doc/jcgp/backend/population/Chromosome.html


1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (1.8.0_05) on Tue May 06 14:28:06 BST 2014 -->
<title>Chromosome</title>
<meta name="date" content="2014-05-06">
<link rel="stylesheet" type="text/css" href="../../../stylesheet.css" title="Style">
<script type="text/javascript" src="../../../script.js"></script>
</head>
<body>
<script type="text/javascript"><!--
    try {
        if (location.href.indexOf('is-external=true') == -1) {
            parent.document.title="Chromosome";
        }
    }
    catch(err) {
    }
//-->
var methods = {"i0":10,"i1":10,"i2":10,"i3":10,"i4":10,"i5":10,"i6":10,"i7":10,"i8":10,"i9":10,"i10":10,"i11":10,"i12":10,"i13":10,"i14":10,"i15":10,"i16":10,"i17":10};
var tabs = {65535:["t0","All Methods"],2:["t2","Instance Methods"],8:["t4","Concrete Methods"]};
var altColor = "altColor";
var rowColor = "rowColor";
var tableTab = "tableTab";
var activeTableTab = "activeTableTab";
</script>
<noscript>
<div>JavaScript is disabled on your browser.</div>
</noscript>
<!-- ========= START OF TOP NAVBAR ======= -->
<div class="topNav"><a name="navbar.top">
<!--   -->
</a>
<div class="skipNav"><a href="#skip.navbar.top" title="Skip navigation links">Skip navigation links</a></div>
<a name="navbar.top.firstrow">
<!--   -->
</a>
<ul class="navList" title="Navigation">
<li><a href="../../../overview-summary.html">Overview</a></li>
<li><a href="package-summary.html">Package</a></li>
<li class="navBarCell1Rev">Class</li>
<li><a href="class-use/Chromosome.html">Use</a></li>
<li><a href="package-tree.html">Tree</a></li>
<li><a href="../../../deprecated-list.html">Deprecated</a></li>
<li><a href="../../../index-files/index-1.html">Index</a></li>
<li><a href="../../../help-doc.html">Help</a></li>
</ul>
</div>
<div class="subNav">
<ul class="navList">
<li>Prev&nbsp;Class</li>
<li><a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
</ul>
<ul class="navList">
<li><a href="../../../index.html?jcgp/backend/population/Chromosome.html" target="_top">Frames</a></li>
<li><a href="Chromosome.html" target="_top">No&nbsp;Frames</a></li>
</ul>
<ul class="navList" id="allclasses_navbar_top">
<li><a href="../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
</ul>
<div>
<script type="text/javascript"><!--
  allClassesLink = document.getElementById("allclasses_navbar_top");
  if(window==top) {
    allClassesLink.style.display = "block";
  }
  else {
    allClassesLink.style.display = "none";
  }
  //-->
</script>
</div>
<div>
<ul class="subNavList">
<li>Summary:&nbsp;</li>
<li>Nested&nbsp;|&nbsp;</li>
<li>Field&nbsp;|&nbsp;</li>
<li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
<li><a href="#method.summary">Method</a></li>
</ul>
<ul class="subNavList">
<li>Detail:&nbsp;</li>
<li>Field&nbsp;|&nbsp;</li>
<li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
<li><a href="#method.detail">Method</a></li>
</ul>
</div>
<a name="skip.navbar.top">
<!--   -->
</a></div>
<!-- ========= END OF TOP NAVBAR ========= -->
<!-- ======== START OF CLASS DATA ======== -->
<div class="header">
<div class="subTitle">jcgp.backend.population</div>
<h2 title="Class Chromosome" class="title">Class Chromosome</h2>
</div>
<div class="contentContainer">
<ul class="inheritance">
<li>java.lang.Object</li>
<li>
<ul class="inheritance">
<li>jcgp.backend.population.Chromosome</li>
</ul>
</li>
</ul>
<div class="description">
<ul class="blockList">
<li class="blockList">
<dl>
<dt>All Implemented Interfaces:</dt>
<dd>java.lang.Comparable&lt;<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&gt;</dd>
</dl>
<hr>
<br>
<pre>public class <span class="typeNameLabel">Chromosome</span>
extends java.lang.Object
implements java.lang.Comparable&lt;<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&gt;</pre>
<div class="block">This class encapsulates a CGP chromosome.
