binaries/src/ViennaRNA/doc/latex/mainpage_8h_source.tex

   1 \hypertarget{mainpage_8h_source}{\section{mainpage.\-h}
   2 }
   3
   4 \begin{DoxyCode}
   5 00001 \textcolor{comment}{/*}
   6 00002 \textcolor{comment}{#############################################################}
   7 00003 \textcolor{comment}{# The next comment is used to order the modules correctly   #}
   8 00004 \textcolor{comment}{#############################################################}
   9 00005 \textcolor{comment}{*/}
  10 00006
  11 00108 \textcolor{comment}{/*}
  12 00109 \textcolor{comment}{#############################################################}
  13 00110 \textcolor{comment}{# Now the mainpage text is following                        #}
  14 00111 \textcolor{comment}{#############################################################}
  15 00112 \textcolor{comment}{*/}
  16 00113
  17 00327    \{   0,   2,   2,   2,   2,   1,   1\},   \textcolor{comment}{/* Null replaced */}
  18 00328    \{   2,   0,   2,   2,   2, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}\},   \textcolor{comment}{/* H    replaced */}
  19 00329    \{   2,   2,   0,   1,   2, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}\},   \textcolor{comment}{/* B    replaced */}
  20 00330    \{   2,   2,   1,   0,   2, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}\},   \textcolor{comment}{/* I    replaced */}
  21 00331    \{   2,   2,   2,   2,   0, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}\},   \textcolor{comment}{/* M    replaced */}
  22 00332    \{   1, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   0, INF\},   \textcolor{comment}{/* S    replaced */}
  23 00333    \{   1, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   0\},   \textcolor{comment}{/* E    replaced */}
  24 00334
  25 00335
  26 00336 \textcolor{comment}{/* Null,   H,   B,   I,   M,   S,   E   */}
  27 00337    \{   0, 100,   5,   5,  75,   5,   5\},   \textcolor{comment}{/* Null replaced */}
  28 00338    \{ 100,   0,   8,   8,   8, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}\},   \textcolor{comment}{/* H    replaced */}
  29 00339    \{   5,   8,   0,   3,   8, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}\},   \textcolor{comment}{/* B    replaced */}
  30 00340    \{   5,   8,   3,   0,   8, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}\},   \textcolor{comment}{/* I    replaced */}
  31 00341    \{  75,   8,   8,   8,   0, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}\},   \textcolor{comment}{/* M    replaced */}
  32 00342    \{   5, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   0, INF\},   \textcolor{comment}{/* S    replaced */}
  33 00343    \{   5, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF}, \hyperlink{energy__const_8h_a12c2040f25d8e3a7b9e1c2024c618cb6}{INF},   0\},   \textcolor{comment}{/* E    replaced */}
  34 00344 \(\backslash\)endverbatim
  35 00345
  36 00346 The lower matrix uses the costs given in \(\backslash\)cite shapiro:1990.
  37 00347 All distance functions use the following global variables:
  38 00348
  39 00349 \(\backslash\)verbatim
  40 00350 \textcolor{keywordtype}{int}  \hyperlink{dist__vars_8h_ab65d8ff14c6937612212526a60f59b3c}{cost\_matrix};
  41 00351 \(\backslash\)endverbatim
  42 00352 \(\backslash\)copybrief cost\_matrix
  43 00353
  44 00354 \(\backslash\)verbatim
  45 00355 \textcolor{keywordtype}{int}   \hyperlink{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{edit\_backtrack};
  46 00356 \(\backslash\)endverbatim
  47 00357 \(\backslash\)copybrief edit\_backtrack
  48 00358
  49 00359 \(\backslash\)verbatim
  50 00360 \textcolor{keywordtype}{char} *\hyperlink{dist__vars_8h_ac1605fe3448ad0a0b809c4fb8f6a854a}{aligned\_line}[4];
  51 00361 \(\backslash\)endverbatim
  52 00362 \(\backslash\)copybrief aligned\_line
  53 00363
  54 00364 \(\backslash\)see utils.h, dist\_vars.h and stringdist.h \textcolor{keywordflow}{for} more details
  55 00365
  56 00366 <h3>Functions \textcolor{keywordflow}{for} \hyperlink{structTree}{Tree} Edit Distances</h3>
  57 00367
  58 00368 \(\backslash\)verbatim
  59 00369 \hyperlink{structTree}{Tree}   *\hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\_tree} (\textcolor{keywordtype}{char} *struc)
  60 00370 \(\backslash\)endverbatim
  61 00371 \(\backslash\)copybrief \hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\_tree}()
