PagelTransform.java

/* PDAP:PDTREE package for Mesquite  copyright 2001-2009 P. Midford & W. MaddisonPDAP:PDTREE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.The web site for PDAP:PDTREE is http://mesquiteproject.org/pdap_mesquite/This source code and its compiled class files are free and modifiable under the terms of GNU Lesser General Public License.  (http://www.gnu.org/copyleft/lesser.html)*/package mesquite.pdap.PagelTransform;/*~~  */import mesquite.lib.*;import mesquite.lib.duties.*;/** ======================================================================== */public class PagelTransform extends BranchLengthsAlterer {	private int [] depth;	/*.................................................................................................................*/	public boolean startJob(String arguments, Object condition, boolean hiredByName) {		return true;  	 }  	 	/*.................................................................................................................*/	/**     *     * @param tree     * @param resultString          * @return true if calling code is responsible for notifying listeners of tree 	 */        public boolean transformTree(AdjustableTree tree, MesquiteString resultString){        doTransform(tree);		return true;	}	        /**     * This procedure sets all the branch lengths to those dictated by     * Pagel's (1992, J. of Theoretical Biol 156:431-442) arbitrary method.     * The depth of a node is equal to the maximum of the number of     * bifurcation levels of the left child and the right child plus one.     * If a node is a polytomy, its depth is set to the maximum of the     * bifurcation levels of the offspring, but one is not added.  This     * results in polytomies being assigned the least depth possible.  This     * was a (PDAP) internal decision, as Pagel(1992, p. 441 paragraph 7) does     * not discuss how to assign a depth to a polytomy node.       *      * @param tree what to transform     */    private void doTransform(AdjustableTree tree) {        final int root = tree.getRoot();        depth = new int[tree.getNumNodeSpaces()];        pagelMe1(tree,root);        pagelMe2(tree,root);    }                /**     *      * This method computes the depths recursively.  The original     * Pagelme procedure was split into 2 pieces to support PDAP's implementation of polytomy.     * Comment from DOS PDAP PEM 9-May-95.                             * @param tree     * @param nd     * @return     */    private int pagelMe1(AdjustableTree tree, int nd) {        int maxBif = 0;           if (!tree.nodeIsInternal(nd)) {            depth[nd] =0;               //set depth to 0}            return 0;        }        else {            // node is either unbranched or branched - don't add depth for unbranched internal nodes            int daughterCount = tree.numberOfDaughtersOfNode(nd);            if (daughterCount == 1){                depth[nd] = pagelMe1(tree,tree.firstDaughterOfNode(nd));                return depth[nd];            }            else{  // it branches, so add one to the depth                for (int daughter=tree.firstDaughterOfNode(nd); tree.nodeExists(daughter); daughter = tree.nextSisterOfNode(daughter) ) {                    int d = pagelMe1(tree,daughter);                    if (d > maxBif)                        maxBif = d;                }                depth[nd] = maxBif+1;   // this should be compatible with DOS PDAP - a polytomy does add exactly one to the depth (nothing for implied internal ZLB's)                return depth[nd];            }        }    }               /**     * This method finishes the transformation (taking     * polytomies into account.  Note that it does its work while going     * back down the tree (toward the root), while pagelme1 does its work     * going up the tree (toward the tips).  Original  9-May-95, Java translation 23-Feb-2001 PEM     *  @param tree     *  @param nd    */    private void pagelMe2(AdjustableTree tree, int nd) {        if (tree.nodeIsInternal(nd)) {            for (int daughter=tree.firstDaughterOfNode(nd); tree.nodeExists(daughter); daughter = tree.nextSisterOfNode(daughter) ) {                 tree.setBranchLength(daughter,depth[nd]-depth[daughter],false);                pagelMe2(tree,daughter);            }        }    }	/*.................................................................................................................*/     public String getName() {		return "Branch Lengths Transformation of Pagel (1992)";   	 }	/*.................................................................................................................*/  	 public String getVersion() {		return "1.15";   	 }	/*.................................................................................................................*/  	 public boolean isPrerelease() {		return false;   	 }     /*................................................................................................................*/     public boolean isSubstantive(){         return true;     }           	 	/*.................................................................................................................*/  	 public String getAuthors() {		return "Peter E. Midford, Ted Garland Jr., and Wayne P. Maddison";   	 }	/*.................................................................................................................*/ 	/** returns an explanation of what the module does.*/ 	public String getExplanation() { 		return ("Adjusts a tree's branch lengths according the method of Pagel (1992): " + 		             "The depth of a node is equal to the maximum of the number of " +				"bifurcation levels of the left child and the right child plus one. ");   	 }}