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source: branches/OKBJavaConnector/ECJClient/src/ec/vector/FloatVectorSpecies.java @ 6152

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Last change on this file since 6152 was 6152, checked in by bfarka, 13 years ago
added ecj and custom statistics to communicate with the okb services #1441
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1	package ec.vector;
2
3	import ec.*;
4	import ec.util.*;
5
6	/*
7	* FloatVectorSpecies.java
8	*
9	* Created: Tue Feb 20 13:26:00 2001
10	* By: Sean Luke
11	*/
12
13	/**
14	* FloatVectorSpecies is a subclass of VectorSpecies with special
15	* constraints for floating-point vectors, namely FloatVectorIndividual and
16	* DoubleVectorIndividual.
17	*
18	* <p>FloatVectorSpecies can specify min/max numeric constraints on gene values
19	* in three different ways.
20	*
21	* <ol>
22	* <li> You may provide a default min and max value.
23	* This is done by specifying:
24	* <p><i>base</i>.<tt>min-gene</tt>
25	* <br><i>base</i>.<tt>max-gene</tt>
26	* <p><i>Note:</i> you <b>must</b> provide these values even if you don't use them,
27	* as they're used as defaults by #2 and #3 below.
28	*<p>
29	* <li> You may provide min and max values for genes in segments (regions) along
30	* the genome. This is done by specifying:
31	* <p><i>base</i>.<tt>num-segments</tt>
32	* The segments may be defined by either start or end indices of genes.
33	* This is controlled by specifying the value of:
34	* <p><i>base</i>.<tt>segment-type</tt>
35	* which can assume the value of start or end, with start being the default.
36	* The indices are defined using Java array style, i.e. the first gene has the index of 0,
37	* and the last gene has the index of genome-size - 1.
38	* <p>Using this method, each segment is specified by<i>j</i>...
39	* <p><i>base</i>.<tt>segment.</tt><i>j</i><tt>.start</tt>
40	* <br><i>base</i>.<tt>segment.</tt><i>j</i><tt>.min-gene</tt>
41	* <br><i>base</i>.<tt>segment.</tt><i>j</i><tt>.max-gene</tt>
42	* if segment-type value was chosen as start or by:
43	* <p><i>base</i>.<tt>segment.</tt><i>j</i><tt>.end</tt>
44	* <br><i>base</i>.<tt>segment.</tt><i>j</i><tt>.min-gene</tt>
45	* <br><i>base</i>.<tt>segment.</tt><i>j</i><tt>.max-gene</tt>
46	* if segment-type value is equal to end.
47	*<p>
48	* <li> You may provide min and max values for each separate gene.
49	* This is done by specifying (for each gene location <i>i</i> you wish to specify)
50	* <p><i>base</i>.<tt>min-gene</tt>.<i>i</i>
51	* <br><i>basn</i>.<tt>max-gene</tt>.<i>i</i>
52	* </ol>
53	*
54	* <p>Any settings for #3 override #2, and both override #1.
55	*
56	* <p>
57	* FloatVectorSpecies provides support for three ways of mutating a gene:
58	* <ul>
59	* <li>replacing the gene's value with a value uniformly-drawn from the gene's
60	* range (the default behavior, legacy from the previous versions).</li>
61	* <li>perturbing the gene's value with gaussian noise; if the gene-by-gene range
62	* is used, than the standard deviation is scaled to reflect each gene's range.
63	* If the gaussian mutation's standard deviation is too large for the range,
64	* than there's a large probability the mutated value will land outside range.
65	* We will try again a number of times (100) before giving up and using the
66	* previous mutation method.</li>
67	* <li>perturbing the gene's value with noise chosen from a <i>polynomial distribution</i>,
68	* similar to the gaussian distribution. The polynomial distribution was popularized
69	* by Kalyanmoy Deb and is found in many of his publications (see http://www.iitk.ac.in/kangal/deb.shtml).
70	* The polynomial distribution has two options. First, there is the <i>index</i>. This
71	* variable defines the shape of the distribution and is in some sense the equivalent of the
72	* standard deviation in the gaussian distribution. The index is an integer. If it is zero,
73	* the polynomial distribution is simply the uniform distribution from [1,-1]. If it is 1, the
74	* polynomial distribution is basically a triangular distribution from [1,-1] peaking at 0. If
75	* it is 2, the polynomial distribution follows a squared function, again peaking at 0. Larger
76	* values result in even more peaking and narrowness. The default values used in nearly all of
77	* the NSGA-II and Deb work is 20. Second, there is whether or not the value is intended for
78	* <i>bounded</i> genes. The default polynomial distribution is used when we assume the gene can
79	* take on literally any value, even beyond the min and max values. For genes which are restricted
80	* to be between min and max, there is an alternative version of the polynomial distribution, used by
81	* Deb's team but not discussed much in the literature, desiged for that situation. We assume boundedness
82	* by default, and have found it to be somewhat better for NSGA-II and SPEA2 problems. For a description
83	* of this alternative version, see "A Niched-Penalty Approach for Constraint Handling in Genetic Algorithms"
84	* by Kalyanmoy Deb and Samir Agrawal. Deb's default implementation bounds the result to min or max;
85	* instead ECJ's implementation of the polynomial distribution retries until it finds a legal value. This
86	* will be just fine for ranges like [0,1], but for smaller ranges you may be waiting a long time.
