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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;
import java.io.File;
import java.io.IOException;
import java.io.FileNotFoundException;
import java.util.ArrayList;
class TreeReader {
float[] distance;
boolean isUnRooted = false;
TreeReader(){
}
// Read a tree from a file and remove branch lengths
//
String readFile(String filename) {
String tree = new String();
ProAlign.log("TreeReader: "+filename);
try {
InFile in = new InFile(filename);
String row = new String();
while((row = in.readLine()) != null) {
tree += row;
}
} catch (Exception e) {}
return tree;
}
// Take a tree and divide it into two subtrees.
// Notice that clustalw root is trifurcating
//
String[] divideTree(String tree) {
// System.out.println("tree "+tree+"\n");
String[] trees = new String[2];
distance = new float[2];
trees[0] = "";
if(tree.endsWith(";")) {
tree = tree.substring(0,tree.length()-1); // remove last ';'
}
tree = tree.substring(1,tree.length()-1); // remove first & last '('
if(tree.charAt(0)!='(') { // only one taxon
String tmp = tree.substring(0,tree.indexOf(","));
trees[0] = tmp.substring(0,tmp.indexOf(":"));
distance[0] = new Float(tmp.substring(tmp.indexOf(":")+1)).floatValue();
boolean trifurc = false;
int open = 0;
for(int j = tree.indexOf(",")+1; j<tree.length(); j++) {
if(tree.charAt(j)=='(') { open++; }
else if(tree.charAt(j)==')') { open--; }
if(open==0 && tree.substring(j).indexOf(",")>0) {
trifurc = true;
}
}
// correction for trifurcating root
if(trifurc) {
isUnRooted = true;
trees[1] = "("+tree.substring(tree.indexOf(",")+1)+")";
distance[0] = distance[0]/2f;
distance[1] = distance[0];
} else {
trees[1] = tree.substring(tree.indexOf(",")+1,tree.lastIndexOf(":"));
tmp = tree.substring(tree.lastIndexOf(":")+1);
distance[1] = new Float(tmp).floatValue();
}
// System.out.println("1o: "+trees[0]+" "+distance[0]+"\n");
// System.out.println("2o: "+trees[1]+" "+distance[1]+"\n");
} else {
int open = 0;
for(int i=0; i<tree.length(); i++) {
// count parentheses that are "open"
if(tree.charAt(i)=='(') { open++; }
else if(tree.charAt(i)==')') { open--; }
trees[0] += ""+tree.charAt(i);
if(open<=0) {
String tmp = tree.substring(i+2,tree.indexOf(",",i+2));
distance[0] = new Float(tmp).floatValue();
boolean trifurc = false;
open = 0;
for(int j = tree.indexOf(",",i+2)+1; j<tree.length(); j++) {
if(tree.charAt(j)=='(') { open++; }
else if(tree.charAt(j)==')') { open--; }
if(open==0 && tree.substring(j).indexOf(",")>0) {
trifurc = true;
}
}
// correction for trifurcating root
if(trifurc) {
isUnRooted = true;
trees[1] = "("+tree.substring(tree.indexOf(",",i+2)+1)+")";
distance[0] = distance[0]/2f;
distance[1] = distance[0];
// System.out.println("1: "+trees[0]+" "+distance[0]+"\n");
// System.out.println("2a: "+trees[1]+" "+distance[1]+"\n");
} else {
tmp = tree.substring(tree.indexOf(",",i+2)+1);
trees[1] = tmp.substring(0,tmp.lastIndexOf(":"));
tmp = tmp.substring(tmp.lastIndexOf(":")+1);
distance[1] = new Float(tmp).floatValue();
// System.out.println("1: "+trees[0]+" "+distance[0]+"\n");
// System.out.println("2b: "+trees[1]+" "+distance[1]+"\n");
}
break;
}
}
}
//System.out.println("0: "+trees[0]+" ["+distance[0]+"]");
//System.out.println("1: "+trees[1]+" ["+distance[1]+"]");
return trees;
}
String[] getAllNodes(String filepath) {
ArrayList nl = new ArrayList();
TreeReader tr = this;
String tree = this.readFile(filepath);
// if(ProAlign.DEBUG) {
// ProAlign.log.println(" reading a list of all the nodes.");
// }
//System.out.println(clustalw);
String[] trees = tr.divideTree(tree);
tr.loopThroughNodes(trees[0],tr,nl);
tr.loopThroughNodes(trees[1],tr,nl);
String[] nodes = new String[nl.size()];
for(int i=0; i<nl.size(); i++) {
nodes[i] = (String) nl.get(i);
}
return nodes;
}
void loopThroughNodes(String tree, TreeReader tr, ArrayList nl) {
if(tree.indexOf(",")>0) {
String[] trees = tr.divideTree(tree);
tr.loopThroughNodes(trees[0],tr,nl);
tr.loopThroughNodes(trees[1],tr,nl);
} else {
nl.add(tree);
//System.out.println(nl.size()+" "+tree);
}
}
// ---DEBUGGING ONLY -->
void loopTreeTest(String tree, TreeReader tr) {
if(tree.indexOf(",")>0) {
String[] trees = tr.divideTree(tree);
tr.loopTreeTest(trees[0],tr);
tr.loopTreeTest(trees[1],tr);
} else {
//System.out.println("l "+tree);
}
}
public static void main(String[] args) {
TreeReader tr = new TreeReader();
String tree = tr.readFile(args[0]);
String[] trees = tr.divideTree(tree);
tr.loopTreeTest(trees[0],tr);
tr.loopTreeTest(trees[1],tr);
System.out.println("OK");
String[] nodes = tr.getAllNodes(args[0]);
for(int i=0; i<nodes.length; i++) {
System.out.println(nodes[i]);
}
}
// <--DEBUGGING ONLY ---
}
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