Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/tax/IDNode.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package tax;
2
3 import java.util.ArrayList;
4 import java.util.BitSet;
5 import java.util.Locale;
6 import java.util.PriorityQueue;
7
8 import shared.Tools;
9
10 /**
11 * Support class for IDTree.
12 * @author Brian Bushnell
13 * @date July 1, 2016
14 *
15 */
16 public class IDNode implements Comparable<IDNode>{
17
18 public static IDNode makeTree(IDNode[] nodes){
19
20 PriorityQueue<IDNode> heap=new PriorityQueue<IDNode>(nodes.length);
21 ArrayList<IDNode> list=new ArrayList<IDNode>(2*nodes.length);
22 for(IDNode n : nodes){
23 list.add(n);
24 heap.add(n);
25 }
26
27 while(heap.size()>1){
28 IDNode a=heap.poll();
29 // System.err.println("Found A node "+a);
30 if(a.parent==null){
31 IDNode b=nodes[a.maxPos];
32 if(b.parent!=null){
33 // System.err.println("Skipped node "+b);
34 }
35 while(b.parent!=null){
36 b=b.parent;
37 // System.err.println("to parent "+b);
38 }
39 // System.err.println("Found B node "+b);
40 IDNode c=new IDNode(a, b, list.size());
41 list.add(c);
42 heap.add(c);
43 // System.err.println("Made C node "+c);
44 // System.err.println(c.toNewick());
45 }
46
47 // System.err.println();
48 }
49
50 return heap.poll();
51 }
52
53 @Override
54 public int compareTo(IDNode idn) {
55 if(max==idn.max){return number-idn.number;}
56 return max<idn.max ? 1 : -1;
57 }
58
59 public IDNode(double[] array_, int number_, String name_){
60 array=array_;
61 number=number_;
62 name=name_;
63 left=right=null;
64 maxPos=(array.length>0 ? Tools.maxIndex(array) : 0);
65 max=(maxPos>=array.length ? 0 : array[maxPos]);
66 bs=new BitSet(number+1);
67 bs.set(number);
68 }
69
70 double[] shorter(double[] a, double[] b){
71 return a.length<b.length ? a : b;
72 }
73
74 double[] longer(double[] a, double[] b){
75 return a.length<b.length ? b : a;
76 }
77
78 public IDNode(IDNode a, IDNode b, int number_){
79 assert(a!=b) : a+"; "+a.parent+"; "+a.left+"; "+a.right;
80 assert(a.parent==null);
81 assert(b.parent==null);
82 assert(a.max>=b.max);
83
84 number=number_;
85
86 double[] array1=longer(a.array, b.array);
87 double[] array2=shorter(a.array, b.array);
88 assert(array1!=array2) : a.array.length+", "+b.array.length+", "+a.array+", "+b.array;
89
90 bs=new BitSet();
91 bs.or(a.bs);
92 bs.or(b.bs);
93 array=array1.clone();
94 for(int i=0; i<array2.length; i++){
95 array[i]=Tools.max(array[i], array2[i]);
96 }
97 array[a.maxPos]=0;
98 for(int i=0; i<array.length; i++){
99 if(bs.get(i)){array[i]=0;}
100 }
101 maxPos=Tools.maxIndex(array);
102 max=array[maxPos];
103 left=a;
104 right=b;
105 a.parent=b.parent=this;
106 }
107
108 public StringBuilder toNewick(){
109 StringBuilder sb=new StringBuilder();
110 toNewick(sb);
111 return sb;
112 }
113
114 private void toNewick(StringBuilder sb){
115 if(left!=null){
116 sb.append('(');
117 left.toNewick(sb);
118 sb.append(',');
119 right.toNewick(sb);
120 sb.append(')');
121 }
122 if(name!=null){
123 for(int i=0; i<name.length(); i++){
124 char c=name.charAt(i);
125 if(c=='(' || c==')' || c==':' || c==',' || c==';' || Character.isWhitespace(c)){c='_';}
126 sb.append(c);
127 }
128 }
129 // sb.append(String.format(Locale.ROOT, ":%.4f", max));
130 if(parent!=null){
131 sb.append(':');
132
133 double len;
134 if(left==null){
135 len=1-Tools.max(parent.left.max, parent.right.max);
136 }else{
137 len=Tools.max(left.max, right.max)-max;
138 }
139
140 sb.append(String.format(Locale.ROOT, "%.4f", len));
141 // assert(Tools.max(parent.left.max, parent.right.max)-parent.max<0.4) : parent+"\n"+parent.left+"\n"+parent.right+"\n";
142 }
143 }
144
145 @Override
146 public String toString(){
147 return "("+number+/*" "+name+*/" "+String.format(Locale.ROOT, "%.4f", max)+" "+toString(array)+")";
148 }
149
150 private static String toString(double[] array){
151 StringBuilder sb=new StringBuilder();
152 sb.append('[');
153 sb.append(' ');
154 for(double d : array){
155 sb.append(String.format(Locale.ROOT, "%.4f ", d));
156 }
157 sb.append(']');
158 return sb.toString();
159 }
160
161 public String name;
162 public double[] array;
163 public final int number;
164 public final int maxPos;
165 public final double max;
166 public final BitSet bs;
167
168 public IDNode parent;
169 public final IDNode left;
170 public final IDNode right;
171
172 }