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comparison libs/commons-math-2.1/docs/apidocs/src-html/org/apache/commons/math/genetics/RandomKey.html @ 13:cbf34dd4d7e6

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commons-math-2.1 added
author dwinter
date Tue, 04 Jan 2011 10:02:07 +0100
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12:970d26a94fb7 13:cbf34dd4d7e6
1 <HTML>
2 <BODY BGCOLOR="white">
3 <PRE>
4 <FONT color="green">001</FONT> /*<a name="line.1"></a>
5 <FONT color="green">002</FONT> * Licensed to the Apache Software Foundation (ASF) under one or more<a name="line.2"></a>
6 <FONT color="green">003</FONT> * contributor license agreements. See the NOTICE file distributed with<a name="line.3"></a>
7 <FONT color="green">004</FONT> * this work for additional information regarding copyright ownership.<a name="line.4"></a>
8 <FONT color="green">005</FONT> * The ASF licenses this file to You under the Apache License, Version 2.0<a name="line.5"></a>
9 <FONT color="green">006</FONT> * (the "License"); you may not use this file except in compliance with<a name="line.6"></a>
10 <FONT color="green">007</FONT> * the License. You may obtain a copy of the License at<a name="line.7"></a>
11 <FONT color="green">008</FONT> *<a name="line.8"></a>
12 <FONT color="green">009</FONT> * http://www.apache.org/licenses/LICENSE-2.0<a name="line.9"></a>
13 <FONT color="green">010</FONT> *<a name="line.10"></a>
14 <FONT color="green">011</FONT> * Unless required by applicable law or agreed to in writing, software<a name="line.11"></a>
15 <FONT color="green">012</FONT> * distributed under the License is distributed on an "AS IS" BASIS,<a name="line.12"></a>
16 <FONT color="green">013</FONT> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.<a name="line.13"></a>
17 <FONT color="green">014</FONT> * See the License for the specific language governing permissions and<a name="line.14"></a>
18 <FONT color="green">015</FONT> * limitations under the License.<a name="line.15"></a>
19 <FONT color="green">016</FONT> */<a name="line.16"></a>
20 <FONT color="green">017</FONT> package org.apache.commons.math.genetics;<a name="line.17"></a>
21 <FONT color="green">018</FONT> <a name="line.18"></a>
22 <FONT color="green">019</FONT> import java.util.ArrayList;<a name="line.19"></a>
23 <FONT color="green">020</FONT> import java.util.Arrays;<a name="line.20"></a>
24 <FONT color="green">021</FONT> import java.util.Collections;<a name="line.21"></a>
25 <FONT color="green">022</FONT> import java.util.Comparator;<a name="line.22"></a>
26 <FONT color="green">023</FONT> import java.util.List;<a name="line.23"></a>
27 <FONT color="green">024</FONT> <a name="line.24"></a>
28 <FONT color="green">025</FONT> /**<a name="line.25"></a>
29 <FONT color="green">026</FONT> * &lt;p&gt;<a name="line.26"></a>
30 <FONT color="green">027</FONT> * Random Key chromosome is used for permutation representation. It is a vector<a name="line.27"></a>
31 <FONT color="green">028</FONT> * of a fixed length of real numbers in [0,1] interval. The index of the i-th<a name="line.28"></a>
32 <FONT color="green">029</FONT> * smallest value in the vector represents an i-th member of the permutation.<a name="line.29"></a>
33 <FONT color="green">030</FONT> * &lt;/p&gt;<a name="line.30"></a>
34 <FONT color="green">031</FONT> *<a name="line.31"></a>
35 <FONT color="green">032</FONT> * &lt;p&gt;<a name="line.32"></a>
36 <FONT color="green">033</FONT> * For example, the random key [0.2, 0.3, 0.8, 0.1] corresponds to the<a name="line.33"></a>
37 <FONT color="green">034</FONT> * permutation of indices (3,0,1,2). If the original (unpermuted) sequence would<a name="line.34"></a>
38 <FONT color="green">035</FONT> * be (a,b,c,d), this would mean the sequence (d,a,b,c).<a name="line.35"></a>
39 <FONT color="green">036</FONT> * &lt;/p&gt;<a name="line.36"></a>