  62 00372
  63 00373 \(\backslash\)verbatim
  64 00374 \textcolor{keywordtype}{float}   \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\_edit\_distance} (\hyperlink{structTree}{Tree} *T1,
  65 00375                             \hyperlink{structTree}{Tree} *T2)
  66 00376 \(\backslash\)endverbatim
  67 00377 \(\backslash\)copybrief \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\_edit\_distance}()
  68 00378
  69 00379 \(\backslash\)verbatim
  70 00380 \textcolor{keywordtype}{void}    \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\_tree}(\hyperlink{structTree}{Tree} *t)
  71 00381 \(\backslash\)endverbatim
  72 00382 \(\backslash\)copybrief \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\_tree}()
  73 00383
  74 00384 \(\backslash\)see dist\_vars.h and treedist.h \textcolor{keywordflow}{for} prototypes and more detailed descriptions
  75 00385
  76 00386 <h3>Functions \textcolor{keywordflow}{for} String Alignment</h3>
  77 00387
  78 00388 \(\backslash\)verbatim
  79 00389 \hyperlink{structswString}{swString} *\hyperlink{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{Make\_swString} (\textcolor{keywordtype}{char} *\textcolor{keywordtype}{string})
  80 00390 \(\backslash\)endverbatim
  81 00391 \(\backslash\)copybrief \hyperlink{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{Make\_swString}()
  82 00392
  83 00393 \(\backslash\)verbatim
  84 00394 \textcolor{keywordtype}{float}     \hyperlink{stringdist_8h_a89e3c335ef17780576d7c0e713830db9}{string\_edit\_distance} (\hyperlink{structswString}{swString} *T1,
  85 00395                                 \hyperlink{structswString}{swString} *T2)
  86 00396 \(\backslash\)endverbatim
  87 00397 \(\backslash\)copybrief \hyperlink{stringdist_8h_a89e3c335ef17780576d7c0e713830db9}{string\_edit\_distance}()
  88 00398
  89 00399 \(\backslash\)see dist\_vars.h and stringdist.h \textcolor{keywordflow}{for} prototypes and more detailed descriptions
  90 00400
  91 00401 <h3>Functions \textcolor{keywordflow}{for} Comparison of Base Pair Probabilities</h3>
  92 00402
  93 00403 For comparison of base pair probability matrices, the matrices are first
  94 00404 condensed into probability profiles which are the compared by alignment.
  95 00405
  96 00406 \(\backslash\)verbatim
  97 00407 \textcolor{keywordtype}{float} *\hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\_bp\_profile\_bppm} ( \textcolor{keywordtype}{double} *bppm,
  98 00408                               \textcolor{keywordtype}{int} length)
  99 00409 \(\backslash\)endverbatim
 100 00410 \(\backslash\)copybrief \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\_bp\_profile\_bppm}()
 101 00411
 102 00412 \(\backslash\)verbatim
 103 00413 \textcolor{keywordtype}{float} \hyperlink{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{profile\_edit\_distance} ( \textcolor{keyword}{const} \textcolor{keywordtype}{float} *T1,
 104 00414                               \textcolor{keyword}{const} \textcolor{keywordtype}{float} *T2)
 105 00415 \(\backslash\)endverbatim
 106 00416 \(\backslash\)copybrief \hyperlink{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{profile\_edit\_distance}()
 107 00417
 108 00418 \(\backslash\)see ProfileDist.h \textcolor{keywordflow}{for} prototypes and more details of the above functions
 109 00419
 110 00420 \(\backslash\)ref mp\_utils \textcolor{stringliteral}{"Next Page: Utilities"}
 111 00421
 112 00422 \(\backslash\)page  mp\_utils     Utilities - Odds and Ends
 113 00423
 114 00424 \(\backslash\)anchor toc
 115 00425
 116 00426 <h3>Table of Contents</h3>
 117 00427 <hr>
 118 00428
 119 00429 \(\backslash\)li \(\backslash\)ref  utils\_ss
 120 00430 \(\backslash\)li \(\backslash\)ref  utils\_dot
 121 00431 \(\backslash\)li \(\backslash\)ref  utils\_aln
 122 00432 \(\backslash\)li \(\backslash\)ref  utils\_seq
 123 00433 \(\backslash\)li \(\backslash\)ref  utils\_struc
 124 00434 \(\backslash\)li \(\backslash\)ref  utils\_misc
 125 00435
 126 00436 <hr>
 127 00437
 128 00438 \(\backslash\)section utils\_ss Producing secondary structure graphs
 129 00439
 130 00440 \(\backslash\)verbatim
 131 00441 \textcolor{keywordtype}{int} \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{PS\_rna\_plot} ( \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 132 00442                   \textcolor{keywordtype}{char} *structure,