87	* </ul>
88	*
89	*
90	* <p>
91	* <b>Parameters</b><br>
92	* <table>
93	* <tr>
94	* <td valign=top><i>base</i>.<tt>min-gene</tt><br>
95	* <font size=-1>double (default=0.0)</font></td>
96	* <td valign=top>(the minimum gene value)</td>
97	* </tr>
98	*
99	* <tr>
100	* <td valign=top><i>base</i>.<tt>max-gene</tt><br>
101	* <font size=-1>double >= <i>base</i>.min-gene</font></td>
102	* <td valign=top>(the maximum gene value)</td>
103	* </tr>
104	*
105	* <tr>
106	* <td valign=top><i>base</i>.<tt>min-gene</tt>.<i>i</i><br>
107	* <font size=-1>double (default=<i>base</i>.<tt>min-gene</tt>)</font></td>
108	* <td valign=top>(the minimum gene value for gene <i>i</i>)</td>
109	* </tr>
110	*
111	* <tr>
112	* <td valign=top><i>base</i>.<tt>max-gene</tt>.<i>i</i><br>
113	* <font size=-1>double >= <i>base</i>.min-gene.<i>i</i> (default=<i>base</i>.<tt>max-gene</tt>)</font></td>
114	* <td valign=top>(the maximum gene value for gene <i>i</i>)</td>
115	* </tr>
116	*
117	* <tr><td valign=top><i>base.</i>.<tt>num-segments</tt><br>
118	* <font size=-1>int >= 1 (default=no segments used)</font></td>
119	* <td valign=top>(the number of gene segments defined)</td>
120	* </tr>
121	*
122	* <tr><td valign=top><i>base.</i>.<tt>segment-type</tt><br>
123	* <font size=-1>start (default) or end</font></td>
124	* <td valign=top>(defines the way in which segments are defined: either by providing start indices (segment-type=start) or by providing end indices (segment-type=end)</td>
125	* </tr>
126	*
127	* <tr><td valign=top><i>base.</i>.<tt>segment</tt>.<i>j</i>.<tt>start</tt><br>
128	* <font size=-1>0 <= int < genome length</font></td>
129	* <td valign=top>(the start index of gene segment <i>j</i> -- the end of a segment is before the start of the next segment)</td>
130	* <td valign=top>(used when the value of segment-type parameter is equal to start)</td>
131	* </tr>
132	*
133	* <tr><td valign=top><i>base.</i>.<tt>segment</tt>.<i>j</i>.<tt>end</tt><br>
134	* <font size=-1>0 <= int < genome length</font></td>
135	* <td valign=top>(the end of gene segment <i>j</i> -- the start of a segment is after the end of the previous segment)</td>
136	* <td valign=top>(used when the value of segment-type parameter is equal to end)</td>
137	* </tr>
138	*
139	* <tr><td valign=top><i>base.</i>.<tt>segment</tt>.<i>j</i>.<tt>min-gene</tt><br>
140	* <font size=-1>double (default=0.0)</font></td>
141	* <td valign=top>(the minimum gene value for segment <i>j</i>)</td>
142	* </tr>
143	*
144	* <tr><td valign=top><i>base.</i>.<tt>segment</tt>.<i>j</i>.<tt>max-gene</tt><br>
145	* <font size=-1>double >= <i>base.</i>.<tt>segment</tt>.<i>j</i>.<tt>min-gene</tt></td>
146	* <td valign=top>(the maximum gene value for segment <i>j</i>)</td>
147	* </tr>
148	*
149	* <tr>
150	* <td valign=top><i>base</i>.<tt>mutation-type</tt><br>
151	* <font size=-1><tt>reset</tt>, <tt>gauss</tt>, or <tt>polynomial</tt> (default=<tt>reset</tt>)</font></td>
152	* <td valign=top>(the mutation type)</td>
153	* </tr>
154	*
155	* <tr>
156	* <td valign=top><i>base</i>.<tt>mutation-stdev</tt><br>
157	* <font size=-1>double ≥ 0</font></td>
158	* <td valign=top>(the standard deviation or the gauss perturbation)</td>
159	* </tr>
160	*
161	* <tr>
162	* <td valign=top><i>base</i>.<tt>out-of-bounds-retries</tt><br>
163	* <font size=-1>int ≥ 0 (default=100)</font></td>
164	* <td valign=top>(number of times the gaussian mutation got the gene out of range
165	* before we give up and reset the gene's value; 0 means "never give up")</td>
166	* </tr>
167	*
168	* <tr>
169	* <td valign=top><i>base</i>.<tt>distribution-index</tt><br>
170	* <font size=-1>int ≥ 0</font></td>
171	* <td valign=top>(the mutation distribution index for the polynomial mutation distribution)</td>
