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segments.h
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1 /* =============================================================================
2  *
3  * segments.h
4  * -- Create random segments from random gene
5  *
6  * =============================================================================
7  *
8  * Copyright (C) Stanford University, 2006. All Rights Reserved.
9  * Author: Chi Cao Minh
10  *
11  * =============================================================================
12  *
13  * For the license of bayes/sort.h and bayes/sort.c, please see the header
14  * of the files.
15  *
16  * ------------------------------------------------------------------------
17  *
18  * For the license of kmeans, please see kmeans/LICENSE.kmeans
19  *
20  * ------------------------------------------------------------------------
21  *
22  * For the license of ssca2, please see ssca2/COPYRIGHT
23  *
24  * ------------------------------------------------------------------------
25  *
26  * For the license of lib/mt19937ar.c and lib/mt19937ar.h, please see the
27  * header of the files.
28  *
29  * ------------------------------------------------------------------------
30  *
31  * For the license of lib/rbtree.h and lib/rbtree.c, please see
32  * lib/LEGALNOTICE.rbtree and lib/LICENSE.rbtree
33  *
34  * ------------------------------------------------------------------------
35  *
36  * Unless otherwise noted, the following license applies to STAMP files:
37  *
38  * Copyright (c) 2007, Stanford University
39  * All rights reserved.
40  *
41  * Redistribution and use in source and binary forms, with or without
42  * modification, are permitted provided that the following conditions are
43  * met:
44  *
45  * * Redistributions of source code must retain the above copyright
46  * notice, this list of conditions and the following disclaimer.
47  *
48  * * Redistributions in binary form must reproduce the above copyright
49  * notice, this list of conditions and the following disclaimer in
50  * the documentation and/or other materials provided with the
51  * distribution.
52  *
53  * * Neither the name of Stanford University nor the names of its
54  * contributors may be used to endorse or promote products derived
55  * from this software without specific prior written permission.
56  *
57  * THIS SOFTWARE IS PROVIDED BY STANFORD UNIVERSITY ``AS IS'' AND ANY
58  * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
59  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
60  * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL STANFORD UNIVERSITY BE LIABLE
61  * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
62  * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
63  * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
64  * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
65  * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
66  * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
67  * THE POSSIBILITY OF SUCH DAMAGE.
68  *
69  * =============================================================================
70  */
71 
72 
73 #ifndef SEGMENTS_H
74 #define SEGMENTS_H 1
75 
76 
77 #include "gene.h"
78 #include "random.h"
79 #include "vector.h"
80 
81 
82 typedef struct segments {
83  long length;
84  long minNum;
85  vector_t* contentsPtr;
86 /* private: */
87  char** strings;
88 } segments_t;
89 
90 
91 /* =============================================================================
92  * segments_alloc
93  * -- Does almost all the memory allocation for random segments
94  * -- The actual number of segments created by 'segments_create' may be larger
95  * than 'minNum' to ensure the segments overlap and cover the entire gene
96  * -- Returns NULL on failure
97  * =============================================================================
98  */
99 segments_t*
100 segments_alloc (long length, long minNum);
101 
102 
103 /* =============================================================================
104  * segments_create
105  * -- Populates 'contentsPtr'
106  * =============================================================================
107  */
108 void
109 segments_create (segments_t* segmentsPtr, gene_t* genePtr, random_t* randomPtr);
110 
111 
112 /* =============================================================================
113  * segments_free
114  * =============================================================================
115  */
116 void
117 segments_free (segments_t* segmentsPtr);
118 
119 
120 #endif /* SEGMENTS_H */
121 
122 
123 /* =============================================================================
124  *
125  * End of segments.h
126  *
127  * =============================================================================
128  */
vector
Definition: vector.h:85
gene
Definition: gene.h:81
segments::strings
char ** strings
Definition: segments.h:87
segments_alloc
segments_t * segments_alloc(long length, long minNum)
Definition: segments.c:92
segments_create
void segments_create(segments_t *segmentsPtr, gene_t *genePtr, random_t *randomPtr)
Definition: segments.c:135
segments::contentsPtr
vector_t * contentsPtr
Definition: segments.h:85
segments::length
long length
Definition: segments.h:83
segments::minNum
long minNum
Definition: segments.h:84
segments
Definition: segments.h:82
segments_t
struct segments segments_t
random
Definition: random.h:86
segments_free
void segments_free(segments_t *segmentsPtr)
Definition: segments.c:213