 <br><br>
 A chromosome contains a matrix of nodes and arrays of inputs and outputs.
 These elements are all interconnected, and actually form the chromosome
 network itself. Individual nodes can be retrieved using <code>getNode()</code>
 which requires the row and column to be specified. The same works for
 inputs and outputs using the associated getters, in which case only the
 index is necessary.
 <br><br>
 In evolutionary computation it is often necessary to make copies of 
 chromosomes; this can be accomplished in JCGP in two ways. The recommended
 way to do this is using <code>copyChromosome()</code> in <code>Population</code>, but alternatively
 it can be done by using the <code>Chromosome</code> copy constructor and specifying the
 object to copy from, or by using the <code>copyGenes()</code> method. 
 <br><br>
 To illustrate this, given two chromosomes, chr1 and chr2, the following code:
 <br><br>
 <code>
 chr1.copyGenes(chr2);
 </code><br><br>
 will modify all of chr1's connections and functions to match those of chr2, without
 creating a new instance. In contrast, 
 <br><br>
 <code>
 chr1 = new Chromosome(chr2);
 </code><br><br>
 creates a new instance of chromosome which is identical to chr2 and assigns it to chr1,
 meaning any old references to chr1 that are not updated will still refer to a chromosome
 that is not identical to chr2. In practice, the most reliable way is to use the copy method
 in <code>Population</code>. Assuming chr1 and chr2 are indexed 1 and 2 in <code>population</code> respectively,
 <br><br>
 population.copyChromosome(2, 1);
 <br><br>
 will copy chr2 into chr1 without creating new instances or requiring access to the underlying
 chromosome array. <code>Chromosome</code> offers a variety of methods to compare chromosomes as well, 
 such as <code>compareGenesTo()</code> and <code>compareActiveGenesTo()</code>. <code>Comparable</code> is implemented
 to compare fitness value, meaning <code>compareTo()</code> returns a value depending the relative fitness
 of the compared chromosomes.
 <br><br>
 In order to set the chromosome's input values for decoding, <code>setInputs()</code> should be used. A few 
 utility methods are provided in order to retrieve random elements from the chromosome, which are used
 internally to initialise with random connections but also externally by mutators when performing 
 mutations.</div>
<dl>
<dt><span class="simpleTagLabel">Author:</span></dt>
<dd>Eduardo Pedroni</dd>
</dl>
</li>
</ul>
</div>
<div class="summary">
<ul class="blockList">
<li class="blockList">
<!-- ======== CONSTRUCTOR SUMMARY ======== -->
<ul class="blockList">
<li class="blockList"><a name="constructor.summary">
<!--   -->
</a>
<h3>Constructor Summary</h3>
<table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
<tr>
<th class="colOne" scope="col">Constructor and Description</th>
</tr>
<tr class="altColor">
<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#Chromosome-jcgp.backend.population.Chromosome-">Chromosome</a></span>(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;clone)</code>
<div class="block">Copy constructor.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#Chromosome-jcgp.backend.resources.Resources-">Chromosome</a></span>(<a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</code>
<div class="block">Initialise a chromosome with the specified parameters.</div>
</td>
</tr>
</table>
</li>
</ul>
<!-- ========== METHOD SUMMARY =========== -->
<ul class="blockList">
<li class="blockList"><a name="method.summary">
<!--   -->
</a>
<h3>Method Summary</h3>
<table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
<caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
<tr>
<th class="colFirst" scope="col">Modifier and Type</th>
<th class="colLast" scope="col">Method and Description</th>
</tr>
<tr id="i0" class="altColor">
<td class="colFirst"><code>boolean</code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#compareActiveGenesTo-jcgp.backend.population.Chromosome-">compareActiveGenesTo</a></span>(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome)</code>
<div class="block">Does the same as <code>compareGenesto()</code> but only looks
 at the active portion of the chromosome.</div>
</td>
</tr>
<tr id="i1" class="rowColor">
<td class="colFirst"><code>boolean</code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#compareGenesTo-jcgp.backend.population.Chromosome-">compareGenesTo</a></span>(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome)</code>
<div class="block">Performs a deep comparison between this chromosome and the provided one.</div>
</td>
</tr>
<tr id="i2" class="altColor">
<td class="colFirst"><code>int</code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#compareTo-jcgp.backend.population.Chromosome-">compareTo</a></span>(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;o)</code>&nbsp;</td>
</tr>
<tr id="i3" class="rowColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#copyGenes-jcgp.backend.population.Chromosome-">copyGenes</a></span>(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;clone)</code>
<div class="block">Creates a deep copy of the specified chromosome in the
 this instance.</div>
</td>
</tr>
<tr id="i4" class="altColor">