40 <FONT color="green">037</FONT> *<a name="line.37"></a>
41 <FONT color="green">038</FONT> * &lt;p&gt;<a name="line.38"></a>
42 <FONT color="green">039</FONT> * With this representation, common operators like n-point crossover can be<a name="line.39"></a>
43 <FONT color="green">040</FONT> * used, because any such chromosome represents a valid permutation.<a name="line.40"></a>
44 <FONT color="green">041</FONT> * &lt;/p&gt;<a name="line.41"></a>
45 <FONT color="green">042</FONT> *<a name="line.42"></a>
46 <FONT color="green">043</FONT> * &lt;p&gt;<a name="line.43"></a>
47 <FONT color="green">044</FONT> * Since the chromosome (and thus its arrayRepresentation) is immutable, the<a name="line.44"></a>
48 <FONT color="green">045</FONT> * array representation is sorted only once in the constructor.<a name="line.45"></a>
49 <FONT color="green">046</FONT> * &lt;/p&gt;<a name="line.46"></a>
50 <FONT color="green">047</FONT> *<a name="line.47"></a>
51 <FONT color="green">048</FONT> * &lt;p&gt;<a name="line.48"></a>
52 <FONT color="green">049</FONT> * For details, see:<a name="line.49"></a>
53 <FONT color="green">050</FONT> * &lt;ul&gt;<a name="line.50"></a>
54 <FONT color="green">051</FONT> * &lt;li&gt;Bean, J.C.: Genetic algorithms and random keys for sequencing and<a name="line.51"></a>
55 <FONT color="green">052</FONT> * optimization. ORSA Journal on Computing 6 (1994) 154–160&lt;/li&gt;<a name="line.52"></a>
56 <FONT color="green">053</FONT> * &lt;li&gt;Rothlauf, F.: Representations for Genetic and Evolutionary Algorithms.<a name="line.53"></a>
57 <FONT color="green">054</FONT> * Volume 104 of Studies in Fuzziness and Soft Computing. Physica-Verlag,<a name="line.54"></a>
58 <FONT color="green">055</FONT> * Heidelberg (2002)&lt;/li&gt;<a name="line.55"></a>
59 <FONT color="green">056</FONT> * &lt;/ul&gt;<a name="line.56"></a>
60 <FONT color="green">057</FONT> * &lt;/p&gt;<a name="line.57"></a>
61 <FONT color="green">058</FONT> *<a name="line.58"></a>
62 <FONT color="green">059</FONT> * @param &lt;T&gt;<a name="line.59"></a>
63 <FONT color="green">060</FONT> * type of the permuted objects<a name="line.60"></a>
64 <FONT color="green">061</FONT> * @since 2.0<a name="line.61"></a>
65 <FONT color="green">062</FONT> * @version $Revision: 811685 $ $Date: 2009-09-05 13:36:48 -0400 (Sat, 05 Sep 2009) $<a name="line.62"></a>
66 <FONT color="green">063</FONT> */<a name="line.63"></a>
67 <FONT color="green">064</FONT> public abstract class RandomKey&lt;T&gt; extends AbstractListChromosome&lt;Double&gt; implements PermutationChromosome&lt;T&gt; {<a name="line.64"></a>
68 <FONT color="green">065</FONT> <a name="line.65"></a>
69 <FONT color="green">066</FONT> /**<a name="line.66"></a>
70 <FONT color="green">067</FONT> * Cache of sorted representation (unmodifiable).<a name="line.67"></a>
71 <FONT color="green">068</FONT> */<a name="line.68"></a>
72 <FONT color="green">069</FONT> private final List&lt;Double&gt; sortedRepresentation;<a name="line.69"></a>
73 <FONT color="green">070</FONT> <a name="line.70"></a>
74 <FONT color="green">071</FONT> /**<a name="line.71"></a>
75 <FONT color="green">072</FONT> * Base sequence [0,1,...,n-1], permuted accorting to the representation (unmodifiable).<a name="line.72"></a>
76 <FONT color="green">073</FONT> */<a name="line.73"></a>
77 <FONT color="green">074</FONT> private final List&lt;Integer&gt; baseSeqPermutation;<a name="line.74"></a>
78 <FONT color="green">075</FONT> <a name="line.75"></a>
79 <FONT color="green">076</FONT> /**<a name="line.76"></a>
80 <FONT color="green">077</FONT> * Constructor.<a name="line.77"></a>
81 <FONT color="green">078</FONT> *<a name="line.78"></a>
82 <FONT color="green">079</FONT> * @param representation list of [0,1] values representing the permutation<a name="line.79"></a>
83 <FONT color="green">080</FONT> */<a name="line.80"></a>
