1 | // This file is a part of Framsticks SDK. http://www.framsticks.com/ |
---|
2 | // Copyright (C) 1999-2020 Maciej Komosinski and Szymon Ulatowski. |
---|
3 | // See LICENSE.txt for details. |
---|
4 | |
---|
5 | |
---|
6 | #include <vector> |
---|
7 | #include <string> |
---|
8 | #include "common/loggers/loggertostdout.h" |
---|
9 | #include "frams/_demos/genotypeloader.h" |
---|
10 | #include "frams/genetics/preconfigured.h" |
---|
11 | #include "common/virtfile/stdiofile.h" |
---|
12 | #include "frams/model/similarity/measure-distribution.h" |
---|
13 | #include "frams/model/similarity/measure-greedy.h" |
---|
14 | #include "frams/model/similarity/measure-hungarian.h" |
---|
15 | |
---|
16 | using namespace std; |
---|
17 | |
---|
18 | int add_double_param(std::vector<string> *args, int pos, std::vector<double> *params, std::vector<string> *params_names) |
---|
19 | { |
---|
20 | for (unsigned int i = 0; i < params_names->size(); i++) |
---|
21 | { |
---|
22 | try |
---|
23 | { |
---|
24 | params->push_back(std::stod(args->at(pos))); |
---|
25 | pos++; |
---|
26 | } |
---|
27 | catch (const std::invalid_argument&) |
---|
28 | { |
---|
29 | printf("%s should be a number\n", params_names->at(i).c_str()); |
---|
30 | return -1; |
---|
31 | } |
---|
32 | catch (const std::out_of_range&) |
---|
33 | { |
---|
34 | printf("%s should be inside double range\n", params_names->at(i).c_str()); |
---|
35 | return -1; |
---|
36 | } |
---|
37 | } |
---|
38 | return 0; |
---|
39 | } |
---|
40 | |
---|
41 | /** Computes a matrix of distances between all genotypes in the specified |
---|
42 | .gen file, using the matching and measure weights as specified in the |
---|
43 | command line. */ |
---|
44 | int main(int argc, char *argv[]) |
---|
45 | { |
---|
46 | typedef double *pDouble; |
---|
47 | LoggerToStdout messages_to_stdout(LoggerBase::Enable); |
---|
48 | SimilMeasure *simil_measure = nullptr; |
---|
49 | if (argc < 5) |
---|
50 | { |
---|
51 | printf("Too few parameters!\n"); |
---|
52 | printf("Command line: [-names] <genotypesFile> <measure (greedy/hungarian)> <w_dP> <w_dDEG> <w_dNEU> <w_dGEO> <fixZaxis?>\n\n"); |
---|
53 | printf("Command line: [-names] <genotypesFile> <measure (distribution)> <desc> <simil> <dens> <bins> <samp_num>\n\n"); |
---|
54 | printf("Parameters:\n"); |
---|
55 | printf(" <genotypesFile> name of a file with genotypes\n"); |
---|
56 | printf(" <measure> similarity measure name (greedy/hungarian/distribution)\n"); |
---|
57 | printf("\n"); |
---|
58 | printf("Parameters of greedy and hungarian measures:\n"); |
---|
59 | printf(" <w_dP> weight of the difference in the number of parts\n"); |
---|
60 | printf(" <w_dDEG> weight of the difference in degrees of matched parts\n"); |
---|
61 | printf(" <w_dNEU> weight of the difference in neurons of matched parts\n"); |
---|
62 | printf(" <w_dGEO> weight of the distance of matched parts\n"); |
---|
63 | printf(" <fixZaxis?> should the 'z' (vertical) coordinate be fixed during the alignment? (0 or 1)\n\n"); |
---|
64 | printf("Parameters of distribution measure:\n"); |
---|
65 | printf(" <dens> sampling density\n"); |
---|
66 | printf(" <bins> number of histogram bins\n"); |
---|
67 | printf(" <samp_num> number of samples taken\n\n"); |
---|
68 | |
---|
69 | printf("Switches:\n"); |
---|
70 | printf(" -names specifies that the number and names of genotypes are to be printed to output\n"); |
---|
71 | printf(" before the distance matrix; by default the number and names are not printed\n\n"); |
---|
72 | |
---|
73 | printf("Outputs a symmetric distance matrix in the format:\n"); |
---|
74 | printf(" <row_1> (columns in a row are separated by TABs)\n"); |
---|
75 | printf(" ...\n"); |
---|
76 | printf(" <row_n>\n"); |
---|
77 | |
---|
78 | return -1; |
---|
79 | } |
---|
80 | |
---|
81 | std::vector<string> args; |
---|
82 | for (int i = 1; i < argc; i++) |
---|
83 | args.push_back(std::string(argv[i])); |
---|
84 | |
---|
85 | bool print_names = false; |
---|
86 | |
---|
87 | int pos = 1; |
---|
88 | if (args.at(0).compare("-names")==0) |
---|
89 | { |
---|
90 | print_names = true; |
---|
91 | pos = 2; |
---|
92 | } |
---|
93 | |
---|
94 | string measure_name = args.at(pos); |
---|
95 | pos++; |
---|
96 | std::vector<double> params; |
---|
97 | |
---|
98 | if (measure_name.compare("greedy")==0 || measure_name.compare("hungarian")==0) |
---|
99 | { |
---|
100 | std::vector<string> params_names{ "<w_dP>", "<w_dDEG>", "<w_dNEU>", "<w_dGEO>", "<fixZaxis?>" }; |
---|
101 | |
---|