<td class="colFirst"><code>java.util.ArrayList&lt;<a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>&gt;</code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getActiveNodes--">getActiveNodes</a></span>()</code>
<div class="block">This method computes a list of active nodes (if necessary) and returns it.</div>
</td>
</tr>
<tr id="i5" class="rowColor">
<td class="colFirst"><code>double</code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getFitness--">getFitness</a></span>()</code>&nbsp;</td>
</tr>
<tr id="i6" class="altColor">
<td class="colFirst"><code><a href="../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a></code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getInput-int-">getInput</a></span>(int&nbsp;index)</code>
<div class="block">Returns a reference to the indexed input.</div>
</td>
</tr>
<tr id="i7" class="rowColor">
<td class="colFirst"><code><a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a></code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getNode-int-int-">getNode</a></span>(int&nbsp;row,
       int&nbsp;column)</code>
<div class="block">Returns a reference to any node, addressed by row and column.</div>
</td>
</tr>
<tr id="i8" class="altColor">
<td class="colFirst"><code><a href="../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a></code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getOutput-int-">getOutput</a></span>(int&nbsp;index)</code>
<div class="block">Returns a reference to the indexed output.</div>
</td>
</tr>
<tr id="i9" class="rowColor">
<td class="colFirst"><code><a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getRandomConnection--">getRandomConnection</a></span>()</code>
<div class="block">This method will pick a completely random connection, independently
 of levels back, including inputs.</div>
</td>
</tr>
<tr id="i10" class="altColor">
<td class="colFirst"><code><a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a></code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getRandomConnection-int-">getRandomConnection</a></span>(int&nbsp;column)</code>
<div class="block">Returns a random allowed connection respecting levels back.<br>
 This method may always pick inputs, as they can be picked
 regardless of the column.</div>
</td>
</tr>
<tr id="i11" class="rowColor">
<td class="colFirst"><code><a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a></code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getRandomMutable--">getRandomMutable</a></span>()</code>
<div class="block">This method is useful for mutating chromosomes.</div>
</td>
</tr>
<tr id="i12" class="altColor">
<td class="colFirst"><code><a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a></code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#getResources--">getResources</a></span>()</code>&nbsp;</td>
</tr>
<tr id="i13" class="rowColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#printNodes--">printNodes</a></span>()</code>
<div class="block">Iterates through the nodes and prints all connections and functions.</div>
</td>
</tr>
<tr id="i14" class="altColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#recomputeActiveNodes--">recomputeActiveNodes</a></span>()</code>
<div class="block">This causes the list of active nodes to be recomputed lazily (once it is actually requested).</div>
</td>
</tr>
<tr id="i15" class="rowColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#reinitialiseConnections--">reinitialiseConnections</a></span>()</code>
<div class="block">Sets random connections and functions across the entire
 chromosome.</div>
</td>
</tr>
<tr id="i16" class="altColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#setFitness-double-">setFitness</a></span>(double&nbsp;newFitness)</code>
<div class="block">Sets the fitness of the chromosome.</div>
</td>
</tr>
<tr id="i17" class="rowColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><span class="memberNameLink"><a href="../../../jcgp/backend/population/Chromosome.html#setInputs-java.lang.Object...-">setInputs</a></span>(java.lang.Object...&nbsp;values)</code>
<div class="block">Loops through the inputs and sets the specified values,
 so that evaluations can be performed.</div>
</td>
</tr>
</table>
<ul class="blockList">
<li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
<!--   -->
</a>
<h3>Methods inherited from class&nbsp;java.lang.Object</h3>
<code>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
<div class="details">
<ul class="blockList">
<li class="blockList">
<!-- ========= CONSTRUCTOR DETAIL ======== -->
<ul class="blockList">
<li class="blockList"><a name="constructor.detail">
<!--   -->
</a>
<h3>Constructor Detail</h3>
<a name="Chromosome-jcgp.backend.resources.Resources-">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>Chromosome</h4>
<pre>public&nbsp;Chromosome(<a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;resources)</pre>
<div class="block">Initialise a chromosome with the specified parameters. Random valid connections
 are created upon initialisation.</div>
<dl>
<dt><span class="paramLabel">Parameters:</span></dt>
<dd><code>resources</code> - the experiment's resources.</dd>
</dl>
</li>
</ul>
<a name="Chromosome-jcgp.backend.population.Chromosome-">
<!--   -->
</a>
<ul class="blockListLast">
<li class="blockList">
<h4>Chromosome</h4>
<pre>public&nbsp;Chromosome(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;clone)</pre>
<div class="block">Copy constructor.
