refactored from newickfile

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@438 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/uk/ac/vamsas/objects/utils/trees/BinaryNode.java b/src/uk/ac/vamsas/objects/utils/trees/BinaryNode.java
new file mode 100644 (file)
index 0000000..ca0739a
--- /dev/null
+++ b/src/uk/ac/vamsas/objects/utils/trees/BinaryNode.java
@@ -0,0 +1,278 @@
+/**\r
+ * \r
+ */\r
+package uk.ac.vamsas.objects.utils.trees;\r
+\r
+import uk.ac.vamsas.client.Vobject;\r
+import uk.ac.vamsas.client.VorbaId;\r
+\r
+public class BinaryNode {\r
+  Vobject element;\r
+\r
+  String name;\r
+\r
+  BinaryNode left;\r
+\r
+  BinaryNode right;\r
+\r
+  BinaryNode parent;\r
+\r
+  /** DOCUMENT ME!! */\r
+  public int bootstrap;\r
+\r
+  /**\r
+   * Creates a new BinaryNode object.\r
+   */\r
+  public BinaryNode() {\r
+    left = right = parent = null;\r
+    bootstrap = 0;\r
+  }\r
+\r
+  /**\r
+   * Creates a new BinaryNode object.\r
+   * \r
+   * @param val\r
+   *          DOCUMENT ME!\r
+   * @param parent\r
+   *          DOCUMENT ME!\r
+   * @param name\r
+   *          DOCUMENT ME!\r
+   */\r
+  public BinaryNode(Vobject val, BinaryNode parent, String name) {\r
+    this.element = val;\r
+    this.parent = parent;\r
+    this.name = name;\r
+\r
+    left = right = null;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public Vobject element() {\r
+    return element;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @param v\r
+   *          DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public Vobject setElement(Vobject v) {\r
+    return element = v;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public BinaryNode left() {\r
+    return left;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @param n\r
+   *          DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public BinaryNode setLeft(BinaryNode n) {\r
+    return left = n;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public BinaryNode right() {\r
+    return right;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @param n\r
+   *          DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public BinaryNode setRight(BinaryNode n) {\r
+    return right = n;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public BinaryNode parent() {\r
+    return parent;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @param n\r
+   *          DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public BinaryNode setParent(BinaryNode n) {\r
+    return parent = n;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public boolean isLeaf() {\r
+    return (left == null) && (right == null);\r
+  }\r
+\r
+  /**\r
+   * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children\r
+   * of this node (removing any old references) a null parameter DOES NOT mean\r
+   * that the pointer to the corresponding child node is set to NULL - you\r
+   * should use setChild(null), or detach() for this.\r
+   * \r
+   */\r
+  public void SetChildren(BinaryNode leftchild, BinaryNode rightchild) {\r
+    if (leftchild != null) {\r
+      this.setLeft(leftchild);\r
+      leftchild.detach();\r
+      leftchild.setParent(this);\r
+    }\r
+\r
+    if (rightchild != null) {\r
+      this.setRight(rightchild);\r
+      rightchild.detach();\r
+      rightchild.setParent(this);\r
+    }\r
+  }\r
+\r
+  /**\r
+   * Detaches the node from the binary tree, along with all its child nodes.\r
+   * \r
+   * @return BinaryNode The detached node.\r
+   */\r
+  public BinaryNode detach() {\r
+    if (this.parent != null) {\r
+      if (this.parent.left == this) {\r
+        this.parent.left = null;\r
+      } else {\r
+        if (this.parent.right == this) {\r
+          this.parent.right = null;\r
+        }\r
+      }\r
+    }\r
+\r
+    this.parent = null;\r
+\r
+    return this;\r
+  }\r
+\r
+  /**\r
+   * Traverses up through the tree until a node with a free leftchild is\r
+   * discovered.\r
+   * \r
+   * @return BinaryNode\r
+   */\r
+  public BinaryNode ascendLeft() {\r
+    BinaryNode c = this;\r
+\r
+    do {\r
+      c = c.parent();\r
+    } while ((c != null) && (c.left() != null) && !c.left().isLeaf());\r
+\r
+    return c;\r
+  }\r
+\r
+  /**\r
+   * Traverses up through the tree until a node with a free rightchild is\r
+   * discovered. Jalview builds trees by descent on the left, so this may be\r
+   * unused.\r
+   * \r
+   * @return BinaryNode\r
+   */\r
+  public BinaryNode ascendRight() {\r
+    BinaryNode c = this;\r
