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| /* 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.GrafensRhoTransform;/*~~ */import mesquite.lib.*;import mesquite.lib.duties.*;/** ======================================================================== */public class GrafensRhoTransform extends BranchLengthsAlterer { double resultNum; double rho; /*.................................................................................................................*/ /** * @param arguments * @param condition * @param hiredByName * * When hired, this module immediately asks for a value for Rho */ public boolean startJob(String arguments, Object condition, boolean hiredByName) { //TODO is this the right place to be doing this if (!MesquiteThread.isScripting()) { rho= MesquiteDouble.queryDouble(containerOfModule(), "Rho Value", "Choose a value for Grafen's Rho", 0.5, 0.0, MesquiteDouble.infinite); if (rho == MesquiteDouble.unassigned) { return false; } } return true; } /*.................................................................................................................*/ //Returns true if calling code is responsible for notifying listeners of tree public boolean transformTree(AdjustableTree tree, MesquiteString resultString){ doTransform(tree); return true; } // This method transforms any set of branch lengths using the rho transform of Grafen (1989). // It then checks the tree's height, and saves it. It then scales the tree to a height of one. // It changes the branch lengths to be a measure of the distance from the top of the tree to each node. // Note that the branch length field is being used for something other than // storing branch lengths. It then raises each distance (stored in branch // length) to the power rho. Finally it changes the distances back to // branch lengths and rescales the tree. Note that if the original tree // had contemporaneous tips, then the transformed tree will also. For a // discussion of transforming branch lengths in the context of Felsenstein's // (1985) method of phylogenetically independent contrasts, see Garland // et al. (1992, Systematic Biology 41:18-32.} private void doTransform(AdjustableTree tree) { MesquiteDouble height = new MesquiteDouble(0.0); //MesquiteDouble checkHeight = new MesquiteDouble(0.0); // debug variable double multiplier; int root = tree.getRoot(); heightCalculation(tree,0,height,root); multiplier = 1/height.getValue(); scl(tree,root,multiplier); //heightCalculation(tree,0,checkHeight,tree.getRoot()); //Debugg.println("After scl, height is: " + checkHeight.getValue()); //checkHeight.setValue(0.0); t1(tree,root,0); //heightCalculation(tree,0,checkHeight,tree.getRoot()); //Debugg.println("After t1, height is: " + checkHeight.getValue()); //checkHeight.setValue(0.0); expMe(tree,root,rho); //heightCalculation(tree,0,checkHeight,tree.getRoot()); //Debugg.println("After expMe, height is: " + checkHeight.getValue()); //checkHeight.setValue(0.0); t2(tree,root); //heightCalculation(tree,0,checkHeight,tree.getRoot()); //Debugg.println("After t2, height is: " + checkHeight.getValue()); //checkHeight.setValue(0.0); scl(tree,root,height.getValue()); //heightCalculation(tree,0,checkHeight,tree.getRoot()); //Debugg.println("After scl, height is: " + checkHeight.getValue()); //checkHeight.setValue(0.0); } // This method just gets the height of the tree. There may be somewhere else I could get this, // but since I don't know where, I'll just copy some code from the diagnostic screens. // This is a little different from DOS PDAP, where calculating the height comes as part of // the tree drawing code. private void heightCalculation(AdjustableTree tree, double ht, MesquiteDouble max, int node) { if (node != tree.getRoot()) ht = ht + tree.getBranchLength(node); else ht = 0; if (tree.nodeIsInternal(node)) { for (int daughter = tree.firstDaughterOfNode(node); tree.nodeExists(daughter); daughter = tree.nextSisterOfNode(daughter)) heightCalculation(tree, ht, max, daughter); } else if (ht > max.getValue()) max.setValue(ht); } // This is another helper method. It is given the scaling factor, and then traverses the tree, multiplying all the branch // lengths by the correct amount. private void scl(AdjustableTree tree, int nd, double mult) { if (nd != tree.getRoot()) { tree.setBranchLength(nd,mult*tree.getBranchLength(nd),false); } if (tree.nodeIsInternal(nd)) for (int daughter = tree.firstDaughterOfNode(nd); tree.nodeExists(daughter); daughter = tree.nextSisterOfNode(daughter)) scl(tree, daughter, mult); } // This method traverses the tree and raises all the branch lengths to a power. private void expMe(AdjustableTree tree, int nd, double power) { if ((tree.getRoot() != nd) && (tree.getBranchLength(nd) > 0.0) && (MesquiteDouble.isCombinable(tree.getBranchLength(nd)))) tree.setBranchLength(nd, Math.exp(power*Math.log(tree.getBranchLength(nd))),false); else if (tree.getRoot() != nd && (MesquiteDouble.isCombinable(tree.getBranchLength(nd)))) tree.setBranchLength(nd,0,false); if (tree.nodeIsInternal(nd)) for (int daughter = tree.firstDaughterOfNode(nd); tree.nodeExists(daughter); daughter = tree.nextSisterOfNode(daughter)) expMe(tree, daughter, power); } // This is the first of two support methods. It transforms the tree so that the branch // length field no longer holds the branch length, but holds the distance // from the highest tip to itself. Because the procedure assumes that // the has already been transformed to a height of one, this distance is // just 1 minus the height of the node. private void t1(AdjustableTree tree, int nd, double ht){ if (nd != tree.getRoot()) ht += tree.getBranchLength(nd); if (tree.nodeIsInternal(nd)) { for (int daughter=tree.firstDaughterOfNode(nd); tree.nodeExists(daughter); daughter = tree.nextSisterOfNode(daughter) ) t1(tree, daughter,ht); } if (nd != tree.getRoot()) tree.setBranchLength(nd,1-ht,false); if (tree.getBranchLength(nd)<1e-18) // length must be due to roundoff error so tree.setBranchLength(nd,0,false); // zero it out; constant changed 12-27-99 PEM } // This is the second of two support methods. // This recursive procedure transforms the tree so that the branch // length field holds the branch length, assuming that it previously held // the distance from the highest tip to the node below previously. // It also assumes that the height of the tree is one to start with. private void t2(AdjustableTree tree, int nd){ if (tree.nodeIsInternal(nd)) { for (int daughter=tree.firstDaughterOfNode(nd); tree.nodeExists(daughter); daughter = tree.nextSisterOfNode(daughter) ) t2(tree, daughter); } boolean rootFamily = false; if (nd == tree.getRoot()) rootFamily = true; for (int daughter=tree.firstDaughterOfNode(tree.getRoot()); tree.nodeExists(daughter); daughter = tree.nextSisterOfNode(daughter) ) if (daughter == nd) rootFamily = true; if (!rootFamily) { tree.setBranchLength(nd,tree.getBranchLength(tree.motherOfNode(nd))-tree.getBranchLength(nd),false); } else if (nd != tree.getRoot()) tree.setBranchLength(nd,1-tree.getBranchLength(nd),false); } /*.................................................................................................................*/ public String getName() { return "Grafen's (1989) Rho transform"; } /*.................................................................................................................*/ 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 Grafen's (1989) Rho transform" ; }} |