172	* </tr>
173	*
174	* <tr>
175	* <td valign=top><i>base</i>.<tt>alternative-polynomial-version</tt><br>
176	* <font size=-1>boolean (default=true)</font></td>
177	* <td valign=top>(whether to use the "bounded" variation of the polynomial mutation or the standard ("unbounded") version)</td>
178	* </tr>
179	*
180	* <tr>
181	* <td valign=top><i>base</i>.<tt>mutation-bounded</tt><br>
182	* <font size=-1>boolean (default=true)</font></td>
183	* <td valign=top>(whether mutation is restricted to only being within the min/max gene values. Does not apply to SimulatedBinaryCrossover (which is always bounded))</td>
184	* </tr>
185	*
186	* </table>
187	* @author Sean Luke, Gabriel Balan, Rafal Kicinger
188	* @version 2.0
189	*/
190	public class FloatVectorSpecies extends VectorSpecies
191	{
192	public final static String P_MINGENE = "min-gene";
193
194	public final static String P_MAXGENE = "max-gene";
195
196	public final static String P_MUTATIONTYPE = "mutation-type";
197
198	public final static String P_STDEV = "mutation-stdev";
199
200	public final static String P_MUTATION_DISTRIBUTION_INDEX = "mutation-distribution-index";
201
202	public final static String P_POLYNOMIAL_ALTERNATIVE = "alternative-polynomial-version";
203
204	public final static String V_RESET_MUTATION = "reset";
205
206	public final static String V_GAUSS_MUTATION = "gauss";
207
208	public final static String V_POLYNOMIAL_MUTATION = "polynomial";
209
210	public final static String P_OUTOFBOUNDS_RETRIES = "out-of-bounds-retries";
211
212	public final static String P_NUM_SEGMENTS = "num-segments";
213
214	public final static String P_SEGMENT_TYPE = "segment-type";
215
216	public final static String P_SEGMENT_START = "start";
217
218	public final static String P_SEGMENT_END = "end";
219
220	public final static String P_SEGMENT = "segment";
221
222	public final static String P_MUTATION_BOUNDED = "mutation-bounded";
223
224	public final static int C_RESET_MUTATION = 0;
225
226	public final static int C_GAUSS_MUTATION = 1;
227
228	public final static int C_POLYNOMIAL_MUTATION = 2;
229
230	public double[] minGenes;
231	public double[] maxGenes;
232
233	/** What kind of mutation do we have? */
234	public int mutationType;
235
236	public double gaussMutationStdev;
237	public boolean mutationIsBounded;
238
239	public int outOfBoundsRetries=100;
240
241	public int mutationDistributionIndex;
242	public boolean polynomialIsAlternative;
243
244	static final double SIMULATED_BINARY_CROSSOVER_EPS = 1.0e-14;
245
246	private boolean outOfBoundsRetriesWarningPrinted = false;
247	public void outOfRangeRetryLimitReached(EvolutionState state)
248	{
249	if(!outOfBoundsRetriesWarningPrinted)
250	{
251	outOfBoundsRetriesWarningPrinted=true;
252	state.output.warning(
253	"The limit of 'out-of-range' retries for gaussian mutation was reached.");
254	}
255	}
256
257	public double maxGene(int gene)
258	{
259	double[] m = maxGenes;
260	if (m.length <= gene)
261	{
262	if (!dynamicInitialSize && !warned) warnAboutGene(gene);
263	gene = m.length - 1;
264	}
265	return m[gene];
266	}
267
268	public double minGene(int gene)
269	{
270	double[] m = minGenes;
271	if (m.length <= gene)
272	{
273	if (!dynamicInitialSize && !warned) warnAboutGene(gene);
274	gene = m.length - 1;
275	}
276	return m[gene];
277	}
278
279	public boolean inNumericalTypeRange(double geneVal)
280	{
281	if (i_prototype instanceof FloatVectorIndividual)
282	return (geneVal <= Float.MAX_VALUE && geneVal >= -Float.MAX_VALUE);
283	else if (i_prototype instanceof DoubleVectorIndividual)
284	return true; // geneVal is valid for all double
285	else
286	return false; // dunno what the individual is...