102 | if (add_double_param(&args, pos, ¶ms, ¶ms_names) == -1) |
---|
103 | return -1; |
---|
104 | |
---|
105 | if (measure_name.compare("greedy")==0) |
---|
106 | simil_measure = new SimilMeasureGreedy(); |
---|
107 | else |
---|
108 | simil_measure = new SimilMeasureHungarian(); |
---|
109 | } |
---|
110 | |
---|
111 | |
---|
112 | else if (measure_name.compare("distribution")==0) |
---|
113 | { |
---|
114 | std::vector<string> params_names{ "<dens>", "<bins>", "<samp_num>" }; |
---|
115 | |
---|
116 | if (add_double_param(&args, pos, ¶ms, ¶ms_names)==-1) |
---|
117 | return -1; |
---|
118 | |
---|
119 | simil_measure = new SimilMeasureDistribution(); |
---|
120 | } |
---|
121 | |
---|
122 | else |
---|
123 | { |
---|
124 | printf("Measure type should be greedy (flexible criteria order and optimal matching), hungarian (vertex degree order and greedy matching) or distribution!\n"); |
---|
125 | return -1; |
---|
126 | } |
---|
127 | |
---|
128 | simil_measure->setParams(params); |
---|
129 | |
---|
130 | // read the input file |
---|
131 | // prepare loading of genotypes from a .gen file |
---|
132 | // create some basic genotype converters |
---|
133 | PreconfiguredGenetics genetics; |
---|
134 | StdioFileSystem_autoselect stdiofilesys; |
---|
135 | |
---|
136 | // prepare output parameters from .gen file |
---|
137 | vector<Geno *> pvGenos; |
---|
138 | vector<char *> pvNames; |
---|
139 | |
---|
140 | long count = 0, totalsize = 0; |
---|
141 | GenotypeMiniLoader loader(args.at(0).c_str()); |
---|
142 | GenotypeMini *loaded; |
---|
143 | while (loaded = loader.loadNextGenotype()) |
---|
144 | { |
---|
145 | // while a valid genotype was loaded |
---|
146 | count++; |
---|
147 | totalsize += loaded->genotype.length(); |
---|
148 | // create a Geno object based on the MiniGenotype |
---|
149 | Geno *pNextGenotype = new Geno(loaded->genotype); |
---|
150 | if ((pNextGenotype != NULL) && (pNextGenotype->isValid())) |
---|
151 | { |
---|
152 | pvGenos.push_back(pNextGenotype); |
---|
153 | char *szNewName = new char[loaded->name.length() + 1]; |
---|
154 | strcpy(szNewName, loaded->name.c_str()); |
---|
155 | pvNames.push_back(szNewName); |
---|
156 | } |
---|
157 | else |
---|
158 | { |
---|
159 | printf("Genotype %2li is not valid\n", count); |
---|
160 | if (pNextGenotype != NULL) delete pNextGenotype; |
---|
161 | } |
---|
162 | } |
---|
163 | if (loader.getStatus() == GenotypeMiniLoader::OnError) |
---|
164 | { |
---|
165 | printf("Error: %s", loader.getError().c_str()); |
---|
166 | } |
---|
167 | |
---|
168 | double dSimilarity = 0.0; |
---|
169 | double **aaSimil = NULL; // array of similarities |
---|
170 | |
---|
171 | // create the empty array of similarities |
---|
172 | aaSimil = new pDouble[pvGenos.size()]; |
---|
173 | for (unsigned int k = 0; k < pvGenos.size(); k++) |
---|
174 | { |
---|
175 | aaSimil[k] = new double[pvGenos.size()]; |
---|
176 | for (unsigned int l = 0; l < pvGenos.size(); l++) |
---|
177 | aaSimil[k][l] = 0.0; |
---|
178 | } |
---|
179 | |
---|
180 | |
---|
181 | |
---|
182 | // compute and remember similarities |
---|
183 | for (unsigned int i = 0; i < pvGenos.size(); i++) |
---|
184 | { |
---|
185 | for (unsigned int j = 0; j < pvGenos.size(); j++) |
---|
186 | { |
---|
187 | dSimilarity = simil_measure->evaluateDistance(pvGenos.operator[](i), pvGenos.operator[](j)); |
---|
188 | aaSimil[i][j] = dSimilarity; |
---|
189 | } |
---|
190 | } |
---|
191 | |
---|
192 | if (print_names) |
---|
193 | { |
---|
194 | // if "-names" switch was given, print the number of genotypes and their names |
---|
195 | printf("%li\n", pvGenos.size()); |
---|
196 | for (unsigned int iGen = 0; iGen < pvNames.size(); iGen++) |
---|
197 | { |
---|
198 | printf("%s\n", pvNames.at(iGen)); |
---|
199 | } |
---|
200 | } |
---|
201 | |
---|
202 | // print out the matrix of similarities |
---|
203 | for (unsigned int i = 0; i < pvGenos.size(); i++) |
---|
204 | { |
---|
205 | for (unsigned int j = 0; j < pvGenos.size(); j++) |
---|
206 | { |
---|
207 | printf("%.2lf\t", aaSimil[i][j]); |
---|
208 | } |
---|
209 | printf("\n"); |
---|
210 | } |
---|
211 | |
---|
212 | // delete vectors and arrays |
---|
213 | for (unsigned int i = 0; i < pvGenos.size(); i++) |
---|
214 | { |
---|
215 | delete pvGenos.operator[](i); |
---|
216 | delete[] pvNames.operator[](i); |
---|
217 | delete[] aaSimil[i]; |
---|
218 | } |
---|
219 | |
---|
220 | delete[] aaSimil; |
---|
221 | delete simil_measure; |
---|
222 | |
---|
223 | return 0; |
---|
224 | } |
---|