+\r
+    do {\r
+      c = c.parent();\r
+    } while ((c != null) && (c.right() != null) && !c.right().isLeaf());\r
+\r
+    return c;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @param name\r
+   *          DOCUMENT ME!\r
+   */\r
+  public void setName(String name) {\r
+    this.name = name;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public String getName() {\r
+    return this.name;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @param boot\r
+   *          DOCUMENT ME!\r
+   */\r
+  public void setBootstrap(int boot) {\r
+    this.bootstrap = boot;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public int getBootstrap() {\r
+    return bootstrap;\r
+  }\r
+  /**\r
+   * \r
+   * @return unquoted string of form VorbaId|v|node name string\r
+  public String getNewickNodeName() {\r
+    if (element!=null || name!=null)\r
+      {\r
+      return ((element!=null) ? element.getVorbaId().getId()+"|v|" : "")\r
+        + ((name == null) ? "" : name);\r
+      }\r
+    return "";\r
+  }\r
+  \r
+   * note we probably don't need this now\r
+\r
+   * public boolean parseNodeNameString(uk.ac.vamsas.client.ClientDocument binder)\r
+  {\r
+    \r
+    if (element==null && name!=null && name.indexOf("|v|")>-1)\r
+    {\r
+      element = binder.getObject(null).getVorbaId(); // TODO: fix THIS ! name.substring(0, name.indexOf("|v")));\r
+      \r
+    }\r
+    return false;\r
+  }*/\r
+}
\ No newline at end of file

diff --git a/src/uk/ac/vamsas/objects/utils/trees/SequenceNode.java b/src/uk/ac/vamsas/objects/utils/trees/SequenceNode.java
new file mode 100644 (file)
index 0000000..9f2a05d
--- /dev/null
+++ b/src/uk/ac/vamsas/objects/utils/trees/SequenceNode.java
@@ -0,0 +1,123 @@
+/**\r
+ * \r
+ */\r
+package uk.ac.vamsas.objects.utils.trees;\r
+\r
+import uk.ac.vamsas.client.Vobject;\r
+import uk.ac.vamsas.client.VorbaId;\r
+\r
+public class SequenceNode extends BinaryNode {\r
+  /** DOCUMENT ME!! */\r
+  public float dist;\r
+\r
+  /** DOCUMENT ME!! */\r
+  public boolean dummy = false;\r
+\r
+  private boolean placeholder = false;\r
+\r
+  /**\r
+   * Creates a new SequenceNode object.\r
+   */\r
+  public SequenceNode() {\r
+    super();\r
+  }\r
+\r
+  /**\r
+   * Creates a new SequenceNode object.\r
+   * \r
+   * @param val\r
+   *          DOCUMENT ME!\r
+   * @param parent\r
+   *          DOCUMENT ME!\r
+   * @param dist\r
+   *          DOCUMENT ME!\r
+   * @param name\r
+   *          DOCUMENT ME!\r
+   */\r
+  public SequenceNode(Vobject val, SequenceNode parent, float dist, String name) {\r
+    super(val, parent, name);\r
+    this.dist = dist;\r
+  }\r
+\r
+  /**\r
+   * Creates a new SequenceNode object.\r
+   * \r
+   * @param val\r
+   *          DOCUMENT ME!\r
+   * @param parent\r
+   *          DOCUMENT ME!\r
+   * @param name\r
+   *          DOCUMENT ME!\r
+   * @param dist\r
+   *          DOCUMENT ME!\r
+   * @param bootstrap\r
+   *          DOCUMENT ME!\r
+   * @param dummy\r
+   *          DOCUMENT ME!\r
+   */\r
+  public SequenceNode(Vobject val, SequenceNode parent, String name,\r
+      float dist, int bootstrap, boolean dummy) {\r
+    super(val, parent, name);\r
+    this.dist = dist;\r
+    this.bootstrap = bootstrap;\r
+    this.dummy = dummy;\r
+  }\r
+\r
+  /**\r
+   * @param dummy\r
+   *          true if node is created for the representation of polytomous\r
+   *          trees\r
+   */\r
+  public boolean isDummy() {\r
+    return dummy;\r
+  }\r
+\r
+  /*\r
+   * @param placeholder is true if the sequence referred to in the element node\r
+   * is not actually present in the associated alignment\r
+   */\r
+  public boolean isPlaceholder() {\r
+    return placeholder;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @param newstate\r
+   *          DOCUMENT ME!\r
+   * \r
+   * @return DOCUMENT ME!\r
+   */\r
+  public boolean setDummy(boolean newstate) {\r
+    boolean oldstate = dummy;\r
+    dummy = newstate;\r
+\r
+    return oldstate;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   * \r
+   * @param Placeholder\r
+   *          DOCUMENT ME!\r
+   */\r
+  public void setPlaceholder(boolean Placeholder) {\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\r
+   * SequenceNodes.\r
+   */\r
+  public SequenceNode AscendTree() {\r
+    SequenceNode c = this;\r
+\r
+    do {\r
+      c = (SequenceNode) c.parent();\r
+    } while ((c != null) && c.dummy);\r
+\r
+    return c;\r
+  }\r
+\r
+}
\ No newline at end of file