287	}
288
289	public void setup(final EvolutionState state, final Parameter base)
290	{
291	super.setup(state, base);
292
293	Parameter def = defaultBase();
294
295	// create the arrays
296	minGenes = new double[genomeSize];
297	maxGenes = new double[genomeSize];
298
299
300
301	// LOADING GLOBAL MIN/MAX GENES
302	double minGene = state.parameters.getDoubleWithDefault(base.push(P_MINGENE), def.push(P_MINGENE), 0);
303	double maxGene = state.parameters.getDouble(base.push(P_MAXGENE), def.push(P_MAXGENE), minGene);
304	if (maxGene < minGene)
305	state.output.fatal("FloatVectorSpecies must have a default min-gene which is <= the default max-gene",
306	base.push(P_MAXGENE), def.push(P_MAXGENE));
307
308	for (int x = 0; x < genomeSize; x++)
309	{
310	minGenes[x] = minGene;
311	maxGenes[x] = maxGene;
312	}
313
314
315	// LOADING SEGMENTS
316
317
318	//Set number of segments to 0 by default
319	int numSegments = 0;
320	// Now check to see if segments of genes (genes having the same min and
321	// max values) exist
322	if (state.parameters.exists(base.push(P_NUM_SEGMENTS), def.push(P_NUM_SEGMENTS)))
323	{
324	if (dynamicInitialSize)
325	state.output.warnOnce("Using dynamic initial sizing, but per-segment min/max gene declarations. This is probably wrong. You probably want to use global min/max declarations.",
326	base.push(P_NUM_SEGMENTS), def.push(P_NUM_SEGMENTS));
327
328	numSegments = state.parameters.getIntWithDefault(base.push(P_NUM_SEGMENTS),
329	def.push(P_NUM_SEGMENTS), 0);
330
331	if(numSegments == 0)
332	state.output.warning(
333	"The number of genome segments has been defined to be equal to 0.\n"
334	+ "Hence, no genome segments will be defined.",
335	base.push(P_NUM_SEGMENTS),
336	def.push(P_NUM_SEGMENTS));
337	else if(numSegments < 0)
338	state.output.fatal(
339	"Invalid number of genome segments: " + numSegments
340	+ "\nIt must be a nonnegative value.",
341	base.push(P_NUM_SEGMENTS),
342	def.push(P_NUM_SEGMENTS));
343
344	//read the type of segment definition using the default start value
345	String segmentType = state.parameters.getStringWithDefault(base.push(P_SEGMENT_TYPE),
346	def.push(P_SEGMENT_TYPE), P_SEGMENT_START);
347
348	if(segmentType.equalsIgnoreCase(P_SEGMENT_START))
349	initializeGenomeSegmentsByStartIndices(state, base, def, numSegments, minGene, maxGene);
350	else if(segmentType.equalsIgnoreCase(P_SEGMENT_END))
351	initializeGenomeSegmentsByEndIndices(state, base, def, numSegments, minGene, maxGene);
352	else
353	state.output.fatal(
354	"Invalid specification of genome segment type: " + segmentType
355	+ "\nThe " + P_SEGMENT_TYPE + " parameter must have the value of " + P_SEGMENT_START + " or " + P_SEGMENT_END,
356	base.push(P_SEGMENT_TYPE),
357	def.push(P_SEGMENT_TYPE));
358
359
360	}
361
362
363
364	// LOADING PER-GENE VALUES
365
366	boolean foundStuff = false;
367	boolean warnedMin = false;
368	boolean warnedMax = false;
369	for (int x = 0; x < genomeSize; x++)
370	{
371	if (!state.parameters.exists(base.push(P_MINGENE).push("" + x), def.push(P_MINGENE).push("" + x)))
372	{
373	if (foundStuff && !warnedMin)
374	{
375	state.output.warning(
376	"FloatVectorSpecies has missing min-gene values for some genes.\n"
377	+ "The first one is gene #" + x + ".",
378	base.push(P_MINGENE).push("" + x), def.push(P_MINGENE).push("" + x));
379	warnedMin = true;
380	}
381	}
382	else
383	{
384	if (dynamicInitialSize)
385	state.output.warnOnce("Using dynamic initial sizing, but per-gene min/max gene declarations. This is probably wrong. You probably want to use global min/max declarations.",
386	base.push(P_MINGENE).push(""+x),base.push(P_MINGENE).push(""+x));
387
388	minGenes[x] = state.parameters.getDoubleWithDefault(base.push(P_MINGENE).push("" + x),
389	def.push(P_MINGENE).push("" + x), minGene);
390	foundStuff = true;
391	}
392
393	if (!state.parameters.exists(base.push(P_MAXGENE).push("" + x), def.push(P_MAXGENE).push("" + x)))
394	{
395	if (foundStuff && !warnedMax)
