Alphabet.cpp
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00011 #include <string.h>
00012 #include <math.h>
00013
00014 #include "features/Alphabet.h"
00015 #include "lib/io.h"
00016
00017
00018 const uint8_t CAlphabet::B_A=0;
00019 const uint8_t CAlphabet::B_C=1;
00020 const uint8_t CAlphabet::B_G=2;
00021 const uint8_t CAlphabet::B_T=3;
00022 const uint8_t CAlphabet::MAPTABLE_UNDEF=0xff;
00023 const char* CAlphabet::alphabet_names[11]={"DNA", "RAWDNA", "RNA", "PROTEIN", "ALPHANUM", "CUBE", "RAW", "IUPAC_NUCLEIC_ACID", "IUPAC_AMINO_ACID", "NONE", "UNKNOWN"};
00024
00025 CAlphabet::CAlphabet(char* al, int32_t len)
00026 : CSGObject()
00027 {
00028 EAlphabet alpha=NONE;
00029
00030 if (len>=(int32_t) strlen("DNA") && !strncmp(al, "DNA", strlen("DNA")))
00031 alpha = DNA;
00032 else if (len>=(int32_t) strlen("RAWDNA") && !strncmp(al, "RAWDNA", strlen("RAWDNA")))
00033 alpha = RAWDNA;
00034 else if (len>=(int32_t) strlen("RNA") && !strncmp(al, "RNA", strlen("RNA")))
00035 alpha = RNA;
00036 else if (len>=(int32_t) strlen("PROTEIN") && !strncmp(al, "PROTEIN", strlen("PROTEIN")))
00037 alpha = PROTEIN;
00038 else if (len>=(int32_t) strlen("ALPHANUM") && !strncmp(al, "ALPHANUM", strlen("ALPHANUM")))
00039 alpha = ALPHANUM;
00040 else if (len>=(int32_t) strlen("CUBE") && !strncmp(al, "CUBE", strlen("CUBE")))
00041 alpha = CUBE;
00042 else if ((len>=(int32_t) strlen("BYTE") && !strncmp(al, "BYTE", strlen("BYTE"))) ||
00043 (len>=(int32_t) strlen("RAW") && !strncmp(al, "RAW", strlen("RAW"))))
00044 alpha = RAWBYTE;
00045 else if (len>=(int32_t) strlen("IUPAC_NUCLEIC_ACID") && !strncmp(al, "IUPAC_NUCLEIC_ACID", strlen("IUPAC_NUCLEIC_ACID")))
00046 alpha = IUPAC_NUCLEIC_ACID;
00047 else if (len>=(int32_t) strlen("IUPAC_AMINO_ACID") && !strncmp(al, "IUPAC_AMINO_ACID", strlen("IUPAC_AMINO_ACID")))
00048 alpha = IUPAC_AMINO_ACID;
00049 else {
00050 SG_ERROR( "unknown alphabet %s\n", al);
00051 }
00052
00053 set_alphabet(alpha);
00054 }
00055
00056 CAlphabet::CAlphabet(EAlphabet alpha)
00057 : CSGObject()
00058 {
00059 set_alphabet(alpha);
00060 }
00061
00062 CAlphabet::CAlphabet(CAlphabet* a)
00063 : CSGObject()
00064 {
00065 ASSERT(a);
00066 set_alphabet(a->get_alphabet());
00067 copy_histogram(a);
00068 }
00069
00070 CAlphabet::~CAlphabet()
00071 {
00072 }
00073
00074 bool CAlphabet::set_alphabet(EAlphabet alpha)
00075 {
00076 bool result=true;
00077 alphabet=alpha;
00078
00079 switch (alphabet)
00080 {
00081 case DNA:
00082 case RAWDNA:
00083 num_symbols = 4;
00084 break;
00085 case RNA:
00086 num_symbols = 4;
00087 break;
00088 case PROTEIN:
00089 num_symbols = 26;
00090 break;
00091 case ALPHANUM:
00092 num_symbols = 36;
00093 break;
00094 case CUBE:
00095 num_symbols = 6;
00096 break;
00097 case RAWBYTE:
00098 num_symbols = 256;
00099 break;
00100 case IUPAC_NUCLEIC_ACID:
00101 num_symbols = 16;