 133 00443                   \textcolor{keywordtype}{char} *file)
 134 00444 \(\backslash\)endverbatim
 135 00445 \(\backslash\)copybrief \hyperlink{PS__dot_8h_a0873c7cc4cd7a11c9a2cea19dde7e9c9}{PS\_rna\_plot}()
 136 00446
 137 00447 \(\backslash\)verbatim
 138 00448 \textcolor{keywordtype}{int} \hyperlink{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{PS\_rna\_plot\_a} (
 139 00449             \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 140 00450             \textcolor{keywordtype}{char} *structure,
 141 00451             \textcolor{keywordtype}{char} *file,
 142 00452             \textcolor{keywordtype}{char} *pre,
 143 00453             \textcolor{keywordtype}{char} *post)
 144 00454 \(\backslash\)endverbatim
 145 00455 \(\backslash\)copybrief \hyperlink{PS__dot_8h_a47856b2504b566588785597b6ebb8271}{PS\_rna\_plot\_a}()
 146 00456
 147 00457 \(\backslash\)verbatim
 148 00458 \textcolor{keywordtype}{int} \hyperlink{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{gmlRNA} (\textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 149 00459             \textcolor{keywordtype}{char} *structure,
 150 00460             \textcolor{keywordtype}{char} *ssfile,
 151 00461             \textcolor{keywordtype}{char} option)
 152 00462 \(\backslash\)endverbatim
 153 00463 \(\backslash\)copybrief \hyperlink{PS__dot_8h_a70834bc8c0aad4fe6824ff76ccb8f329}{gmlRNA}()
 154 00464
 155 00465 \(\backslash\)verbatim
 156 00466 \textcolor{keywordtype}{int} \hyperlink{PS__dot_8h_add368528755f9a830727b680243541df}{ssv\_rna\_plot} (\textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 157 00467                   \textcolor{keywordtype}{char} *structure,
 158 00468                   \textcolor{keywordtype}{char} *ssfile)
 159 00469 \(\backslash\)endverbatim
 160 00470 \(\backslash\)copybrief \hyperlink{PS__dot_8h_add368528755f9a830727b680243541df}{ssv\_rna\_plot}()
 161 00471
 162 00472 \(\backslash\)verbatim
 163 00473 \textcolor{keywordtype}{int} \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\_rna\_plot} (\textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 164 00474                   \textcolor{keywordtype}{char} *structure,
 165 00475                   \textcolor{keywordtype}{char} *ssfile)
 166 00476 \(\backslash\)endverbatim
 167 00477 \(\backslash\)copybrief \hyperlink{PS__dot_8h_ae7853539b5df98f294b4af434e979304}{svg\_rna\_plot}()
 168 00478
 169 00479 \(\backslash\)verbatim
 170 00480 \textcolor{keywordtype}{int} \hyperlink{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{xrna\_plot} ( \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 171 00481                 \textcolor{keywordtype}{char} *structure,
 172 00482                 \textcolor{keywordtype}{char} *ssfile)
 173 00483 \(\backslash\)endverbatim
 174 00484 \(\backslash\)copybrief \hyperlink{PS__dot_8h_a2f6d5953e6a323df898896b8d6614483}{xrna\_plot}()
 175 00485
 176 00486 \(\backslash\)verbatim
 177 00487 \textcolor{keywordtype}{int} rna\_plot\_type
 178 00488 \(\backslash\)endverbatim
 179 00489 \(\backslash\)copybrief \hyperlink{plot__layouts_8h_a5964c4581431b098b80027d6e14dcdd4}{rna\_plot\_type}
 180 00490
 181 00491 Two low-level functions provide direct access to the graph lauyouting
 182 00492 algorithms:
 183 00493
 184 00494 \(\backslash\)verbatim
 185 00495 \textcolor{keywordtype}{int} \hyperlink{plot__layouts_8h_af4b9173e7d3fd361c3c85e6def194123}{simple\_xy\_coordinates} ( \textcolor{keywordtype}{short} *pair\_table,
 186 00496                             \textcolor{keywordtype}{float} *X,
 187 00497                             \textcolor{keywordtype}{float} *Y)
 188 00498 \(\backslash\)endverbatim
 189 00499 \(\backslash\)copybrief \hyperlink{plot__layouts_8h_af4b9173e7d3fd361c3c85e6def194123}{simple\_xy\_coordinates}()
 190 00500
 191 00501 \(\backslash\)verbatim
 192 00502 \textcolor{keywordtype}{int} naview\_xy\_coordinates ( \textcolor{keywordtype}{short} *pair\_table,
 193 00503                             \textcolor{keywordtype}{float} *X,
 194 00504                             \textcolor{keywordtype}{float} *Y)
 195 00505 \(\backslash\)endverbatim
 196 00506 \(\backslash\)copybrief naview\_xy\_coordinates()
 197 00507
 198 00508 \(\backslash\)see PS\_dot.h and naview.h \textcolor{keywordflow}{for} more detailed descriptions.