 
 Initialise a new chromosome with the exact same connections as a given instance of Chromosome.</div>
<dl>
<dt><span class="paramLabel">Parameters:</span></dt>
<dd><code>clone</code> - the chromosome to be copied.</dd>
</dl>
</li>
</ul>
</li>
</ul>
<!-- ============ METHOD DETAIL ========== -->
<ul class="blockList">
<li class="blockList"><a name="method.detail">
<!--   -->
</a>
<h3>Method Detail</h3>
<a name="reinitialiseConnections--">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>reinitialiseConnections</h4>
<pre>public&nbsp;void&nbsp;reinitialiseConnections()</pre>
<div class="block">Sets random connections and functions across the entire
 chromosome. This method can be used more than once for
 each instance, if entirely random chromosomes are desired.</div>
</li>
</ul>
<a name="copyGenes-jcgp.backend.population.Chromosome-">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>copyGenes</h4>
<pre>public&nbsp;void&nbsp;copyGenes(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;clone)</pre>
<div class="block">Creates a deep copy of the specified chromosome in the
 this instance. In practice, this iterates through the
 entire chromosome making equivalent connections and
 setting functions to the same values as those in the
 specified chromosome. It also sets the fitness of the
 copy to the same value as the original.
 <br>
 It is assumed that both chromosomes have the same 
 topology; while this method will still run if that is not
 the case, the effects might be undesirable and null pointer
 access might occur.</div>
<dl>
<dt><span class="paramLabel">Parameters:</span></dt>
<dd><code>clone</code> - the chromosome to clone.</dd>
</dl>
</li>
</ul>
<a name="getNode-int-int-">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>getNode</h4>
<pre>public&nbsp;<a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>&nbsp;getNode(int&nbsp;row,
                    int&nbsp;column)</pre>
<div class="block">Returns a reference to any node, addressed by row and column.</div>
<dl>
<dt><span class="paramLabel">Parameters:</span></dt>
<dd><code>row</code> - the row of the node.</dd>
<dd><code>column</code> - the column of the node.</dd>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>the addressed node.</dd>
</dl>
</li>
</ul>
<a name="getOutput-int-">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>getOutput</h4>
<pre>public&nbsp;<a href="../../../jcgp/backend/population/Output.html" title="class in jcgp.backend.population">Output</a>&nbsp;getOutput(int&nbsp;index)</pre>
<div class="block">Returns a reference to the indexed output.</div>
<dl>
<dt><span class="paramLabel">Parameters:</span></dt>
<dd><code>index</code> - the output index.</dd>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>the output reference.</dd>
</dl>
</li>
</ul>
<a name="getInput-int-">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>getInput</h4>
<pre>public&nbsp;<a href="../../../jcgp/backend/population/Input.html" title="class in jcgp.backend.population">Input</a>&nbsp;getInput(int&nbsp;index)</pre>
<div class="block">Returns a reference to the indexed input.</div>
<dl>
<dt><span class="paramLabel">Parameters:</span></dt>
<dd><code>index</code> - the input index.</dd>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>the input reference.</dd>
</dl>
</li>
</ul>
<a name="getFitness--">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>getFitness</h4>
<pre>public&nbsp;double&nbsp;getFitness()</pre>
<dl>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>the fitness of the chromosome.</dd>
</dl>
</li>
</ul>
<a name="setFitness-double-">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>setFitness</h4>
<pre>public&nbsp;void&nbsp;setFitness(double&nbsp;newFitness)</pre>
<div class="block">Sets the fitness of the chromosome. This method
 should be used by the experiment problem when the
 population is evaluated in order to assign a fitness
 to each individual.</div>
<dl>
<dt><span class="paramLabel">Parameters:</span></dt>
<dd><code>newFitness</code> - the fitness to assign.</dd>
</dl>
</li>
</ul>
<a name="setInputs-java.lang.Object...-">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>setInputs</h4>
<pre>public&nbsp;void&nbsp;setInputs(java.lang.Object...&nbsp;values)</pre>
<div class="block">Loops through the inputs and sets the specified values,
 so that evaluations can be performed. If the number of
 elements in the array of values does not match the
 number of inputs exactly, an exception is thrown.</div>
<dl>
<dt><span class="paramLabel">Parameters:</span></dt>
<dd><code>values</code> - the values the input should take.</dd>
</dl>
