X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceNode.java;h=0a694c2117efc1590029f0193f941d8971118bd5;hb=d1e20f6a5654ea6baf378afa3277b4e751c69a96;hp=905bd15dda65009149dc327e96a2e899ffb24c6b;hpb=f008025f6aa0c2df0e1fbf556a89393e7052db72;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 905bd15..0a694c2 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,54 +1,189 @@
-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 boolean dummy = false;
-  public SequenceNode() {
-    super();
-  }
-
-  public SequenceNode(Object val, SequenceNode parent, float dist,String name) {
-    super(val,parent,name);
-    this.dist = dist;
-  }
-  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;
-  }
-  public boolean setDummy(boolean newstate) {
-    boolean oldstate = dummy;
-    dummy = newstate;
-    return oldstate;
-  }
-
-  /**
-   * 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;
-  }
-}
+/*
+ * 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;
+
+import java.awt.Color;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceNode extends BinaryNode
+{
+  /** DOCUMENT ME!! */
+  public double dist;
+
+  /** DOCUMENT ME!! */
+  public int count;
+
+  /** DOCUMENT ME!! */
+  public double 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, double 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,
+          double 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;
+  }
+}