84 <FONT color="green">081</FONT> public RandomKey(List&lt;Double&gt; representation) {<a name="line.81"></a>
85 <FONT color="green">082</FONT> super(representation);<a name="line.82"></a>
86 <FONT color="green">083</FONT> // store the sorted representation<a name="line.83"></a>
87 <FONT color="green">084</FONT> List&lt;Double&gt; sortedRepr = new ArrayList&lt;Double&gt; (getRepresentation());<a name="line.84"></a>
88 <FONT color="green">085</FONT> Collections.sort(sortedRepr);<a name="line.85"></a>
89 <FONT color="green">086</FONT> sortedRepresentation = Collections.unmodifiableList(sortedRepr);<a name="line.86"></a>
90 <FONT color="green">087</FONT> // store the permutation of [0,1,...,n-1] list for toString() and isSame() methods<a name="line.87"></a>
91 <FONT color="green">088</FONT> baseSeqPermutation = Collections.unmodifiableList(<a name="line.88"></a>
92 <FONT color="green">089</FONT> decodeGeneric(baseSequence(getLength()), getRepresentation(), sortedRepresentation)<a name="line.89"></a>
93 <FONT color="green">090</FONT> );<a name="line.90"></a>
94 <FONT color="green">091</FONT> }<a name="line.91"></a>
95 <FONT color="green">092</FONT> <a name="line.92"></a>
96 <FONT color="green">093</FONT> /**<a name="line.93"></a>
97 <FONT color="green">094</FONT> * Constructor.<a name="line.94"></a>
98 <FONT color="green">095</FONT> *<a name="line.95"></a>
99 <FONT color="green">096</FONT> * @param representation array of [0,1] values representing the permutation<a name="line.96"></a>
100 <FONT color="green">097</FONT> */<a name="line.97"></a>
101 <FONT color="green">098</FONT> public RandomKey(Double[] representation) {<a name="line.98"></a>
102 <FONT color="green">099</FONT> this(Arrays.asList(representation));<a name="line.99"></a>
103 <FONT color="green">100</FONT> }<a name="line.100"></a>
104 <FONT color="green">101</FONT> <a name="line.101"></a>
105 <FONT color="green">102</FONT> /**<a name="line.102"></a>
106 <FONT color="green">103</FONT> * {@inheritDoc}<a name="line.103"></a>
107 <FONT color="green">104</FONT> */<a name="line.104"></a>
108 <FONT color="green">105</FONT> public List&lt;T&gt; decode(List&lt;T&gt; sequence) {<a name="line.105"></a>
109 <FONT color="green">106</FONT> return decodeGeneric(sequence, getRepresentation(), sortedRepresentation);<a name="line.106"></a>
110 <FONT color="green">107</FONT> }<a name="line.107"></a>
111 <FONT color="green">108</FONT> <a name="line.108"></a>
112 <FONT color="green">109</FONT> /**<a name="line.109"></a>
113 <FONT color="green">110</FONT> * Decodes a permutation represented by &lt;code&gt;representation&lt;/code&gt; and<a name="line.110"></a>
114 <FONT color="green">111</FONT> * returns a (generic) list with the permuted values.<a name="line.111"></a>
115 <FONT color="green">112</FONT> *<a name="line.112"></a>
116 <FONT color="green">113</FONT> * @param &lt;S&gt; generic type of the sequence values<a name="line.113"></a>
117 <FONT color="green">114</FONT> * @param sequence the unpermuted sequence<a name="line.114"></a>
118 <FONT color="green">115</FONT> * @param representation representation of the permutation ([0,1] vector)<a name="line.115"></a>
119 <FONT color="green">116</FONT> * @param sortedRepr sorted &lt;code&gt;representation&lt;/code&gt;<a name="line.116"></a>
120 <FONT color="green">117</FONT> * @return list with the sequence values permuted according to the representation<a name="line.117"></a>
121 <FONT color="green">118</FONT> */<a name="line.118"></a>
122 <FONT color="green">119</FONT> private static &lt;S&gt; List&lt;S&gt; decodeGeneric(List&lt;S&gt; sequence, List&lt;Double&gt; representation, List&lt;Double&gt; sortedRepr) {<a name="line.119"></a>
123 <FONT color="green">120</FONT> int l = sequence.size();<a name="line.120"></a>
124 <FONT color="green">121</FONT> <a name="line.121"></a>