 199 00509
 200 00510 \(\backslash\)htmlonly
 201 00511 <hr>
 202 00512 <a href=\textcolor{stringliteral}{"#toc"}>Table of Contents</a>
 203 00513 <hr>
 204 00514 \(\backslash\)endhtmlonly
 205 00515
 206 00516 \(\backslash\)section utils\_dot Producing (colored) dot plots for base pair probabilities
 207 00517
 208 00518 \(\backslash\)verbatim
 209 00519 \textcolor{keywordtype}{int} PS\_color\_dot\_plot ( \textcolor{keywordtype}{char} *\textcolor{keywordtype}{string},
 210 00520                         \hyperlink{structcpair}{cpair} *pi,
 211 00521                         \textcolor{keywordtype}{char} *filename)
 212 00522 \(\backslash\)endverbatim
 213 00523 \(\backslash\)copybrief PS\_color\_dot\_plot()
 214 00524
 215 00525 \(\backslash\)verbatim
 216 00526 \textcolor{keywordtype}{int} PS\_color\_dot\_plot\_turn (\textcolor{keywordtype}{char} *seq,
 217 00527                             \hyperlink{structcpair}{cpair} *pi,
 218 00528                             \textcolor{keywordtype}{char} *filename,
 219 00529                             \textcolor{keywordtype}{int} winSize)
 220 00530 \(\backslash\)endverbatim
 221 00531 \(\backslash\)copybrief PS\_color\_dot\_plot\_turn()
 222 00532
 223 00533 \(\backslash\)verbatim
 224 00534 \textcolor{keywordtype}{int} \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{PS\_dot\_plot\_list} (\textcolor{keywordtype}{char} *seq,
 225 00535                       \textcolor{keywordtype}{char} *filename,
 226 00536                       \hyperlink{structplist}{plist} *pl,
 227 00537                       \hyperlink{structplist}{plist} *mf,
 228 00538                       \textcolor{keywordtype}{char} *comment)
 229 00539 \(\backslash\)endverbatim
 230 00540 \(\backslash\)copybrief \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{PS\_dot\_plot\_list}()
 231 00541
 232 00542 \(\backslash\)verbatim
 233 00543 \textcolor{keywordtype}{int} PS\_dot\_plot\_turn (\textcolor{keywordtype}{char} *seq,
 234 00544                       struct \hyperlink{structplist}{plist} *pl,
 235 00545                       \textcolor{keywordtype}{char} *filename,
 236 00546                       \textcolor{keywordtype}{int} winSize)
 237 00547 \(\backslash\)endverbatim
 238 00548 \(\backslash\)copybrief PS\_dot\_plot\_turn()
 239 00549
 240 00550 \(\backslash\)see PS\_dot.h for more detailed descriptions.
 241 00551
 242 00552 \(\backslash\)section utils\_aln Producing (colored) alignments
 243 00553
 244 00554 \(\backslash\)verbatim
 245 00555 \textcolor{keywordtype}{int} PS\_color\_aln (
 246 00556             const \textcolor{keywordtype}{char} *structure,
 247 00557             const \textcolor{keywordtype}{char} *filename,
 248 00558             const \textcolor{keywordtype}{char} *seqs[],
 249 00559             const \textcolor{keywordtype}{char} *names[])
 250 00560 \(\backslash\)endverbatim
 251 00561 \(\backslash\)copybrief PS\_color\_aln()
 252 00562
 253 00563 \(\backslash\)htmlonly
 254 00564 <hr>
 255 00565 <a href="\textcolor{preprocessor}{#toc">Table of Contents</a>}
 256 00566 \textcolor{preprocessor}{}<hr>
 257 00567 \(\backslash\)endhtmlonly
 258 00568
 259 00569 \(\backslash\)section  utils\_seq   RNA sequence related utilities
 260 00570
 261 00571 Several functions provide useful applications to RNA sequences
 262 00572
 263 00573 \(\backslash\)verbatim
 264 00574 \textcolor{keywordtype}{char}  *\hyperlink{utils_8h_a1b95eac365a021572e1c37e5993a89be}{random\_string} (\textcolor{keywordtype}{int} l,
 265 00575                       \textcolor{keyword}{const} \textcolor{keywordtype}{char} symbols[])
 266 00576 \(\backslash\)endverbatim
 267 00577 \(\backslash\)copybrief \hyperlink{utils_8h_a1b95eac365a021572e1c37e5993a89be}{random\_string}()
 268 00578
 269 00579 \(\backslash\)verbatim
 270 00580 \textcolor{keywordtype}{int}   \hyperlink{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{hamming} ( \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s1,
 271 00581                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *s2)
 272 00582 \(\backslash\)endverbatim
 273 00583 \(\backslash\)copybrief \hyperlink{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{hamming}()
 274 00584
 275 00585 \(\backslash\)verbatim
 276 00586 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{str\_DNA2RNA}(\textcolor{keywordtype}{char} *sequence);
 277 00587 \(\backslash\)endverbatim
 278 00588 \(\backslash\)copybrief \hyperlink{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{str\_DNA2RNA}()
 279 00589
 280 00590 \(\backslash\)verbatim
 281 00591 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a17b796b806f96b70382077fb5bc519bb}{str\_uppercase}(\textcolor{keywordtype}{char} *sequence);
 282 00592 \(\backslash\)endverbatim
