preliminary methods for detecting internal sequence nodes

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 943751e..ca09301 100755 (executable)
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,149 +1,167 @@
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-import java.awt.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class SequenceNode\r
-    extends BinaryNode\r
-{\r
-  /** DOCUMENT ME!! */\r
-  public float dist;\r
-\r
-  /** DOCUMENT ME!! */\r
-  public int count;\r
-\r
-  /** DOCUMENT ME!! */\r
-  public float height;\r
-\r
-  /** DOCUMENT ME!! */\r
-  public float ycount;\r
-\r
-  /** DOCUMENT ME!! */\r
-  public Color color = Color.black;\r
-\r
-  /** DOCUMENT ME!! */\r
-  public boolean dummy = false;\r
-  private boolean placeholder = false;\r
-\r
-  /**\r
-   * Creates a new SequenceNode object.\r
-   */\r
-  public SequenceNode()\r
-  {\r
-    super();\r
-  }\r
-\r
-  /**\r
-   * Creates a new SequenceNode object.\r
-   *\r
-   * @param val DOCUMENT ME!\r
-   * @param parent DOCUMENT ME!\r
-   * @param dist DOCUMENT ME!\r
-   * @param name DOCUMENT ME!\r
-   */\r
-  public SequenceNode(Object val, SequenceNode parent, float dist, String name)\r
-  {\r
-    super(val, parent, name);\r
-    this.dist = dist;\r
-  }\r
-\r
-  /**\r
-   * Creates a new SequenceNode object.\r
-   *\r
-   * @param val DOCUMENT ME!\r
-   * @param parent DOCUMENT ME!\r
-   * @param name DOCUMENT ME!\r
-   * @param dist DOCUMENT ME!\r
-   * @param bootstrap DOCUMENT ME!\r
-   * @param dummy DOCUMENT ME!\r
-   */\r
-  public SequenceNode(Object val, SequenceNode parent, String name,\r
-                      float dist, int bootstrap, boolean dummy)\r
-  {\r
-    super(val, parent, name);\r
-    this.dist = dist;\r
-    this.bootstrap = bootstrap;\r
-    this.dummy = dummy;\r
-  }\r
-\r
-  /**\r
-   * @param dummy true if node is created for the representation of polytomous trees\r
-   */\r
-  public boolean isDummy()\r
-  {\r
-    return dummy;\r
-  }\r
-\r
-  /* @param placeholder is true if the sequence refered to in the\r
-   *  element node is not actually present in the associated alignment\r
-   */\r
-  public boolean isPlaceholder()\r
-  {\r
-    return placeholder;\r
-  }\r
-\r
-  /**\r
-   * DOCUMENT ME!\r
-   *\r
-   * @param newstate DOCUMENT ME!\r
-   *\r
-   * @return DOCUMENT ME!\r
-   */\r
-  public boolean setDummy(boolean newstate)\r
-  {\r
-    boolean oldstate = dummy;\r
-    dummy = newstate;\r
-\r
-    return oldstate;\r
-  }\r
-\r
-  /**\r
-   * DOCUMENT ME!\r
-   *\r
-   * @param Placeholder DOCUMENT ME!\r
-   */\r
-  public void setPlaceholder(boolean Placeholder)\r
-  {\r
-    this.placeholder = Placeholder;\r
-  }\r
-\r
-  /**\r
-   * ascends the tree but doesn't stop until a non-dummy node is discovered.\r
-   * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.\r
-   */\r
-  public SequenceNode AscendTree()\r
-  {\r
-    SequenceNode c = this;\r
-\r
-    do\r
-    {\r
-      c = (SequenceNode) c.parent();\r
-    }\r
-    while ( (c != null) && c.dummy);\r
-\r
-    return c;\r
-  }\r
-}\r
+/*
+ * 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;
+  }
+}