@ import java.awt.*;
 public class SequenceNode extends BinaryNode
 {
   /** DOCUMENT ME!! */
-  public float dist;
+  public double dist;
 
   /** DOCUMENT ME!! */
   public int count;
 
   /** DOCUMENT ME!! */
-  public float height;
+  public double height;
 
   /** DOCUMENT ME!! */
   public float ycount;
@@ -60,15 +62,15 @@ public class SequenceNode extends BinaryNode
    * Creates a new SequenceNode object.
    * 
    * @param val
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param parent
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param dist
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
-  public SequenceNode(Object val, SequenceNode parent, float dist,
+  public SequenceNode(Object val, SequenceNode parent, double dist,
           String name)
   {
     super(val, parent, name);
@@ -79,20 +81,20 @@ public class SequenceNode extends BinaryNode
    * Creates a new SequenceNode object.
    * 
    * @param val
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param parent
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param dist
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param bootstrap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param dummy
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public SequenceNode(Object val, SequenceNode parent, String name,
-          float dist, int bootstrap, boolean dummy)
+          double dist, int bootstrap, boolean dummy)
   {
     super(val, parent, name);
     this.dist = dist;
@@ -102,8 +104,7 @@ public class SequenceNode extends BinaryNode
 
   /**
    * @param dummy
-   *                true if node is created for the representation of polytomous
-   *                trees
+   *          true if node is created for the representation of polytomous trees
    */
   public boolean isDummy()
   {
@@ -123,7 +124,7 @@ public class SequenceNode extends BinaryNode
    * DOCUMENT ME!
    * 
    * @param newstate
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -139,7 +140,7 @@ public class SequenceNode extends BinaryNode
    * DOCUMENT ME!
    * 
    * @param Placeholder
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setPlaceholder(boolean Placeholder)
   {
@@ -177,7 +178,9 @@ public class SequenceNode extends BinaryNode
       {
         char q = name.charAt(c);
         if ('0' <= q && q <= '9')
+        {
           continue;
+        }
         return true;
       }
     }