 283 00593 \(\backslash\)copybrief \hyperlink{utils_8h_a17b796b806f96b70382077fb5bc519bb}{str\_uppercase}()
 284 00594
 285 00595 \(\backslash\)htmlonly
 286 00596 <hr>
 287 00597 <a href=\textcolor{stringliteral}{"#toc"}>Table of Contents</a>
 288 00598 <hr>
 289 00599 \(\backslash\)endhtmlonly
 290 00600
 291 00601 \(\backslash\)section utils\_struc  RNA secondary structure related utilities
 292 00602
 293 00603 \(\backslash\)verbatim
 294 00604 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\_structure} (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *struc)
 295 00605 \(\backslash\)endverbatim
 296 00606 \(\backslash\)copybrief \hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\_structure}()
 297 00607
 298 00608 \(\backslash\)verbatim
 299 00609 \textcolor{keywordtype}{char} *\hyperlink{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{unpack\_structure} (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *packed)
 300 00610 \(\backslash\)endverbatim
 301 00611 \(\backslash\)copybrief \hyperlink{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{unpack\_structure}()
 302 00612
 303 00613 \(\backslash\)verbatim
 304 00614 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\_pair\_table} (\textcolor{keyword}{const} \textcolor{keywordtype}{char} *structure)
 305 00615 \(\backslash\)endverbatim
 306 00616 \(\backslash\)copybrief \hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\_pair\_table}()
 307 00617
 308 00618 \(\backslash\)verbatim
 309 00619 \textcolor{keywordtype}{short} *\hyperlink{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{copy\_pair\_table} (\textcolor{keyword}{const} \textcolor{keywordtype}{short} *pt)
 310 00620 \(\backslash\)endverbatim
 311 00621 \(\backslash\)copybrief \hyperlink{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{copy\_pair\_table}()
 312 00622
 313 00623 \(\backslash\)htmlonly
 314 00624 <hr>
 315 00625 <a href=\textcolor{stringliteral}{"#toc"}>Table of Contents</a>
 316 00626 <hr>
 317 00627 \(\backslash\)endhtmlonly
 318 00628
 319 00629 \(\backslash\)section  utils\_misc  Miscellaneous Utilities
 320 00630
 321 00631 \(\backslash\)verbatim
 322 00632 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{print\_tty\_input\_seq} (\textcolor{keywordtype}{void})
 323 00633 \(\backslash\)endverbatim
 324 00634 \(\backslash\)copybrief \hyperlink{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{print\_tty\_input\_seq}()
 325 00635
 326 00636 \(\backslash\)verbatim
 327 00637 \textcolor{keywordtype}{void} \hyperlink{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{print\_tty\_constraint\_full} (\textcolor{keywordtype}{void})
 328 00638 \(\backslash\)endverbatim
 329 00639 \(\backslash\)copybrief \hyperlink{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{print\_tty\_constraint\_full}()
 330 00640
 331 00641 \(\backslash\)verbatim
 332 00642 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a4d167deb70bb51723e44374dc981deb2}{print\_tty\_constraint} (\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} option)
 333 00643 \(\backslash\)endverbatim
 334 00644 \(\backslash\)copybrief \hyperlink{utils_8h_a4d167deb70bb51723e44374dc981deb2}{print\_tty\_constraint}()
 335 00645
 336 00646 \(\backslash\)verbatim
 337 00647 \textcolor{keywordtype}{int}   *\hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\_iindx} (\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length)
 338 00648 \(\backslash\)endverbatim
 339 00649 \(\backslash\)copybrief \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\_iindx}()
 340 00650
 341 00651 \(\backslash\)verbatim
 342 00652 \textcolor{keywordtype}{int}   *\hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\_indx} (\textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length)
 343 00653 \(\backslash\)endverbatim
 344 00654 \(\backslash\)copybrief \hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\_indx}()
 345 00655
 346 00656 \(\backslash\)verbatim
 347 00657 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a36c3a6c3218b041f992052767bc74549}{constrain\_ptypes} (
 348 00658                 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *constraint,
 349 00659                 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} length,
 350 00660                 \textcolor{keywordtype}{char} *ptype,
 351 00661                 \textcolor{keywordtype}{int} *BP,
 352 00662                 \textcolor{keywordtype}{int} min\_loop\_size,
 353 00663                 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} idx\_type)
 354 00664 \(\backslash\)endverbatim
 355 00665 \(\backslash\)copybrief \hyperlink{utils_8h_a36c3a6c3218b041f992052767bc74549}{constrain\_ptypes}()
 356 00666
 357 00667 \(\backslash\)verbatim