125 <FONT color="green">122</FONT> if (representation.size() != l) {<a name="line.122"></a>
126 <FONT color="green">123</FONT> throw new IllegalArgumentException(String.format("Length of sequence for decoding (%s) has to be equal to the length of the RandomKey (%s)", l, representation.size()));<a name="line.123"></a>
127 <FONT color="green">124</FONT> }<a name="line.124"></a>
128 <FONT color="green">125</FONT> if (representation.size() != sortedRepr.size()) {<a name="line.125"></a>
129 <FONT color="green">126</FONT> throw new IllegalArgumentException(String.format("Representation and sortedRepr must have same sizes, %d != %d", representation.size(), sortedRepr.size()));<a name="line.126"></a>
130 <FONT color="green">127</FONT> }<a name="line.127"></a>
131 <FONT color="green">128</FONT> <a name="line.128"></a>
132 <FONT color="green">129</FONT> List&lt;Double&gt; reprCopy = new ArrayList&lt;Double&gt; (representation);// do not modify the orig. representation<a name="line.129"></a>
133 <FONT color="green">130</FONT> <a name="line.130"></a>
134 <FONT color="green">131</FONT> // now find the indices in the original repr and use them for permuting<a name="line.131"></a>
135 <FONT color="green">132</FONT> List&lt;S&gt; res = new ArrayList&lt;S&gt; (l);<a name="line.132"></a>
136 <FONT color="green">133</FONT> for (int i=0; i&lt;l; i++) {<a name="line.133"></a>
137 <FONT color="green">134</FONT> int index = reprCopy.indexOf(sortedRepr.get(i));<a name="line.134"></a>
138 <FONT color="green">135</FONT> res.add(sequence.get(index));<a name="line.135"></a>
139 <FONT color="green">136</FONT> reprCopy.set(index, null);<a name="line.136"></a>
140 <FONT color="green">137</FONT> }<a name="line.137"></a>
141 <FONT color="green">138</FONT> return res;<a name="line.138"></a>
142 <FONT color="green">139</FONT> }<a name="line.139"></a>
143 <FONT color="green">140</FONT> <a name="line.140"></a>
144 <FONT color="green">141</FONT> /**<a name="line.141"></a>
145 <FONT color="green">142</FONT> * Returns &lt;code&gt;true&lt;/code&gt; iff &lt;code&gt;another&lt;/code&gt; is a RandomKey and<a name="line.142"></a>
146 <FONT color="green">143</FONT> * encodes the same permutation.<a name="line.143"></a>
147 <FONT color="green">144</FONT> *<a name="line.144"></a>
148 <FONT color="green">145</FONT> * @param another chromosome to compare<a name="line.145"></a>
149 <FONT color="green">146</FONT> * @return true iff chromosomes encode the same permutation<a name="line.146"></a>
150 <FONT color="green">147</FONT> */<a name="line.147"></a>
151 <FONT color="green">148</FONT> @Override<a name="line.148"></a>
152 <FONT color="green">149</FONT> protected boolean isSame(Chromosome another) {<a name="line.149"></a>
153 <FONT color="green">150</FONT> // type check<a name="line.150"></a>
154 <FONT color="green">151</FONT> if (! (another instanceof RandomKey&lt;?&gt;))<a name="line.151"></a>
155 <FONT color="green">152</FONT> return false;<a name="line.152"></a>
156 <FONT color="green">153</FONT> RandomKey&lt;?&gt; anotherRk = (RandomKey&lt;?&gt;) another;<a name="line.153"></a>
157 <FONT color="green">154</FONT> // size check<a name="line.154"></a>
158 <FONT color="green">155</FONT> if (getLength() != anotherRk.getLength())<a name="line.155"></a>
159 <FONT color="green">156</FONT> return false;<a name="line.156"></a>
160 <FONT color="green">157</FONT> <a name="line.157"></a>
161 <FONT color="green">158</FONT> // two different representations can still encode the same permutation<a name="line.158"></a>
162 <FONT color="green">159</FONT> // the ordering is what counts<a name="line.159"></a>
163 <FONT color="green">160</FONT> List&lt;Integer&gt; thisPerm = this.baseSeqPermutation;<a name="line.160"></a>
164 <FONT color="green">161</FONT> List&lt;Integer&gt; anotherPerm = anotherRk.baseSeqPermutation;<a name="line.161"></a>
165 <FONT color="green">162</FONT> <a name="line.162"></a>
