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/**
* Title: ProAlign<p>
* Description: <p>
* Copyright: Copyright (c) Ari Loytynoja<p>
* License: GNU GENERAL PUBLIC LICENSE<p>
* @see http://www.gnu.org/copyleft/gpl.html
* Company: ULB<p>
* @author Ari Loytynoja
* @version 1.0
*/
package proalign;
class TreeNode {
String tree;
String[] subTrees;
String[] revTrees;
static String mpTree;
TreeNode parent;
TreeNode child0;
TreeNode child1;
static float halfLength;
static float maxSpan;
static float minDiff;
float[] subDistances;
float maxLength = 0f;
float totalDist = 0f; // weight
boolean isLast = true;
TreeNode(String t) {
mpTree = new String();
minDiff = 100f;
ProAlign.log("TreeNode");
tree = t;
TreeReader tr = new TreeReader();
subTrees = tr.divideTree(tree);
subDistances = tr.distance;
subDistances[0] = Math.abs(subDistances[0]);
subDistances[1] = Math.abs(subDistances[1]);
// System.out.println(subTrees[0]+" "+subTrees[1]);
float tot = subDistances[0]+subDistances[1];
revTrees = new String[2];
revTrees[0] = subTrees[1]+":"+tot;
revTrees[1] = subTrees[0]+":"+tot;
child0 = new TreeNode(tr,subTrees[0],TreeNode.this,0);
child1 = new TreeNode(tr,subTrees[1],TreeNode.this,1);
totalDist = subDistances[0]+subDistances[1]+
child0.totalDist+child1.totalDist;
float currPair = subDistances[0]+child0.maxLength+
subDistances[1]+child1.maxLength;
if(currPair > TreeNode.maxSpan) {
TreeNode.maxSpan = currPair;
// System.out.println("ms0 "+child0.tree+":"+subDistances[0]+" | "+
// child1.tree+":"+subDistances[1]+" "+currPair);
}
}
TreeNode(TreeReader tr,String t,TreeNode p,int branch) {
tree = t;
parent = p;
if(tree.indexOf(",")>0) {
isLast = false;
subTrees = tr.divideTree(tree);
subDistances = tr.distance;
subDistances[0] = Math.abs(subDistances[0]);
subDistances[1] = Math.abs(subDistances[1]);
revTrees = new String[2];
revTrees[0] = "("+parent.revTrees[branch]+","+
subTrees[1]+":"+subDistances[1]+"):"+subDistances[0];
revTrees[1] = "("+parent.revTrees[branch]+","+
subTrees[0]+":"+subDistances[0]+"):"+subDistances[1];
child0 = new TreeNode(tr,subTrees[0],TreeNode.this,0);
child1 = new TreeNode(tr,subTrees[1],TreeNode.this,1);
totalDist = subDistances[0]+subDistances[1]+
child0.totalDist+child1.totalDist;
float currPair = subDistances[0]+child0.maxLength+
subDistances[1]+child1.maxLength;
if(currPair > TreeNode.maxSpan) {
TreeNode.maxSpan = currPair;
// System.out.println("ms1 "+child0.tree+":"+subDistances[0]+" | "+
// child1.tree+":"+subDistances[1]+" "+currPair);
}
if(subDistances[0]+child0.maxLength > subDistances[1]+child1.maxLength) {
maxLength = subDistances[0]+child0.maxLength;
} else {
maxLength = subDistances[1]+child1.maxLength;
}
// System.out.println("ml "+maxLength);
}
}
String findMiddlePoint() {
TreeNode.halfLength = TreeNode.maxSpan/2f;
if(TreeNode.halfLength > child0.maxLength &&
TreeNode.halfLength < child0.maxLength+subDistances[0]+subDistances[1]) {
float b0 = TreeNode.halfLength-child0.maxLength;
float b1 = subDistances[0]+subDistances[1]-b0;
TreeNode.mpTree = "("+child0.tree+": "+b0+","+child1.tree+":"+b1+");";
}
child0.findMiddle(1);
child1.findMiddle(0);
ProAlign.log("mprooted: "+TreeNode.mpTree);
return TreeNode.mpTree;
}
void findMiddle(int branch) {
if(!isLast) {
if(branch==0) {
if(TreeNode.halfLength > child0.maxLength &&
TreeNode.halfLength < child0.maxLength+subDistances[0]) {
float b0 = TreeNode.halfLength-child0.maxLength;
float b1 = subDistances[0]-b0;
TreeNode.mpTree = "("+child0.tree+": "+b0+",("+parent.revTrees[1]+","+
subTrees[1]+":"+subDistances[1]+"):"+b1+");";
// System.out.println("nt "+branch+": "+child0.tree+" "+child0.maxLength+" "+
// child1.tree+" "+child1.maxLength+" "+TreeNode.halfLength+" "+TreeNode.minDiff);
}
if(TreeNode.halfLength > child1.maxLength &&
TreeNode.halfLength < child1.maxLength+subDistances[1]) {
float b0 = TreeNode.halfLength-child1.maxLength;
float b1 = subDistances[1]-b0;
TreeNode.mpTree = "("+child1.tree+": "+b0+",("+parent.revTrees[1]+","+
subTrees[0]+":"+subDistances[0]+"):"+b1+");";
// System.out.println("nt "+branch+": "+child0.tree+" "+child0.maxLength+" "+
// child1.tree+" "+child1.maxLength+" "+TreeNode.halfLength+" "+TreeNode.minDiff);
}
child0.findMiddle(1);
child1.findMiddle(0);
} else {
if(TreeNode.halfLength > child0.maxLength &&
TreeNode.halfLength < child0.maxLength+subDistances[0]) {
float b0 = TreeNode.halfLength-child0.maxLength;
float b1 = subDistances[0]-b0;
TreeNode.mpTree = "("+child0.tree+": "+b0+",("+parent.revTrees[0]+
","+subTrees[1]+":"+subDistances[1]+"):"+b1+");";
// System.out.println("nt "+branch+": "+child0.tree+" "+child0.maxLength+" "+
// child1.tree+" "+child1.maxLength+" "+TreeNode.halfLength+" "+TreeNode.minDiff);
}
if(TreeNode.halfLength > child1.maxLength &&
TreeNode.halfLength < child1.maxLength+subDistances[1]) {
float b0 = TreeNode.halfLength-child1.maxLength;
float b1 = subDistances[1]-b0;
TreeNode.mpTree = "("+child1.tree+": "+b0+",("+parent.revTrees[0]+
","+subTrees[0]+":"+subDistances[0]+"):"+b1+");";
// System.out.println("nt "+branch+": "+child0.tree+" "+child0.maxLength+" "+
// child1.tree+" "+child1.maxLength+" "+TreeNode.halfLength+" "+TreeNode.minDiff);
}
child0.findMiddle(1);
child1.findMiddle(0);
}
}
}
/*
This was the first attempt for the tree rooting. Not used anymore.