 358 00668 \textcolor{keywordtype}{char}  *\hyperlink{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{get\_line}(FILE *fp);
 359 00669 \(\backslash\)endverbatim
 360 00670 \(\backslash\)copybrief \hyperlink{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{get\_line}()
 361 00671
 362 00672 \(\backslash\)verbatim
 363 00673 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\_record}(
 364 00674                 \textcolor{keywordtype}{char} **header,
 365 00675                 \textcolor{keywordtype}{char} **sequence,
 366 00676                 \textcolor{keywordtype}{char} ***rest,
 367 00677                 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} options);
 368 00678 \(\backslash\)endverbatim
 369 00679 \(\backslash\)copybrief \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\_record}()
 370 00680
 371 00681 \(\backslash\)verbatim
 372 00682 \textcolor{keywordtype}{char}  *\hyperlink{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{time\_stamp} (\textcolor{keywordtype}{void})
 373 00683 \(\backslash\)endverbatim
 374 00684 \(\backslash\)copybrief \hyperlink{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{time\_stamp}()
 375 00685
 376 00686 \(\backslash\)verbatim
 377 00687 \textcolor{keywordtype}{void} \hyperlink{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{warn\_user} (\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[])
 378 00688 \(\backslash\)endverbatim
 379 00689 \(\backslash\)copybrief \hyperlink{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{warn\_user}()
 380 00690
 381 00691 \(\backslash\)verbatim
 382 00692 \textcolor{keywordtype}{void} \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror} (\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[])
 383 00693 \(\backslash\)endverbatim
 384 00694 \(\backslash\)copybrief \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror}()
 385 00695
 386 00696 \(\backslash\)verbatim
 387 00697 \textcolor{keywordtype}{void}   \hyperlink{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{init\_rand} (\textcolor{keywordtype}{void})
 388 00698 \(\backslash\)endverbatim
 389 00699 \(\backslash\)copybrief \hyperlink{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{init\_rand}()
 390 00700
 391 00701 \(\backslash\)verbatim
 392 00702 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{short} \hyperlink{utils_8h_af9a866c8417afda7368bbac939ab3c47}{xsubi}[3];
 393 00703 \(\backslash\)endverbatim
 394 00704 \(\backslash\)copybrief xsubi
 395 00705
 396 00706 \(\backslash\)verbatim
 397 00707 \textcolor{keywordtype}{double} \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn} (\textcolor{keywordtype}{void})
 398 00708 \(\backslash\)endverbatim
 399 00709 \(\backslash\)copybrief \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn}()
 400 00710
 401 00711 \(\backslash\)verbatim
 402 00712 \textcolor{keywordtype}{int}    \hyperlink{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{int\_urn} (\textcolor{keywordtype}{int} from, \textcolor{keywordtype}{int} to)
 403 00713 \(\backslash\)endverbatim
 404 00714 \(\backslash\)copybrief \hyperlink{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{int\_urn}()
 405 00715
 406 00716 \(\backslash\)verbatim
 407 00717 \textcolor{keywordtype}{void}  *\hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space} (\textcolor{keywordtype}{unsigned} size)
 408 00718 \(\backslash\)endverbatim
 409 00719 \(\backslash\)copybrief \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}()
 410 00720
 411 00721 \(\backslash\)verbatim
 412 00722 \textcolor{keywordtype}{void}  *\hyperlink{utils_8h_a9037ada838835b1b9db41581a021b0c8}{xrealloc} ( \textcolor{keywordtype}{void} *p,
 413 00723                   \textcolor{keywordtype}{unsigned} size)
 414 00724 \(\backslash\)endverbatim
 415 00725 \(\backslash\)copybrief \hyperlink{utils_8h_a9037ada838835b1b9db41581a021b0c8}{xrealloc}()
 416 00726
 417 00727 \(\backslash\)see  utils.h \textcolor{keywordflow}{for} a complete overview and detailed description of the utility functions
 418 00728
 419 00729 \(\backslash\)htmlonly
 420 00730 <hr>
 421 00731 <a href=\textcolor{stringliteral}{"#toc"}>Table of Contents</a>
 422 00732 <hr>
 423 00733 \(\backslash\)endhtmlonly
 424 00734
 425 00735 \(\backslash\)ref mp\_example \textcolor{stringliteral}{"Next Page: Examples"}
 426 00736
 427 00737 \(\backslash\)page  mp\_example   Example - A Small Example Program
 428 00738
 429 00739 The following program exercises most commonly used functions of the library.
 430 00740 The program folds two sequences \textcolor{keyword}{using} both the mfe and partition \textcolor{keyword}{function}
 431 00741 algorithms and calculates the tree edit and profile distance of the
 432 00742 resulting structures and base pairing probabilities.