00102 break;
00103 case IUPAC_AMINO_ACID:
00104 num_symbols = 23;
00105 break;
00106 case NONE:
00107 num_symbols = 0;
00108 break;
00109 default:
00110 num_symbols = 0;
00111 result=false;
00112 break;
00113 }
00114
00115 num_bits=(int32_t) ceil(log((float64_t) num_symbols)/log((float64_t) 2));
00116 init_map_table();
00117 clear_histogram();
00118
00119 SG_DEBUG( "initialised alphabet %s\n", get_alphabet_name(alphabet));
00120
00121 return result;
00122 }
00123
00124 void CAlphabet::init_map_table()
00125 {
00126 int32_t i;
00127 for (i=0; i<(1<<(8*sizeof(uint8_t))); i++)
00128 {
00129 maptable_to_bin[i] = MAPTABLE_UNDEF;
00130 maptable_to_char[i] = MAPTABLE_UNDEF;
00131 valid_chars[i] = false;
00132 }
00133
00134 switch (alphabet)
00135 {
00136 case CUBE:
00137 valid_chars[(uint8_t) '1']=true;
00138 valid_chars[(uint8_t) '2']=true;
00139 valid_chars[(uint8_t) '3']=true;
00140 valid_chars[(uint8_t) '4']=true;
00141 valid_chars[(uint8_t) '5']=true;
00142 valid_chars[(uint8_t) '6']=true;
00143
00144 maptable_to_bin[(uint8_t) '1']=0;
00145 maptable_to_bin[(uint8_t) '2']=1;
00146 maptable_to_bin[(uint8_t) '3']=2;
00147 maptable_to_bin[(uint8_t) '4']=3;
00148 maptable_to_bin[(uint8_t) '5']=4;
00149 maptable_to_bin[(uint8_t) '6']=5;
00150
00151 maptable_to_char[(uint8_t) 0]='1';
00152 maptable_to_char[(uint8_t) 1]='2';
00153 maptable_to_char[(uint8_t) 2]='3';
00154 maptable_to_char[(uint8_t) 3]='4';
00155 maptable_to_char[(uint8_t) 4]='5';
00156 maptable_to_char[(uint8_t) 5]='6';
00157 break;
00158
00159 case PROTEIN:
00160 {
00161 int32_t skip=0 ;
00162 for (i=0; i<21; i++)
00163 {
00164 if (i==1) skip++ ;
00165 if (i==8) skip++ ;
00166 if (i==12) skip++ ;
00167 if (i==17) skip++ ;
00168 valid_chars['A'+i+skip]=true;
00169 maptable_to_bin['A'+i+skip]=i ;
00170 maptable_to_char[i]='A'+i+skip ;
00171 } ;
00172 } ;
00173 break;
00174
00175 case ALPHANUM:
00176 {
00177 for (i=0; i<26; i++)
00178 {
00179 valid_chars['A'+i]=true;
00180 maptable_to_bin['A'+i]=i ;
00181 maptable_to_char[i]='A'+i ;
00182 } ;
00183 for (i=0; i<10; i++)
00184 {
00185 valid_chars['0'+i]=true;
00186 maptable_to_bin['0'+i]=26+i ;
00187 maptable_to_char[26+i]='0'+i ;
00188 } ;
00189 } ;
00190 break;
00191
00192 case RAWBYTE:
00193 {
00194
00195 for (i=0; i<256; i++)
00196 {
00197 valid_chars[i]=true;
00198 maptable_to_bin[i]=i;
00199 maptable_to_char[i]=i;
00200 }
00201 }
00202 break;
00203
00204 case DNA:
00205 valid_chars[(uint8_t) 'A']=true;
00206 valid_chars[(uint8_t) 'C']=true;
00207 valid_chars[(uint8_t) 'G']=true;
00208 valid_chars[(uint8_t) 'T']=true;
00209
00210 maptable_to_bin[(uint8_t) 'A']=B_A;
00211 maptable_to_bin[(uint8_t) 'C']=B_C;
00212 maptable_to_bin[(uint8_t) 'G']=B_G;
00213 maptable_to_bin[(uint8_t) 'T']=B_T;
00214
00215 maptable_to_char[B_A]='A';
00216 maptable_to_char[B_C]='C';
00217 maptable_to_char[B_G]='G';