</li>
</ul>
<a name="getRandomMutable--">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>getRandomMutable</h4>
<pre>public&nbsp;<a href="../../../jcgp/backend/population/Mutable.html" title="interface in jcgp.backend.population">Mutable</a>&nbsp;getRandomMutable()</pre>
<div class="block">This method is useful for mutating chromosomes. It returns any
 random <code>Mutable</code> out of the chromosome with equal
 probability.</div>
<dl>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>a random element that can be mutated - node or output.</dd>
</dl>
</li>
</ul>
<a name="getRandomConnection-int-">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>getRandomConnection</h4>
<pre>public&nbsp;<a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;getRandomConnection(int&nbsp;column)</pre>
<div class="block">Returns a random allowed connection respecting levels back.<br>
 This method may always pick inputs, as they can be picked
 regardless of the column.</div>
<dl>
<dt><span class="paramLabel">Parameters:</span></dt>
<dd><code>column</code> - the column to use as reference.</dd>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>a random connection.</dd>
</dl>
</li>
</ul>
<a name="getRandomConnection--">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>getRandomConnection</h4>
<pre>public&nbsp;<a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population">Connection</a>&nbsp;getRandomConnection()</pre>
<div class="block">This method will pick a completely random connection, independently
 of levels back, including inputs. It is useful for setting outputs.</div>
<dl>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>a random connection regardless of levels back.</dd>
</dl>
</li>
</ul>
<a name="recomputeActiveNodes--">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>recomputeActiveNodes</h4>
<pre>public&nbsp;void&nbsp;recomputeActiveNodes()</pre>
<div class="block">This causes the list of active nodes to be recomputed lazily (once it is actually requested).</div>
</li>
</ul>
<a name="getActiveNodes--">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>getActiveNodes</h4>
<pre>public&nbsp;java.util.ArrayList&lt;<a href="../../../jcgp/backend/population/Node.html" title="class in jcgp.backend.population">Node</a>&gt;&nbsp;getActiveNodes()</pre>
<div class="block">This method computes a list of active nodes (if necessary) and returns it.</div>
<dl>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>the list of active nodes.</dd>
</dl>
</li>
</ul>
<a name="compareGenesTo-jcgp.backend.population.Chromosome-">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>compareGenesTo</h4>
<pre>public&nbsp;boolean&nbsp;compareGenesTo(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome)</pre>
<div class="block">Performs a deep comparison between this chromosome and the provided one.
 This is done on a gene-by-gene basis.
 
 This method returns true if and only if:
 <ul>
 <li>the chromosomes being compared are not the same instance;</li>
 <li>the connections of the compared chromosomes are not the same instance;</li>
 <li>the grid position of the chromosome's elements are the same;</li>
 </ul>
 <br><br>
 The relationship computed by this method is:
 <ul>
 <li>symmetric: a.copyOf(b) == b.copyOf(a);</li>
 <li>not reflexive: a.copyOf(a) returns false;</li>
 <li>not transitive: if a.copyOf(b) is true and b.copyOf(c) is true, a.copyOf(c) is
    not necessarily true since it is possible that a == c.</li>
 </ul></div>
<dl>
<dt><span class="paramLabel">Parameters:</span></dt>
<dd><code>chromosome</code> - the chromosome to compare to.</dd>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>true if it is a copy of this chromosome, but not the same chromosome.</dd>
</dl>
</li>
</ul>
<a name="compareActiveGenesTo-jcgp.backend.population.Chromosome-">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>compareActiveGenesTo</h4>
<pre>public&nbsp;boolean&nbsp;compareActiveGenesTo(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;chromosome)</pre>
<div class="block">Does the same as <code>compareGenesto()</code> but only looks
 at the active portion of the chromosome.</div>
<dl>
<dt><span class="paramLabel">Parameters:</span></dt>
<dd><code>chromosome</code> - the chromosome to compare to.</dd>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>true if the two active portions are identical.</dd>
</dl>
</li>
</ul>
<a name="printNodes--">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>printNodes</h4>
<pre>public&nbsp;void&nbsp;printNodes()</pre>
<div class="block">Iterates through the nodes and prints all connections and functions.
