X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceNode.java;h=ac2e9e25eb6bd7865c0e3a58a2a592a9f85b588e;hb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;hp=f86c63e2df32a87de9a6b8cdb33a3b8ea93c3ae6;hpb=9257b8510c7354cbd7e43a3fc2817978cc8e4ae9;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index f86c63e..ac2e9e2 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,46 +1,88 @@
 /*
-* 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
-*/
+ * 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.*;
 
 
-public class SequenceNode extends BinaryNode {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceNode extends BinaryNode
+{
+    /** DOCUMENT ME!! */
     public float dist;
+
+    /** DOCUMENT ME!! */
     public int count;
+
+    /** DOCUMENT ME!! */
     public float height;
+
+    /** DOCUMENT ME!! */
     public float ycount;
+
+    /** DOCUMENT ME!! */
     public Color color = Color.black;
+
+    /** DOCUMENT ME!! */
     public boolean dummy = false;
     private boolean placeholder = false;
 
-    public SequenceNode() {
+    /**
+     * Creates a new SequenceNode object.
+     */
+    public SequenceNode()
+    {
         super();
     }
 
-    public SequenceNode(Object val, SequenceNode parent, float dist, String name) {
+    /**
+     * Creates a new SequenceNode object.
+     *
+     * @param val DOCUMENT ME!
+     * @param parent DOCUMENT ME!
+     * @param dist DOCUMENT ME!
+     * @param name DOCUMENT ME!
+     */
+    public SequenceNode(Object val, SequenceNode parent, float dist, String name)
+    {
         super(val, parent, name);
         this.dist = dist;
     }
 
+    /**
+     * Creates a new SequenceNode object.
+     *
+     * @param val DOCUMENT ME!
+     * @param parent DOCUMENT ME!
+     * @param name DOCUMENT ME!
+     * @param dist DOCUMENT ME!
+     * @param bootstrap DOCUMENT ME!
+     * @param dummy DOCUMENT ME!
+     */
     public SequenceNode(Object val, SequenceNode parent, String name,
-        float dist, int bootstrap, boolean dummy) {
+        float dist, int bootstrap, boolean dummy)
+    {
         super(val, parent, name);
         this.dist = dist;
         this.bootstrap = bootstrap;
@@ -50,25 +92,41 @@ public class SequenceNode extends BinaryNode {
     /**
      * @param dummy true if node is created for the representation of polytomous trees
      */
-    public boolean isDummy() {
+    public boolean isDummy()
+    {
         return dummy;
     }
 
     /* @param placeholder is true if the sequence refered to in the
      *  element node is not actually present in the associated alignment
      */
-    public boolean isPlaceholder() {
+    public boolean isPlaceholder()
+    {
         return placeholder;
     }
 
-    public boolean setDummy(boolean newstate) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param newstate DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean setDummy(boolean newstate)
+    {
         boolean oldstate = dummy;
         dummy = newstate;
 
         return oldstate;
     }
 
-    public void setPlaceholder(boolean Placeholder) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param Placeholder DOCUMENT ME!
+     */
+    public void setPlaceholder(boolean Placeholder)
+    {
         this.placeholder = Placeholder;
     }
 
@@ -76,12 +134,15 @@ public class SequenceNode extends BinaryNode {
      * ascends the tree but doesn't stop until a non-dummy node is discovered.
      * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.
      */
-    public SequenceNode AscendTree() {
+    public SequenceNode AscendTree()
+    {
         SequenceNode c = this;
 
-        do {
+        do
+        {
             c = (SequenceNode) c.parent();
-        } while ((c != null) && c.dummy);
+        }
+        while ((c != null) && c.dummy);
 
         return c;
     }