 433 00743
 434 00744 \(\backslash\)code\{.c\}
 435 00745 \textcolor{preprocessor}{#include  <stdio.h>}
 436 00746 \textcolor{preprocessor}{#include  <stdlib.h>}
 437 00747 \textcolor{preprocessor}{#include  <math.h>}
 438 00748 \textcolor{preprocessor}{#include  <string.h>}
 439 00749 \textcolor{preprocessor}{#include  "\hyperlink{utils_8h}{utils.h}"}
 440 00750 \textcolor{preprocessor}{#include  "\hyperlink{fold__vars_8h}{fold\_vars.h}"}
 441 00751 \textcolor{preprocessor}{#include  "\hyperlink{fold_8h}{fold.h}"}
 442 00752 \textcolor{preprocessor}{#include  "\hyperlink{part__func_8h}{part\_func.h}"}
 443 00753 \textcolor{preprocessor}{#include  "\hyperlink{inverse_8h}{inverse.h}"}
 444 00754 \textcolor{preprocessor}{#include  "\hyperlink{RNAstruct_8h}{RNAstruct.h}"}
 445 00755 \textcolor{preprocessor}{#include  "\hyperlink{treedist_8h}{treedist.h}"}
 446 00756 \textcolor{preprocessor}{#include  "\hyperlink{stringdist_8h}{stringdist.h}"}
 447 00757 \textcolor{preprocessor}{#include  "\hyperlink{profiledist_8h}{profiledist.h}"}
 448 00758
 449 00759 \textcolor{keywordtype}{void} main()
 450 00760 \{
 451 00761    \textcolor{keywordtype}{char} *seq1=\textcolor{stringliteral}{"CGCAGGGAUACCCGCG"}, *seq2=\textcolor{stringliteral}{"GCGCCCAUAGGGACGC"},
 452 00762         *struct1,* struct2,* xstruc;
 453 00763    \textcolor{keywordtype}{float} e1, e2, tree\_dist, string\_dist, profile\_dist, kT;
 454 00764    \hyperlink{structTree}{Tree} *T1, *T2;
 455 00765    \hyperlink{structswString}{swString} *S1, *S2;
 456 00766    \textcolor{keywordtype}{float} *pf1, *pf2;
 457 00767    FLT\_OR\_DBL *bppm;
 458 00768    \textcolor{comment}{/* fold at 30C instead of the default 37C */}
 459 00769    \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature} = 30.;      \textcolor{comment}{/* must be set *before* initializing  */}
 460 00770
 461 00771    \textcolor{comment}{/* allocate memory for structure and fold */}
 462 00772    struct1 = (\textcolor{keywordtype}{char}* ) \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}(\textcolor{keyword}{sizeof}(\textcolor{keywordtype}{char})*(strlen(seq1)+1));
 463 00773    e1 =  \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold}(seq1, struct1);
 464 00774
 465 00775    struct2 = (\textcolor{keywordtype}{char}* ) \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}(\textcolor{keyword}{sizeof}(\textcolor{keywordtype}{char})*(strlen(seq2)+1));
 466 00776    e2 =  \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold}(seq2, struct2);
 467 00777
 468 00778    \hyperlink{group__mfe__fold_ga107fdfe5fd641868156bfd849f6866c7}{free\_arrays}();     \textcolor{comment}{/* free arrays used in fold() */}
 469 00779
 470 00780    \textcolor{comment}{/* produce tree and string representations for comparison */}
 471 00781    xstruc = \hyperlink{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{expand\_Full}(struct1);
 472 00782    T1 = \hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\_tree}(xstruc);
 473 00783    S1 = \hyperlink{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{Make\_swString}(xstruc);
 474 00784    free(xstruc);
 475 00785
 476 00786    xstruc = \hyperlink{RNAstruct_8h_a78d73cd54a068ef2812812771cdddc6f}{expand\_Full}(struct2);
 477 00787    T2 = \hyperlink{treedist_8h_a08fe4d5afd385dce593b86eaf010c6e3}{make\_tree}(xstruc);
 478 00788    S2 = \hyperlink{stringdist_8h_a3125991b3a403b3f89230474deb3f22e}{Make\_swString}(xstruc);
 479 00789    free(xstruc);
 480 00790
 481 00791    \textcolor{comment}{/* calculate tree edit distance and aligned structures with gaps */}
 482 00792    \hyperlink{dist__vars_8h_aa03194c513af6b860e7b33e370b82bdb}{edit\_backtrack} = 1;
 483 00793    tree\_dist = \hyperlink{treedist_8h_a3b21f1925f7071f46d93431a835217bb}{tree\_edit\_distance}(T1, T2);
 484 00794    \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\_tree}(T1); \hyperlink{treedist_8h_acbc1cb9bce582ea945e4a467c76a57aa}{free\_tree}(T2);
 485 00795    \hyperlink{RNAstruct_8h_a1054c4477d53b31d79d4cb132100e87a}{unexpand\_aligned\_F}(aligned\_line);