 This is intended for debugging purposes only and does not print to the
 GUI console.</div>
</li>
</ul>
<a name="getResources--">
<!--   -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>getResources</h4>
<pre>public&nbsp;<a href="../../../jcgp/backend/resources/Resources.html" title="class in jcgp.backend.resources">Resources</a>&nbsp;getResources()</pre>
<dl>
<dt><span class="returnLabel">Returns:</span></dt>
<dd>a reference to the resources based on which the chromosome was built.</dd>
</dl>
</li>
</ul>
<a name="compareTo-jcgp.backend.population.Chromosome-">
<!--   -->
</a>
<ul class="blockListLast">
<li class="blockList">
<h4>compareTo</h4>
<pre>public&nbsp;int&nbsp;compareTo(<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&nbsp;o)</pre>
<dl>
<dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
<dd><code>compareTo</code>&nbsp;in interface&nbsp;<code>java.lang.Comparable&lt;<a href="../../../jcgp/backend/population/Chromosome.html" title="class in jcgp.backend.population">Chromosome</a>&gt;</code></dd>
</dl>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>
<!-- ========= END OF CLASS DATA ========= -->
<!-- ======= START OF BOTTOM NAVBAR ====== -->
<div class="bottomNav"><a name="navbar.bottom">
<!--   -->
</a>
<div class="skipNav"><a href="#skip.navbar.bottom" title="Skip navigation links">Skip navigation links</a></div>
<a name="navbar.bottom.firstrow">
<!--   -->
</a>
<ul class="navList" title="Navigation">
<li><a href="../../../overview-summary.html">Overview</a></li>
<li><a href="package-summary.html">Package</a></li>
<li class="navBarCell1Rev">Class</li>
<li><a href="class-use/Chromosome.html">Use</a></li>
<li><a href="package-tree.html">Tree</a></li>
<li><a href="../../../deprecated-list.html">Deprecated</a></li>
<li><a href="../../../index-files/index-1.html">Index</a></li>
<li><a href="../../../help-doc.html">Help</a></li>
</ul>
</div>
<div class="subNav">
<ul class="navList">
<li>Prev&nbsp;Class</li>
<li><a href="../../../jcgp/backend/population/Connection.html" title="interface in jcgp.backend.population"><span class="typeNameLink">Next&nbsp;Class</span></a></li>
</ul>
<ul class="navList">
<li><a href="../../../index.html?jcgp/backend/population/Chromosome.html" target="_top">Frames</a></li>
<li><a href="Chromosome.html" target="_top">No&nbsp;Frames</a></li>
</ul>
<ul class="navList" id="allclasses_navbar_bottom">
<li><a href="../../../allclasses-noframe.html">All&nbsp;Classes</a></li>
</ul>
<div>
<script type="text/javascript"><!--
  allClassesLink = document.getElementById("allclasses_navbar_bottom");
  if(window==top) {
    allClassesLink.style.display = "block";
  }
  else {
    allClassesLink.style.display = "none";
  }
  //-->
</script>
</div>
<div>
<ul class="subNavList">
<li>Summary:&nbsp;</li>
<li>Nested&nbsp;|&nbsp;</li>
<li>Field&nbsp;|&nbsp;</li>
<li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
<li><a href="#method.summary">Method</a></li>
</ul>
<ul class="subNavList">
<li>Detail:&nbsp;</li>
<li>Field&nbsp;|&nbsp;</li>
<li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
<li><a href="#method.detail">Method</a></li>
</ul>
</div>
<a name="skip.navbar.bottom">
<!--   -->
</a></div>
<!-- ======== END OF BOTTOM NAVBAR ======= -->
</body>
</html>