00218 maptable_to_char[B_T]='T';
00219 break;
00220 case RAWDNA:
00221 {
00222
00223 for (i=0; i<4; i++)
00224 {
00225 valid_chars[i]=true;
00226 maptable_to_bin[i]=i;
00227 maptable_to_char[i]=i;
00228 }
00229 }
00230 break;
00231
00232 case RNA:
00233 valid_chars[(uint8_t) 'A']=true;
00234 valid_chars[(uint8_t) 'C']=true;
00235 valid_chars[(uint8_t) 'G']=true;
00236 valid_chars[(uint8_t) 'U']=true;
00237
00238 maptable_to_bin[(uint8_t) 'A']=B_A;
00239 maptable_to_bin[(uint8_t) 'C']=B_C;
00240 maptable_to_bin[(uint8_t) 'G']=B_G;
00241 maptable_to_bin[(uint8_t) 'U']=B_T;
00242
00243 maptable_to_char[B_A]='A';
00244 maptable_to_char[B_C]='C';
00245 maptable_to_char[B_G]='G';
00246 maptable_to_char[B_T]='U';
00247 break;
00248
00249 case IUPAC_NUCLEIC_ACID:
00250 valid_chars[(uint8_t) 'A']=true;
00251 valid_chars[(uint8_t) 'C']=true;
00252 valid_chars[(uint8_t) 'G']=true;
00253 valid_chars[(uint8_t) 'T']=true;
00254 valid_chars[(uint8_t) 'U']=true;
00255 valid_chars[(uint8_t) 'R']=true;
00256 valid_chars[(uint8_t) 'Y']=true;
00257 valid_chars[(uint8_t) 'M']=true;
00258 valid_chars[(uint8_t) 'K']=true;
00259 valid_chars[(uint8_t) 'W']=true;
00260 valid_chars[(uint8_t) 'S']=true;
00261 valid_chars[(uint8_t) 'B']=true;
00262 valid_chars[(uint8_t) 'D']=true;
00263 valid_chars[(uint8_t) 'H']=true;
00264 valid_chars[(uint8_t) 'V']=true;
00265 valid_chars[(uint8_t) 'N']=true;
00266
00267 maptable_to_bin[(uint8_t) 'A']=0;
00268 maptable_to_bin[(uint8_t) 'C']=1;
00269 maptable_to_bin[(uint8_t) 'G']=2;
00270 maptable_to_bin[(uint8_t) 'T']=3;
00271 maptable_to_bin[(uint8_t) 'U']=4;
00272 maptable_to_bin[(uint8_t) 'R']=5;
00273 maptable_to_bin[(uint8_t) 'Y']=6;
00274 maptable_to_bin[(uint8_t) 'M']=7;
00275 maptable_to_bin[(uint8_t) 'K']=8;
00276 maptable_to_bin[(uint8_t) 'W']=9;
00277 maptable_to_bin[(uint8_t) 'S']=10;
00278 maptable_to_bin[(uint8_t) 'B']=11;
00279 maptable_to_bin[(uint8_t) 'D']=12;
00280 maptable_to_bin[(uint8_t) 'H']=13;
00281 maptable_to_bin[(uint8_t) 'V']=14;
00282 maptable_to_bin[(uint8_t) 'N']=15;
00283
00284 maptable_to_char[0]=(uint8_t) 'A';
00285 maptable_to_char[1]=(uint8_t) 'C';
00286 maptable_to_char[2]=(uint8_t) 'G';
00287 maptable_to_char[3]=(uint8_t) 'T';
00288 maptable_to_char[4]=(uint8_t) 'U';
00289 maptable_to_char[5]=(uint8_t) 'R';
00290 maptable_to_char[6]=(uint8_t) 'Y';
00291 maptable_to_char[7]=(uint8_t) 'M';
00292 maptable_to_char[8]=(uint8_t) 'K';
00293 maptable_to_char[9]=(uint8_t) 'W';
00294 maptable_to_char[10]=(uint8_t) 'S';
00295 maptable_to_char[11]=(uint8_t) 'B';
00296 maptable_to_char[12]=(uint8_t) 'D';
00297 maptable_to_char[13]=(uint8_t) 'H';
00298 maptable_to_char[14]=(uint8_t) 'V';
00299 maptable_to_char[15]=(uint8_t) 'N';
00300 break;
00301
00302 case IUPAC_AMINO_ACID:
00303 valid_chars[(uint8_t) 'A']=true;
00304 valid_chars[(uint8_t) 'R']=true;
