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package tax;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Locale;
import java.util.PriorityQueue;
import shared.Tools;
/**
* Support class for IDTree.
* @author Brian Bushnell
* @date July 1, 2016
*
*/
public class IDNode implements Comparable<IDNode>{
public static IDNode makeTree(IDNode[] nodes){
PriorityQueue<IDNode> heap=new PriorityQueue<IDNode>(nodes.length);
ArrayList<IDNode> list=new ArrayList<IDNode>(2*nodes.length);
for(IDNode n : nodes){
list.add(n);
heap.add(n);
}
while(heap.size()>1){
IDNode a=heap.poll();
// System.err.println("Found A node "+a);
if(a.parent==null){
IDNode b=nodes[a.maxPos];
if(b.parent!=null){
// System.err.println("Skipped node "+b);
}
while(b.parent!=null){
b=b.parent;
// System.err.println("to parent "+b);
}
// System.err.println("Found B node "+b);
IDNode c=new IDNode(a, b, list.size());
list.add(c);
heap.add(c);
// System.err.println("Made C node "+c);
// System.err.println(c.toNewick());
}
// System.err.println();
}
return heap.poll();
}
@Override
public int compareTo(IDNode idn) {
if(max==idn.max){return number-idn.number;}
return max<idn.max ? 1 : -1;
}
public IDNode(double[] array_, int number_, String name_){
array=array_;
number=number_;
name=name_;
left=right=null;
maxPos=(array.length>0 ? Tools.maxIndex(array) : 0);
max=(maxPos>=array.length ? 0 : array[maxPos]);
bs=new BitSet(number+1);
bs.set(number);
}
double[] shorter(double[] a, double[] b){
return a.length<b.length ? a : b;
}
double[] longer(double[] a, double[] b){
return a.length<b.length ? b : a;
}
public IDNode(IDNode a, IDNode b, int number_){
assert(a!=b) : a+"; "+a.parent+"; "+a.left+"; "+a.right;
assert(a.parent==null);
assert(b.parent==null);
assert(a.max>=b.max);
number=number_;
double[] array1=longer(a.array, b.array);
double[] array2=shorter(a.array, b.array);
assert(array1!=array2) : a.array.length+", "+b.array.length+", "+a.array+", "+b.array;
bs=new BitSet();
bs.or(a.bs);
bs.or(b.bs);
array=array1.clone();
for(int i=0; i<array2.length; i++){
array[i]=Tools.max(array[i], array2[i]);
}
array[a.maxPos]=0;
for(int i=0; i<array.length; i++){
if(bs.get(i)){array[i]=0;}
}
maxPos=Tools.maxIndex(array);
max=array[maxPos];
left=a;
right=b;
a.parent=b.parent=this;
}
public StringBuilder toNewick(){
StringBuilder sb=new StringBuilder();
toNewick(sb);
return sb;
}
private void toNewick(StringBuilder sb){
if(left!=null){
sb.append('(');
left.toNewick(sb);
sb.append(',');
right.toNewick(sb);
sb.append(')');
}
if(name!=null){
for(int i=0; i<name.length(); i++){
char c=name.charAt(i);
if(c=='(' || c==')' || c==':' || c==',' || c==';' || Character.isWhitespace(c)){c='_';}
sb.append(c);
}
}
// sb.append(String.format(Locale.ROOT, ":%.4f", max));
if(parent!=null){
sb.append(':');
double len;
if(left==null){
len=1-Tools.max(parent.left.max, parent.right.max);
}else{
len=Tools.max(left.max, right.max)-max;
}
sb.append(String.format(Locale.ROOT, "%.4f", len));
// assert(Tools.max(parent.left.max, parent.right.max)-parent.max<0.4) : parent+"\n"+parent.left+"\n"+parent.right+"\n";
}
}
@Override
public String toString(){
return "("+number+/*" "+name+*/" "+String.format(Locale.ROOT, "%.4f", max)+" "+toString(array)+")";
}
private static String toString(double[] array){
StringBuilder sb=new StringBuilder();
sb.append('[');
sb.append(' ');
for(double d : array){
sb.append(String.format(Locale.ROOT, "%.4f ", d));
}
sb.append(']');
return sb.toString();
}
public String name;
public double[] array;
public final int number;
public final int maxPos;
public final double max;
public final BitSet bs;
public IDNode parent;
public final IDNode left;
public final IDNode right;
}
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