166 <FONT color="green">163</FONT> for (int i=0; i&lt;getLength(); i++) {<a name="line.163"></a>
167 <FONT color="green">164</FONT> if (thisPerm.get(i) != anotherPerm.get(i))<a name="line.164"></a>
168 <FONT color="green">165</FONT> return false;<a name="line.165"></a>
169 <FONT color="green">166</FONT> }<a name="line.166"></a>
170 <FONT color="green">167</FONT> // the permutations are the same<a name="line.167"></a>
171 <FONT color="green">168</FONT> return true;<a name="line.168"></a>
172 <FONT color="green">169</FONT> }<a name="line.169"></a>
173 <FONT color="green">170</FONT> <a name="line.170"></a>
174 <FONT color="green">171</FONT> /**<a name="line.171"></a>
175 <FONT color="green">172</FONT> * {@inheritDoc}<a name="line.172"></a>
176 <FONT color="green">173</FONT> */<a name="line.173"></a>
177 <FONT color="green">174</FONT> @Override<a name="line.174"></a>
178 <FONT color="green">175</FONT> protected void checkValidity(java.util.List&lt;Double&gt; chromosomeRepresentation) throws InvalidRepresentationException {<a name="line.175"></a>
179 <FONT color="green">176</FONT> for (double val : chromosomeRepresentation) {<a name="line.176"></a>
180 <FONT color="green">177</FONT> if (val &lt; 0 || val &gt; 1) {<a name="line.177"></a>
181 <FONT color="green">178</FONT> throw new InvalidRepresentationException("Values of representation must be in [0,1] interval");<a name="line.178"></a>
182 <FONT color="green">179</FONT> }<a name="line.179"></a>
183 <FONT color="green">180</FONT> }<a name="line.180"></a>
184 <FONT color="green">181</FONT> }<a name="line.181"></a>
185 <FONT color="green">182</FONT> <a name="line.182"></a>
186 <FONT color="green">183</FONT> <a name="line.183"></a>
187 <FONT color="green">184</FONT> /**<a name="line.184"></a>
188 <FONT color="green">185</FONT> * Generates a representation corresponding to a random permutation of<a name="line.185"></a>
189 <FONT color="green">186</FONT> * length l which can be passed to the RandomKey constructor.<a name="line.186"></a>
190 <FONT color="green">187</FONT> *<a name="line.187"></a>
191 <FONT color="green">188</FONT> * @param l<a name="line.188"></a>
192 <FONT color="green">189</FONT> * length of the permutation<a name="line.189"></a>
193 <FONT color="green">190</FONT> * @return representation of a random permutation<a name="line.190"></a>
194 <FONT color="green">191</FONT> */<a name="line.191"></a>
195 <FONT color="green">192</FONT> public static final List&lt;Double&gt; randomPermutation(int l) {<a name="line.192"></a>
196 <FONT color="green">193</FONT> List&lt;Double&gt; repr = new ArrayList&lt;Double&gt;(l);<a name="line.193"></a>
197 <FONT color="green">194</FONT> for (int i=0; i&lt;l; i++) {<a name="line.194"></a>
198 <FONT color="green">195</FONT> repr.add(GeneticAlgorithm.getRandomGenerator().nextDouble());<a name="line.195"></a>
199 <FONT color="green">196</FONT> }<a name="line.196"></a>
200 <FONT color="green">197</FONT> return repr;<a name="line.197"></a>
201 <FONT color="green">198</FONT> }<a name="line.198"></a>
202 <FONT color="green">199</FONT> <a name="line.199"></a>
203 <FONT color="green">200</FONT> /**<a name="line.200"></a>
204 <FONT color="green">201</FONT> * Generates a representation corresponding to an identity permutation of<a name="line.201"></a>
205 <FONT color="green">202</FONT> * length l which can be passed to the RandomKey constructor.<a name="line.202"></a>
206 <FONT color="green">203</FONT> *<a name="line.203"></a>
207 <FONT color="green">204</FONT> * @param l<a name="line.204"></a>
208 <FONT color="green">205</FONT> * length of the permutation<a name="line.205"></a>
209 <FONT color="green">206</FONT> * @return representation of an identity permutation<a name="line.206"></a>
210 <FONT color="green">207</FONT> */<a name="line.207"></a>