396	{
397	state.output.warning(
398	"FloatVectorSpecies has missing max-gene values for some genes.\n"
399	+ "The first one is gene #" + x + ".",
400	base.push(P_MAXGENE).push("" + x), def.push(P_MAXGENE).push("" + x));
401	warnedMax = true;
402	}
403	}
404	else
405	{
406	if (dynamicInitialSize)
407	state.output.warnOnce("Using dynamic initial sizing, but per-gene min/max gene declarations. This is probably wrong. You probably want to use global min/max declarations.",
408	base.push(P_MINGENE).push(""+x),base.push(P_MINGENE).push(""+x));
409
410	maxGenes[x] = state.parameters.getDoubleWithDefault(base.push(P_MAXGENE).push("" + x),
411	def.push(P_MAXGENE).push("" + x), maxGene);
412	foundStuff = true;
413	}
414	}
415
416
417
418
419
420
421	// VERIFY
422	for(int x=0 ; x < genomeSize; x++)
423	{
424	if (maxGenes[x] != maxGenes[x]) // uh oh, NaN
425	state.output.fatal("FloatVectorSpecies found that max-gene[" + x + "] is NaN");
426
427	if (minGenes[x] != minGenes[x]) // uh oh, NaN
428	state.output.fatal("FloatVectorSpecies found that min-gene[" + x + "] is NaN");
429
430	if (maxGenes[x] < minGenes[x])
431	state.output.fatal("FloatVectorSpecies must have a min-gene[" + x + "] which is <= the max-gene[" + x + "]");
432
433	// check to see if these longs are within the data type of the particular individual
434	if (!inNumericalTypeRange(minGenes[x]))
435	state.output.fatal("This FloatvectorSpecies has a prototype of the kind: "
436	+ i_prototype.getClass().getName()
437	+ ", but doesn't have a min-gene["
438	+ x
439	+ "] value within the range of this prototype's genome's data types");
440	if (!inNumericalTypeRange(maxGenes[x]))
441	state.output.fatal("This FloatvectorSpecies has a prototype of the kind: "
442	+ i_prototype.getClass().getName()
443	+ ", but doesn't have a max-gene["
444	+ x
445	+ "] value within the range of this prototype's genome's data types");
446	}
447
448
449
450
451
452	/// MUTATION
453
454
455	mutationIsBounded = state.parameters.getBoolean(base.push(P_MUTATION_BOUNDED), def.push(P_MUTATION_BOUNDED), true);
456	String mtype = state.parameters.getStringWithDefault(base.push(P_MUTATIONTYPE), def.push(P_MUTATIONTYPE), null);
457	mutationType = C_RESET_MUTATION;
458	if (mtype == null)
459	state.output.warning("No mutation type given for FloatVectorSpecies, assuming 'reset' mutation",
460	base.push(P_MUTATIONTYPE), def.push(P_MUTATIONTYPE));
461	else if (mtype.equalsIgnoreCase(V_RESET_MUTATION))
462	mutationType = C_RESET_MUTATION; // redundant
463	else if (mtype.equalsIgnoreCase(V_POLYNOMIAL_MUTATION))
464	mutationType = C_POLYNOMIAL_MUTATION; // redundant
465	else if (mtype.equalsIgnoreCase(V_GAUSS_MUTATION))
466	mutationType = C_GAUSS_MUTATION;
467	else
468	state.output.fatal("FloatVectorSpecies given a bad mutation type: "
469	+ mtype, base.push(P_MUTATIONTYPE), def.push(P_MUTATIONTYPE));
470
471	if (mutationType == C_POLYNOMIAL_MUTATION)
472	{
473	mutationDistributionIndex = state.parameters.getInt(base.push(P_MUTATION_DISTRIBUTION_INDEX), def.push(P_MUTATION_DISTRIBUTION_INDEX), 0);
474	if (mutationDistributionIndex < 0)
475	state.output.fatal("If FloatVectorSpecies is going to use polynomial mutation, the distribution index must be defined and >= 0.",
476	base.push(P_MUTATION_DISTRIBUTION_INDEX), def.push(P_MUTATION_DISTRIBUTION_INDEX));
477	polynomialIsAlternative = state.parameters.getBoolean(base.push(P_POLYNOMIAL_ALTERNATIVE), def.push(P_POLYNOMIAL_ALTERNATIVE), true);
478
479	outOfBoundsRetries = state.parameters.getIntWithDefault(base.push(P_OUTOFBOUNDS_RETRIES), def.push(P_OUTOFBOUNDS_RETRIES), outOfBoundsRetries);
480	if(outOfBoundsRetries<0)
481	{
482	state.output.fatal(
483	"If it's going to use polynomial mutation, FloatvectorSpecies must have a positive number of out-of-bounds retries or 0 (for don't give up). " +
484	"This is even the case if doing so-called \"bounded\" polynomial mutation, which auto-bounds anyway, or if the mutation is unbounded. " +