00305 valid_chars[(uint8_t) 'N']=true;
00306 valid_chars[(uint8_t) 'D']=true;
00307 valid_chars[(uint8_t) 'C']=true;
00308 valid_chars[(uint8_t) 'Q']=true;
00309 valid_chars[(uint8_t) 'E']=true;
00310 valid_chars[(uint8_t) 'G']=true;
00311 valid_chars[(uint8_t) 'H']=true;
00312 valid_chars[(uint8_t) 'I']=true;
00313 valid_chars[(uint8_t) 'L']=true;
00314 valid_chars[(uint8_t) 'K']=true;
00315 valid_chars[(uint8_t) 'M']=true;
00316 valid_chars[(uint8_t) 'F']=true;
00317 valid_chars[(uint8_t) 'P']=true;
00318 valid_chars[(uint8_t) 'S']=true;
00319 valid_chars[(uint8_t) 'T']=true;
00320 valid_chars[(uint8_t) 'W']=true;
00321 valid_chars[(uint8_t) 'Y']=true;
00322 valid_chars[(uint8_t) 'V']=true;
00323 valid_chars[(uint8_t) 'B']=true;
00324 valid_chars[(uint8_t) 'Z']=true;
00325 valid_chars[(uint8_t) 'X']=true;
00326
00327 maptable_to_bin[(uint8_t) 'A']=0;
00328 maptable_to_bin[(uint8_t) 'R']=1;
00329 maptable_to_bin[(uint8_t) 'N']=2;
00330 maptable_to_bin[(uint8_t) 'D']=3;
00331 maptable_to_bin[(uint8_t) 'C']=4;
00332 maptable_to_bin[(uint8_t) 'Q']=5;
00333 maptable_to_bin[(uint8_t) 'E']=6;
00334 maptable_to_bin[(uint8_t) 'G']=7;
00335 maptable_to_bin[(uint8_t) 'H']=8;
00336 maptable_to_bin[(uint8_t) 'I']=9;
00337 maptable_to_bin[(uint8_t) 'L']=10;
00338 maptable_to_bin[(uint8_t) 'K']=11;
00339 maptable_to_bin[(uint8_t) 'M']=12;
00340 maptable_to_bin[(uint8_t) 'F']=13;
00341 maptable_to_bin[(uint8_t) 'P']=14;
00342 maptable_to_bin[(uint8_t) 'S']=15;
00343 maptable_to_bin[(uint8_t) 'T']=16;
00344 maptable_to_bin[(uint8_t) 'W']=17;
00345 maptable_to_bin[(uint8_t) 'Y']=18;
00346 maptable_to_bin[(uint8_t) 'V']=19;
00347 maptable_to_bin[(uint8_t) 'B']=20;
00348 maptable_to_bin[(uint8_t) 'Z']=21;
00349 maptable_to_bin[(uint8_t) 'X']=22;
00350
00351 maptable_to_char[0]=(uint8_t) 'A';
00352 maptable_to_char[1]=(uint8_t) 'R';
00353 maptable_to_char[2]=(uint8_t) 'N';
00354 maptable_to_char[3]=(uint8_t) 'D';
00355 maptable_to_char[4]=(uint8_t) 'C';
00356 maptable_to_char[5]=(uint8_t) 'Q';
00357 maptable_to_char[6]=(uint8_t) 'E';
00358 maptable_to_char[7]=(uint8_t) 'G';
00359 maptable_to_char[8]=(uint8_t) 'H';
00360 maptable_to_char[9]=(uint8_t) 'I';
00361 maptable_to_char[10]=(uint8_t) 'L';
00362 maptable_to_char[11]=(uint8_t) 'K';
00363 maptable_to_char[12]=(uint8_t) 'M';
00364 maptable_to_char[13]=(uint8_t) 'F';
00365 maptable_to_char[14]=(uint8_t) 'P';
00366 maptable_to_char[15]=(uint8_t) 'S';
00367 maptable_to_char[16]=(uint8_t) 'T';
00368 maptable_to_char[17]=(uint8_t) 'W';
00369 maptable_to_char[18]=(uint8_t) 'Y';
00370 maptable_to_char[19]=(uint8_t) 'V';
00371 maptable_to_char[20]=(uint8_t) 'B';
00372 maptable_to_char[21]=(uint8_t) 'Z';
00373 maptable_to_char[22]=(uint8_t) 'X';
00374 default:
00375 break;
00376 };
00377 }
00378
00379 void CAlphabet::clear_histogram()
00380 {
00381 memset(histogram, 0, sizeof(histogram));
