X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceNode.java;h=ca0930158ef1b96d104c11dafa1e7108c882f614;hb=ae9d8eab907d3f49a529cc86f6dfa6689b50e3d3;hp=6e35ee34363044087b4a05b3b32b94cc40999e77;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 6e35ee3..ca09301 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,21 +1,167 @@
-package jalview.datamodel;
-
-import java.awt.Color;
-
-public class SequenceNode extends BinaryNode {
-
-  public float dist;
-  public int count;
-  public float height;
-  public float ycount;
-  public Color color = Color.black;
-
-  public SequenceNode() {
-    super();
-  }
-  
-  public SequenceNode(Object val, SequenceNode parent, float dist,String name) {
-    super(val,parent,name);
-    this.dist = dist;
-  }
-}
+/*
+ * 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;
+
+import java.awt.*;
+
+/**
+ * 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;
+
+  /**
+   * Creates a new SequenceNode object.
+   */
+  public SequenceNode()
+  {
+    super();
+  }
+
+  /**
+   * 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)
+  {
+    super(val, parent, name);
+    this.dist = dist;
+    this.bootstrap = bootstrap;
+    this.dummy = dummy;
+  }
+
+  /**
+   * @param dummy true if node is created for the representation of polytomous trees
+   */
+  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()
+  {
+    return placeholder;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param newstate DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public boolean setDummy(boolean newstate)
+  {
+    boolean oldstate = dummy;
+    dummy = newstate;
+
+    return oldstate;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param Placeholder DOCUMENT ME!
+   */
+  public void setPlaceholder(boolean Placeholder)
+  {
+    this.placeholder = Placeholder;
+  }
+
+  /**
+   * 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()
+  {
+    SequenceNode c = this;
+
+    do
+    {
+      c = (SequenceNode) c.parent();
+    }
+    while ( (c != null) && c.dummy);
+
+    return c;
+  }
+  /**
+   * test if this node has a name that might be a label rather than a bootstrap value
+   * @return true if node has a non-numeric label
+   */
+  public boolean isSequenceLabel()
+  {
+    if (name!=null && name.length()>0)
+    {
+      for (int c=0,s=name.length(); c<s; c++)
+      {
+        char q = name.charAt(c);
+        if ('0'<=q && q<='9')
+          continue;
+        return true;
+      }
+    }
+    return false;
+  }
+}