485	"In either case, just provide an arbitrary value, which will be ignored.",
486	base.push(P_OUTOFBOUNDS_RETRIES), def.push(P_OUTOFBOUNDS_RETRIES));
487	}
488	}
489
490	if (mutationType == C_GAUSS_MUTATION)
491	{
492	gaussMutationStdev = state.parameters.getDouble(base.push(P_STDEV),def.push(P_STDEV), 0);
493	if (gaussMutationStdev <= 0)
494	state.output.fatal("If it's going to use gaussian mutation, FloatvectorSpecies must have a strictly positive standard deviation",
495	base.push(P_STDEV), def.push(P_STDEV));
496
497	outOfBoundsRetries = state.parameters.getIntWithDefault(base.push(P_OUTOFBOUNDS_RETRIES), def.push(P_OUTOFBOUNDS_RETRIES), outOfBoundsRetries);
498	if(outOfBoundsRetries<0)
499	{
500	state.output.fatal(
501	"If it's going to use gaussian mutation, FloatvectorSpecies must have a positive number of out-of-bounds retries or 0 (for don't give up). " +
502	"This is even the case if the mutation is unbounded. In that case, just provide an arbitrary value, which will be ignored.",
503	base.push(P_OUTOFBOUNDS_RETRIES), def.push(P_OUTOFBOUNDS_RETRIES));
504	}
505	}
506	/*
507	//Debugging
508	for(int i = 0; i < minGenes.length; i++)
509	System.out.println("Min: " + minGenes[i] + ", Max: " + maxGenes[i]);
510	*/
511	}
512
513
514	private void initializeGenomeSegmentsByStartIndices(final EvolutionState state,
515	final Parameter base,
516	final Parameter def,
517	int numSegments,
518	double minGene, double maxGene)
519	{
520	boolean warnedMin = false;
521	boolean warnedMax = false;
522	double currentSegmentMinGeneValue = Double.MAX_VALUE;
523	double currentSegmentMaxGeneValue = Double.MIN_VALUE;
524
525	//loop in reverse order
526	int previousSegmentEnd = genomeSize;
527	int currentSegmentEnd = 0;
528
529	for (int i = numSegments - 1; i >= 0; i--)
530	{
531	//check if the segment data exist
532	if (state.parameters.exists(base.push(P_SEGMENT).push(""+i).push(P_SEGMENT_START),
533	def.push(P_SEGMENT).push(""+i).push(P_SEGMENT_START)))
534	{
535	//Read the index of the end gene specifying current segment
536	currentSegmentEnd = state.parameters.getInt(base.push(P_SEGMENT).push(""+i).push(P_SEGMENT_START),
537	def.push(P_SEGMENT).push(""+i).push(P_SEGMENT_START));
538
539	}
540	else
541	{
542	state.output.fatal("Genome segment " + i + " has not been defined!" +
543	"\nYou must specify start indices for " + numSegments + " segment(s)",
544	base.push(P_SEGMENT).push(""+i).push(P_SEGMENT_START),
545	base.push(P_SEGMENT).push(""+i).push(P_SEGMENT_START));
546	}
547
548	//check if the start index is valid
549	if(currentSegmentEnd >= previousSegmentEnd \|\| currentSegmentEnd < 0)
550	state.output.fatal(
551	"Invalid start index value for segment " + i + ": " + currentSegmentEnd
552	+ "\nThe value must be smaller than " + previousSegmentEnd +
553	" and greater than or equal to " + 0);
554
555	//check if the index of the first segment is equal to 0
556	if(i == 0 && currentSegmentEnd != 0)
557	state.output.fatal(
558	"Invalid start index value for the first segment " + i + ": " + currentSegmentEnd
559	+ "\nThe value must be equal to " + 0);
560
561
562	//get min and max values of genes in this segment
563	if (!state.parameters.exists(base.push(P_SEGMENT).push(""+i).push(P_MINGENE),
564	base.push(P_SEGMENT).push(""+i).push(P_MINGENE)))
565	{
566	if (!warnedMin)
567	{
568	state.output.warning(
569	"IntegerVectorSpecies has missing min-gene values for some segments.\n"
570	+ "The first segment is #" + i + ".",
571	base.push(P_SEGMENT).push(""+i),
572	base.push(P_SEGMENT).push(""+i));
573	warnedMin = true;
574	}
575
576	//the min-gene value has not been defined for this segment so assume the global min value
577	currentSegmentMinGeneValue = minGene;
578	}
579	else //get the min value for this segment
580	{
581	currentSegmentMinGeneValue = state.parameters.getDoubleWithDefault(
582	base.push(P_SEGMENT).push(""+i).push(P_MINGENE),
583	base.push(P_SEGMENT).push(""+i).push(P_MINGENE),
