X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceNode.java;h=f72382d7f24ba19fea1eb3a2b7519c3d8d43b6e4;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=f86c63e2df32a87de9a6b8cdb33a3b8ea93c3ae6;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index f86c63e..f72382d 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,88 +1,185 @@
-/*
-* 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 {
-    public float dist;
-    public int count;
-    public float height;
-    public float ycount;
-    public Color color = Color.black;
-    public boolean dummy = false;
-    private boolean placeholder = 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;
-    }
-
-    /* @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;
-    }
-
-    public boolean setDummy(boolean newstate) {
-        boolean oldstate = dummy;
-        dummy = newstate;
-
-        return oldstate;
-    }
-
-    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;
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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.*;
+
+/**
+ * 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;
+  }
+}