*/
String findMiddleWeightPoint() {
TreeNode.halfLength = totalDist/2f;
child0.findMiddle(1);
child1.findMiddle(0);
ProAlign.log("mprooted: "+TreeNode.mpTree);
return TreeNode.mpTree;
}
void findMiddleWeight(int branch) {
if(!isLast) {
if(branch==0) {
if(Math.abs(TreeNode.halfLength-child0.totalDist)<TreeNode.minDiff) {
TreeNode.minDiff = Math.abs(TreeNode.halfLength-child0.totalDist);
float b0,b1;
if(TreeNode.halfLength>child0.totalDist) {
b0 = TreeNode.halfLength-child0.totalDist;
b1 = subDistances[0]-b0;
} else if(subDistances[0]>0.001f) {
b0 = 0.001f;
b1 = subDistances[0]-b0;
} else {
b0 = 0f;
b1 = subDistances[0];
}
TreeNode.mpTree = "("+child0.tree+": "+b0+",("+parent.revTrees[1]+","+
subTrees[1]+":"+subDistances[1]+"):"+b1+");";
}
if(Math.abs(TreeNode.halfLength-child1.totalDist)<TreeNode.minDiff) {
TreeNode.minDiff = Math.abs(TreeNode.halfLength-child1.totalDist);
float b0,b1;
if(TreeNode.halfLength>child1.totalDist) {
b0 = TreeNode.halfLength-child1.totalDist;
b1 = subDistances[1]-b0;
} else if(subDistances[1]>0.001f) {
b0 = 0.001f;
b1 = subDistances[1]-b0;
} else {
b0 = 0f;
b1 = subDistances[1];
}
TreeNode.mpTree = "("+child1.tree+": "+b0+",("+parent.revTrees[1]+","+
subTrees[0]+":"+subDistances[0]+"):"+b1+");";
}
child0.findMiddle(1);
child1.findMiddle(0);
} else {
if(Math.abs(TreeNode.halfLength-child0.totalDist)<TreeNode.minDiff) {
TreeNode.minDiff = Math.abs(TreeNode.halfLength-child0.totalDist);
float b0,b1;
if(TreeNode.halfLength>child0.totalDist) {
b0 = TreeNode.halfLength-child0.totalDist;
b1 = subDistances[0]-b0;
} else if(subDistances[0]>0.001f) {
b0 = 0.001f;
b1 = subDistances[0]-b0;
} else {
b0 = 0f;
b1 = subDistances[0];
}
TreeNode.mpTree = "("+child0.tree+": "+b0+",("+parent.revTrees[0]+
","+subTrees[1]+":"+subDistances[1]+"):"+b1+");";
}
if(Math.abs(TreeNode.halfLength-child1.totalDist)<TreeNode.minDiff) {
TreeNode.minDiff = Math.abs(TreeNode.halfLength-child1.totalDist);
float b0,b1;
if(TreeNode.halfLength>child1.totalDist) {
b0 = TreeNode.halfLength-child1.totalDist;
b1 = subDistances[1]-b0;
} else if(subDistances[1]>0.001f) {
b0 = 0.001f;
b1 = subDistances[1]-b0;
} else {
b0 = 0f;
b1 = subDistances[1];
}
TreeNode.mpTree = "("+child1.tree+": "+b0+",("+parent.revTrees[0]+
","+subTrees[0]+":"+subDistances[0]+"):"+b1+")";
}
child0.findMiddle(1);
child1.findMiddle(0);
}
}
}
void printNames() {
if(isLast) {
System.out.println(tree);
} else {
child0.printNames();
child1.printNames();
System.out.println("node: "+totalDist);
}
}
/*
public static void main(String[] args) {
TreeReader2 tr = new TreeReader2();
String tree = tr.readFile(args[0]);
TreeNode root = new TreeNode(tree);
TreeNode.halfLength = root.totalDist/2f;
System.out.println(root.findMiddlePoint());
}
//*/
}
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