584	minGene);
585
586	//check if the value is in range
587	if (!inNumericalTypeRange(currentSegmentMinGeneValue))
588	state.output
589	.error(
590	"This IntegerVectorSpecies has a prototype of the kind: "
591	+ i_prototype.getClass()
592	.getName()
593	+ ", but doesn't have a min-gene "
594	+ " value for segment " + i
595	+ " within the range of this prototype's genome's data types",
596	base.push(P_SEGMENT).push(""+i).push(P_MINGENE),
597	base.push(P_SEGMENT).push(""+i).push(P_MINGENE));
598
599	}
600
601	if (!state.parameters.exists(base.push(P_SEGMENT).push(""+i).push(P_MAXGENE),
602	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE)))
603	{
604	if (!warnedMax)
605	{
606	state.output.warning(
607	"IntegerVectorSpecies has missing max-gene values for some segments.\n"
608	+ "The first segment is #" + i + ".",
609	base.push(P_SEGMENT).push(""+i),
610	base.push(P_SEGMENT).push(""+i));
611	warnedMax = true;
612	}
613
614	//the max-gen value has not been defined for this segment so assume the global max value
615	currentSegmentMaxGeneValue = maxGene;
616
617	}
618	else //get the max value for this segment
619	{
620	currentSegmentMaxGeneValue = state.parameters.getDoubleWithDefault(
621	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE),
622	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE),
623	maxGene);
624
625	//check if the value is in range
626	if (!inNumericalTypeRange(currentSegmentMaxGeneValue))
627	state.output
628	.fatal(
629	"This IntegerVectorSpecies has a prototype of the kind: "
630	+ i_prototype.getClass()
631	.getName()
632	+ ", but doesn't have a max-gene "
633	+ " value for segment " + i
634	+ " within the range of this prototype's genome's data types",
635	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE),
636	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE));
637	}
638
639	//check is min is smaller than or equal to max
640	if (currentSegmentMaxGeneValue < currentSegmentMinGeneValue)
641	state.output.fatal(
642	"IntegerVectorSpecies must have a min-gene value for segment "
643	+ i + " which is <= the max-gene value",
644	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE),
645	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE));
646
647
648	//and assign min and max values for all genes in this segment
649	for(int j = previousSegmentEnd-1; j >= currentSegmentEnd; j--)
650	{
651	minGenes[j] = currentSegmentMinGeneValue;
652	maxGenes[j] = currentSegmentMaxGeneValue;
653	}
654
655	previousSegmentEnd = currentSegmentEnd;
656
657	}
658
659	}
660
661	private void initializeGenomeSegmentsByEndIndices(final EvolutionState state,
662	final Parameter base,
663	final Parameter def,
664	int numSegments,
665	double minGene, double maxGene)
666	{
667	boolean warnedMin = false;
668	boolean warnedMax = false;
669	double currentSegmentMinGeneValue = Double.MAX_VALUE;
670	double currentSegmentMaxGeneValue = Double.MIN_VALUE;
671
672	int previousSegmentEnd = -1;
673	int currentSegmentEnd = 0;
674	// iterate over segments and set genes values for each segment
675	for (int i = 0; i < numSegments; i++)
676	{
677	//check if the segment data exist
678	if (state.parameters.exists(base.push(P_SEGMENT).push(""+i).push(P_SEGMENT_END), def.push(P_SEGMENT).push(""+i).push(P_SEGMENT_END)))
679	{
680	//Read the index of the end gene specifying current segment
681	currentSegmentEnd = state.parameters.getInt(base.push(P_SEGMENT).push(""+i).push(P_SEGMENT_END),
682	def.push(P_SEGMENT).push(""+i).push(P_SEGMENT_END));
683
684	}
685	else
686	{
687	state.output.fatal("Genome segment " + i + " has not been defined!" +
688	"\nYou must specify end indices for " + numSegments + " segment(s)",
689	base.push(P_SEGMENT).push(""+i).push(P_SEGMENT_END),
690	base.push(P_SEGMENT).push(""+i).push(P_SEGMENT_END));
691	}
692
693	//check if the end index is valid
694	if(currentSegmentEnd <= previousSegmentEnd \|\| currentSegmentEnd >= genomeSize)
695	state.output.fatal(