00382 print_histogram();
00383 }
00384
00385 int32_t CAlphabet::get_max_value_in_histogram()
00386 {
00387 int32_t max_sym=-1;
00388 for (int32_t i=(int32_t) (1 <<(sizeof(uint8_t)*8))-1;i>=0; i--)
00389 {
00390 if (histogram[i])
00391 {
00392 max_sym=i;
00393 break;
00394 }
00395 }
00396
00397 return max_sym;
00398 }
00399
00400 int32_t CAlphabet::get_num_symbols_in_histogram()
00401 {
00402 int32_t num_sym=0;
00403 for (int32_t i=0; i<(int32_t) (1 <<(sizeof(uint8_t)*8)); i++)
00404 {
00405 if (histogram[i])
00406 num_sym++;
00407 }
00408
00409 return num_sym;
00410 }
00411
00412 int32_t CAlphabet::get_num_bits_in_histogram()
00413 {
00414 int32_t num_sym=get_num_symbols_in_histogram();
00415 if (num_sym>0)
00416 return (int32_t) ceil(log((float64_t) num_sym)/log((float64_t) 2));
00417 else
00418 return 0;
00419 }
00420
00421 void CAlphabet::print_histogram()
00422 {
00423 for (int32_t i=0; i<(int32_t) (1 <<(sizeof(uint8_t)*8)); i++)
00424 {
00425 if (histogram[i])
00426 SG_PRINT( "hist[%d]=%lld\n", i, histogram[i]);
00427 }
00428 }
00429
00430 bool CAlphabet::check_alphabet(bool print_error)
00431 {
00432 bool result = true;
00433
00434 for (int32_t i=0; i<(int32_t) (1 <<(sizeof(uint8_t)*8)); i++)
00435 {
00436 if (histogram[i]>0 && valid_chars[i]==0)
00437 {
00438 result=false;
00439 break;
00440 }
00441 }
00442
00443 if (!result && print_error)
00444 {
00445 print_histogram();
00446 SG_ERROR( "ALPHABET does not contain all symbols in histogram\n");
00447 }
00448
00449 return result;
00450 }
00451
00452 bool CAlphabet::check_alphabet_size(bool print_error)
00453 {
00454 if (get_num_bits_in_histogram() > get_num_bits())
00455 {
00456 if (print_error)
00457 {
00458 print_histogram();
00459 fprintf(stderr, "get_num_bits_in_histogram()=%i > get_num_bits()=%i\n", get_num_bits_in_histogram(), get_num_bits()) ;
00460 SG_ERROR( "ALPHABET too small to contain all symbols in histogram\n");
00461 }
00462 return false;
00463 }
00464 else
00465 return true;
00466
00467 }
00468
00469 void CAlphabet::copy_histogram(CAlphabet* a)
00470 {
00471 memcpy(histogram, a->get_histogram(), sizeof(histogram));
00472 }
00473
00474 const char* CAlphabet::get_alphabet_name(EAlphabet alphabet)
00475 {
00476
00477 int32_t idx;
00478 switch (alphabet)
00479 {
00480 case DNA:
00481 idx=0;
00482 break;
00483 case RAWDNA:
00484 idx=1;
00485 break;
00486 case RNA:
00487 idx=2;
00488 break;
00489 case PROTEIN:
00490 idx=3;
00491 break;
00492 case ALPHANUM:
00493 idx=4;
00494 break;
00495 case CUBE:
00496 idx=5;
00497 break;
00498 case RAWBYTE:
00499 idx=6;
00500 break;
00501 case IUPAC_NUCLEIC_ACID:
00502 idx=7;
00503 break;
00504 case IUPAC_AMINO_ACID:
00505 idx=8;
00506 break;
00507 case NONE:
00508 idx=9;
00509 break;
00510 default:
00511 idx=10;
00512 break;
00513 }
00514 return alphabet_names[idx];
00515 }