211 <FONT color="green">208</FONT> public static final List&lt;Double&gt; identityPermutation(int l) {<a name="line.208"></a>
212 <FONT color="green">209</FONT> List&lt;Double&gt; repr = new ArrayList&lt;Double&gt;(l);<a name="line.209"></a>
213 <FONT color="green">210</FONT> for (int i=0; i&lt;l; i++) {<a name="line.210"></a>
214 <FONT color="green">211</FONT> repr.add((double)i/l);<a name="line.211"></a>
215 <FONT color="green">212</FONT> }<a name="line.212"></a>
216 <FONT color="green">213</FONT> return repr;<a name="line.213"></a>
217 <FONT color="green">214</FONT> }<a name="line.214"></a>
218 <FONT color="green">215</FONT> <a name="line.215"></a>
219 <FONT color="green">216</FONT> /**<a name="line.216"></a>
220 <FONT color="green">217</FONT> * Generates a representation of a permutation corresponding to the<a name="line.217"></a>
221 <FONT color="green">218</FONT> * &lt;code&gt;data&lt;/code&gt; sorted by &lt;code&gt;comparator&lt;/code&gt;. The<a name="line.218"></a>
222 <FONT color="green">219</FONT> * &lt;code&gt;data&lt;/code&gt; is not modified during the process.<a name="line.219"></a>
223 <FONT color="green">220</FONT> *<a name="line.220"></a>
224 <FONT color="green">221</FONT> * This is useful if you want to inject some permutations to the initial<a name="line.221"></a>
225 <FONT color="green">222</FONT> * population.<a name="line.222"></a>
226 <FONT color="green">223</FONT> *<a name="line.223"></a>
227 <FONT color="green">224</FONT> * @param &lt;S&gt; type of the data<a name="line.224"></a>
228 <FONT color="green">225</FONT> * @param data list of data determining the order<a name="line.225"></a>
229 <FONT color="green">226</FONT> * @param comparator how the data will be compared<a name="line.226"></a>
230 <FONT color="green">227</FONT> * @return list representation of the permutation corresponding to the parameters<a name="line.227"></a>
231 <FONT color="green">228</FONT> */<a name="line.228"></a>
232 <FONT color="green">229</FONT> public static &lt;S&gt; List&lt;Double&gt; comparatorPermutation(List&lt;S&gt; data, Comparator&lt;S&gt; comparator) {<a name="line.229"></a>
233 <FONT color="green">230</FONT> List&lt;S&gt; sortedData = new ArrayList&lt;S&gt; (data);<a name="line.230"></a>
234 <FONT color="green">231</FONT> Collections.sort(sortedData, comparator);<a name="line.231"></a>
235 <FONT color="green">232</FONT> <a name="line.232"></a>
236 <FONT color="green">233</FONT> return inducedPermutation(data, sortedData);<a name="line.233"></a>
237 <FONT color="green">234</FONT> }<a name="line.234"></a>
238 <FONT color="green">235</FONT> <a name="line.235"></a>
239 <FONT color="green">236</FONT> /**<a name="line.236"></a>
240 <FONT color="green">237</FONT> * Generates a representation of a permutation corresponding to a<a name="line.237"></a>
241 <FONT color="green">238</FONT> * permutation which yields &lt;code&gt;permutedData&lt;/code&gt; when applied to<a name="line.238"></a>
242 <FONT color="green">239</FONT> * &lt;code&gt;originalData&lt;/code&gt;.<a name="line.239"></a>
243 <FONT color="green">240</FONT> *<a name="line.240"></a>
244 <FONT color="green">241</FONT> * This method can be viewed as an inverse to {@link #decode(List)}.<a name="line.241"></a>
245 <FONT color="green">242</FONT> *<a name="line.242"></a>
246 <FONT color="green">243</FONT> * @param &lt;S&gt; type of the data<a name="line.243"></a>
247 <FONT color="green">244</FONT> * @param originalData the original, unpermuted data<a name="line.244"></a>
248 <FONT color="green">245</FONT> * @param permutedData the data, somehow permuted<a name="line.245"></a>
249 <FONT color="green">246</FONT> * @return representation of a permutation corresponding to the permutation &lt;code&gt;originalData -&gt; permutedData&lt;/code&gt;<a name="line.246"></a>
250 <FONT color="green">247</FONT> * @throws IllegalArgumentException iff the &lt;code&gt;permutedData&lt;/code&gt; and &lt;code&gt;originalData&lt;/code&gt; contains different data<a name="line.247"></a>