 486 00796    printf(\textcolor{stringliteral}{"%s\(\backslash\)n%s  %3.2f\(\backslash\)n"}, aligned\_line[0], aligned\_line[1], tree\_dist);
 487 00797
 488 00798    \textcolor{comment}{/* same thing using string edit (alignment) distance */}
 489 00799    string\_dist = \hyperlink{stringdist_8h_a89e3c335ef17780576d7c0e713830db9}{string\_edit\_distance}(S1, S2);
 490 00800    free(S1); free(S2);
 491 00801    printf(\textcolor{stringliteral}{"%s  mfe=%5.2f\(\backslash\)n%s  mfe=%5.2f  dist=%3.2f\(\backslash\)n"},
 492 00802           aligned\_line[0], e1, aligned\_line[1], e2, string\_dist);
 493 00803
 494 00804    \textcolor{comment}{/* for longer sequences one should also set a scaling factor for}
 495 00805 \textcolor{comment}{      partition function folding, e.g: */}
 496 00806    kT = (\hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}+273.15)*1.98717/1000.;  \textcolor{comment}{/* kT in kcal/mol */}
 497 00807    \hyperlink{fold__vars_8h_ad3b22044065acc6dee0af68931b52cfd}{pf\_scale} = exp(-e1/kT/strlen(seq1));
 498 00808
 499 00809    \textcolor{comment}{/* calculate partition function and base pair probabilities */}
 500 00810    e1 = \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_fold}(seq1, struct1);
 501 00811    \textcolor{comment}{/* get the base pair probability matrix for the previous run of pf\_fold() */}
 502 00812    bppm = \hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export\_bppm}();
 503 00813    pf1 = \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\_bp\_profile\_bppm}(bppm, strlen(seq1));
 504 00814
 505 00815    e2 = \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\_fold}(seq2, struct2);
 506 00816    \textcolor{comment}{/* get the base pair probability matrix for the previous run of pf\_fold() */}
 507 00817    bppm = \hyperlink{group__pf__fold_ga6d463707d5f64bdc4d21515b7dd9b115}{export\_bppm}();
 508 00818    pf2 = \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\_bp\_profile\_bppm}(bppm, strlen(seq2));
 509 00819
 510 00820    \hyperlink{group__pf__fold_gae73db3f49a94f0f72e067ecd12681dbd}{free\_pf\_arrays}();  \textcolor{comment}{/* free space allocated for pf\_fold() */}
 511 00821
 512 00822    profile\_dist = \hyperlink{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{profile\_edit\_distance}(pf1, pf2);
 513 00823    printf(\textcolor{stringliteral}{"%s  free energy=%5.2f\(\backslash\)n%s  free energy=%5.2f  dist=%3.2f\(\backslash\)n"},
 514 00824           aligned\_line[0], e1, aligned\_line[1], e2, profile\_dist);
 515 00825
 516 00826    \hyperlink{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{free\_profile}(pf1); \hyperlink{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{free\_profile}(pf2);
 517 00827 \}
 518 00828 \(\backslash\)endcode
 519 00829
 520 00830 In a typical Unix environment you would compile \textcolor{keyword}{this} program \textcolor{keyword}{using}:
 521 00831 \(\backslash\)verbatim
 522 00832 cc $\{OPENMP\_CFLAGS\} -c example.c -I$\{hpath\}
 523 00833 \(\backslash\)endverbatim
 524 00834 and link using
 525 00835 \(\backslash\)verbatim
 526 00836 cc $\{OPENMP\_CFLAGS\} -o example -L$\{lpath\} -lRNA -lm
 527 00837 \(\backslash\)endverbatim
 528 00838 where \(\backslash\)e $\{hpath\} and \(\backslash\)e $\{lpath\} point to the location of the header
 529 00839 files and library, respectively.
 530 00840 \(\backslash\)note As \textcolor{keywordflow}{default}, the RNAlib is compiled with build-in \(\backslash\)e OpenMP multithreading
 531 00841 support. Thus, when linking your own \textcolor{keywordtype}{object} files to the library you have to pass
 532 00842 the compiler specific \(\backslash\)e $\{OPENMP\_CFLAGS\} (e.g. \textcolor{stringliteral}{'-fopenmp'} for \(\backslash\)b gcc) even \textcolor{keywordflow}{if} your code does not
 533 00843 use openmp specific code. However, in that \textcolor{keywordflow}{case} the \(\backslash\)e OpenMP flags may be ommited when compiling
 534 00844 example.c
 535 00845
 536 00846
 537 00847 **/
 538 00848
 539 \end{DoxyCode}