696	"Invalid end index value for segment " + i + ": " + currentSegmentEnd
697	+ "\nThe value must be greater than " + previousSegmentEnd +
698	" and smaller than " + genomeSize);
699
700	//check if the index of the final segment is equal to the genomeSize
701	if(i == numSegments - 1 && currentSegmentEnd != (genomeSize-1))
702	state.output.fatal(
703	"Invalid end index value for the last segment " + i + ": " + currentSegmentEnd
704	+ "\nThe value must be equal to the index of the last gene in the genome: " + (genomeSize-1));
705
706
707	//get min and max values of genes in this segment
708	if (!state.parameters.exists(base.push(P_SEGMENT).push(""+i).push(P_MINGENE),
709	base.push(P_SEGMENT).push(""+i).push(P_MINGENE)))
710	{
711	if (!warnedMin)
712	{
713	state.output.warning(
714	"IntegerVectorSpecies has missing min-gene values for some segments.\n"
715	+ "The first segment is #" + i + ".",
716	base.push(P_SEGMENT).push(""+i),
717	base.push(P_SEGMENT).push(""+i));
718	warnedMin = true;
719	}
720
721	//the min-gene value has not been defined for this segment so assume the global min value
722	currentSegmentMinGeneValue = minGene;
723	}
724	else //get the min value for this segment
725	{
726	currentSegmentMinGeneValue = state.parameters.getDoubleWithDefault(
727	base.push(P_SEGMENT).push(""+i).push(P_MINGENE),
728	base.push(P_SEGMENT).push(""+i).push(P_MINGENE),
729	minGene);
730
731	//check if the value is in range
732	if (!inNumericalTypeRange(currentSegmentMinGeneValue))
733	state.output
734	.error(
735	"This IntegerVectorSpecies has a prototype of the kind: "
736	+ i_prototype.getClass()
737	.getName()
738	+ ", but doesn't have a min-gene "
739	+ " value for segment " + i
740	+ " within the range of this prototype's genome's data types",
741	base.push(P_SEGMENT).push(""+i).push(P_MINGENE),
742	base.push(P_SEGMENT).push(""+i).push(P_MINGENE));
743
744	}
745
746	if (!state.parameters.exists(base.push(P_SEGMENT).push(""+i).push(P_MAXGENE),
747	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE)))
748	{
749	if (!warnedMax)
750	{
751	state.output.warning(
752	"IntegerVectorSpecies has missing max-gene values for some segments.\n"
753	+ "The first segment is #" + i + ".",
754	base.push(P_SEGMENT).push(""+i),
755	base.push(P_SEGMENT).push(""+i));
756	warnedMax = true;
757	}
758
759	//the max-gen value has not been defined for this segment so assume the global max value
760	currentSegmentMaxGeneValue = maxGene;
761
762	}
763	else //get the max value for this segment
764	{
765	currentSegmentMaxGeneValue = state.parameters.getDoubleWithDefault(
766	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE),
767	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE),
768	maxGene);
769
770	//check if the value is in range
771	if (!inNumericalTypeRange(currentSegmentMaxGeneValue))
772	state.output
773	.fatal(
774	"This IntegerVectorSpecies has a prototype of the kind: "
775	+ i_prototype.getClass()
776	.getName()
777	+ ", but doesn't have a max-gene "
778	+ " value for segment " + i
779	+ " within the range of this prototype's genome's data types",
780	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE),
781	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE));
782	}
783
784	//check is min is smaller than or equal to max
785	if (currentSegmentMaxGeneValue < currentSegmentMinGeneValue)
786	state.output.fatal(
787	"IntegerVectorSpecies must have a min-gene value for segment "
788	+ i + " which is <= the max-gene value",
789	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE),
790	base.push(P_SEGMENT).push(""+i).push(P_MAXGENE));
791
792
793	//and assign min and max values for all genes in this segment
794	for(int j = previousSegmentEnd+1; j <= currentSegmentEnd; j++)
795	{
796	minGenes[j] = currentSegmentMinGeneValue;
797	maxGenes[j] = currentSegmentMaxGeneValue;
798	}
799
800	previousSegmentEnd = currentSegmentEnd;
801
802	}
803	}
804	}

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