251 <FONT color="green">248</FONT> */<a name="line.248"></a>
252 <FONT color="green">249</FONT> public static &lt;S&gt; List&lt;Double&gt; inducedPermutation(List&lt;S&gt; originalData, List&lt;S&gt; permutedData) throws IllegalArgumentException {<a name="line.249"></a>
253 <FONT color="green">250</FONT> if (originalData.size() != permutedData.size()) {<a name="line.250"></a>
254 <FONT color="green">251</FONT> throw new IllegalArgumentException("originalData and permutedData must have same length");<a name="line.251"></a>
255 <FONT color="green">252</FONT> }<a name="line.252"></a>
256 <FONT color="green">253</FONT> int l = originalData.size();<a name="line.253"></a>
257 <FONT color="green">254</FONT> <a name="line.254"></a>
258 <FONT color="green">255</FONT> List&lt;S&gt; origDataCopy = new ArrayList&lt;S&gt; (originalData);<a name="line.255"></a>
259 <FONT color="green">256</FONT> <a name="line.256"></a>
260 <FONT color="green">257</FONT> Double[] res = new Double[l];<a name="line.257"></a>
261 <FONT color="green">258</FONT> for (int i=0; i&lt;l; i++) {<a name="line.258"></a>
262 <FONT color="green">259</FONT> int index = origDataCopy.indexOf(permutedData.get(i));<a name="line.259"></a>
263 <FONT color="green">260</FONT> if (index == -1) {<a name="line.260"></a>
264 <FONT color="green">261</FONT> throw new IllegalArgumentException("originalData and permutedData must contain the same objects.");<a name="line.261"></a>
265 <FONT color="green">262</FONT> }<a name="line.262"></a>
266 <FONT color="green">263</FONT> res[index] = (double) i / l;<a name="line.263"></a>
267 <FONT color="green">264</FONT> origDataCopy.set(index, null);<a name="line.264"></a>
268 <FONT color="green">265</FONT> }<a name="line.265"></a>
269 <FONT color="green">266</FONT> return Arrays.asList(res);<a name="line.266"></a>
270 <FONT color="green">267</FONT> }<a name="line.267"></a>
271 <FONT color="green">268</FONT> <a name="line.268"></a>
272 <FONT color="green">269</FONT> /**<a name="line.269"></a>
273 <FONT color="green">270</FONT> * {@inheritDoc}<a name="line.270"></a>
274 <FONT color="green">271</FONT> */<a name="line.271"></a>
275 <FONT color="green">272</FONT> @Override<a name="line.272"></a>
276 <FONT color="green">273</FONT> public String toString() {<a name="line.273"></a>
277 <FONT color="green">274</FONT> return String.format("(f=%s pi=(%s))", getFitness(), baseSeqPermutation);<a name="line.274"></a>
278 <FONT color="green">275</FONT> }<a name="line.275"></a>
279 <FONT color="green">276</FONT> <a name="line.276"></a>
280 <FONT color="green">277</FONT> /**<a name="line.277"></a>
281 <FONT color="green">278</FONT> * Helper for constructor. Generates a list of natural numbers (0,1,...,l-1).<a name="line.278"></a>
282 <FONT color="green">279</FONT> *<a name="line.279"></a>
283 <FONT color="green">280</FONT> * @param l length of list to generate<a name="line.280"></a>
284 <FONT color="green">281</FONT> * @return list of integers from 0 to l-1<a name="line.281"></a>
285 <FONT color="green">282</FONT> */<a name="line.282"></a>
286 <FONT color="green">283</FONT> private static List&lt;Integer&gt; baseSequence(int l) {<a name="line.283"></a>
287 <FONT color="green">284</FONT> List&lt;Integer&gt; baseSequence = new ArrayList&lt;Integer&gt; (l);<a name="line.284"></a>
288 <FONT color="green">285</FONT> for (int i=0; i&lt;l; i++) {<a name="line.285"></a>
289 <FONT color="green">286</FONT> baseSequence.add(i);<a name="line.286"></a>
290 <FONT color="green">287</FONT> }<a name="line.287"></a>
291 <FONT color="green">288</FONT> return baseSequence;<a name="line.288"></a>
292 <FONT color="green">289</FONT> }<a name="line.289"></a>
293 <FONT color="green">290</FONT> }<a name="line.290"></a>
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