binaries/src/ViennaRNA/doc/latex/utils_8h.tex

   1 \hypertarget{utils_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/utils.h File Reference}
   2 \label{utils_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/utils.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/utils.\-h}}
   3 }
   4
   5
   6 Various utility-\/ and helper-\/functions used throughout the Vienna R\-N\-A package.
   7
   8
   9 This graph shows which files directly or indirectly include this file\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=250pt]{utils_8h__dep__incl}
  15 \end{center}
  16 \end{figure}
  17 \subsection*{Macros}
  18 \begin{DoxyCompactItemize}
  19 \item
  20 \#define \hyperlink{utils_8h_ad403c9ea58f1836689404c2931419c8c}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R}~1\-U
  21 \item
  22 \#define \hyperlink{utils_8h_a72f3c6ca5c83d2b9baed2922d19c403d}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T}~2\-U
  23 \item
  24 \#define \hyperlink{utils_8h_a8e3241b321c9c1a78a69e59e2e019a71}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C}~4\-U
  25 \item
  26 \#define \hyperlink{utils_8h_a2f0d8069e93d3ac54d9320d6bdb8e7e7}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R}~8\-U
  27 \item
  28 \#define \hyperlink{utils_8h_a8566d6787972100e68b5a2a159b4cf45}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E}~16\-U
  29 \item
  30 \#define \hyperlink{utils_8h_ac08a9df45b9721b97a47dbfe7a6e5f85}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T}~32\-U
  31 \item
  32 \#define \hyperlink{utils_8h_a086742158293217a46ae2f71bb296937}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N}~256\-U
  33 \item
  34 \#define \hyperlink{utils_8h_a7a2e8c50a0c7ce82e60da1016e1367fd}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T}~512\-U
  35 \item
  36 \#define \hyperlink{utils_8h_a0de536599b881c787b0943a2671da476}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N}~1024\-U
  37 \item
  38 \#define \hyperlink{utils_8h_ab4db885222b3b69608310d7c7e63e286}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S}~2048\-U
  39 \item
  40 \#define \hyperlink{utils_8h_a305474b93ccb79ae4c7754016a8ddd84}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E}~4096\-U
  41 \item
  42 \#define \hyperlink{utils_8h_a0f6311f11bed1842e3a527ab27b294c6}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S}~128\-U
  43 \item
  44 \#define \hyperlink{utils_8h_af2062e0eeefffd3ed639af460b3d4fab}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T}~8192\-U
  45 \item
  46 \#define \hyperlink{utils_8h_a4e8d7120619b21df0309af425acbc9a2}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E}~1\-U
  47 \item
  48 \#define \hyperlink{utils_8h_a55e1d16fd693ae9ec8e987b0750da804}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T}~2\-U
  49 \item
  50 \#define \hyperlink{utils_8h_a077c56550c915d4516d84a5ed8d051f4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X}~4\-U
  51 \item
  52 \#define \hyperlink{utils_8h_a0512d790f738742cbdcf3f7c87b46f48}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K}~8\-U
  53 \item
  54 \#define \hyperlink{utils_8h_aa20bfca4bb2903c8548000a33d7bbb53}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K}~16\-U
  55 \item
  56 \#define \hyperlink{utils_8h_a7d725ef525b29891abef3f1ed42599a4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}~32\-U
  57 \item
  58 \#define \hyperlink{utils_8h_a08d12a9a846ea593b7171d277c9f033f}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R}~64\-U
  59 \item
  60 \#define \hyperlink{utils_8h_a0a697f77a6fbb10f34e16fa68ed9e655}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L}~128\-U
  61 \item
  62 \#define \hyperlink{utils_8h_a99dc6b23dc4080a76e2ed1a81c20e94d}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G}~256\-U
  63 \item
  64 \#define \hyperlink{utils_8h_abec89c09874528c6cb73140a4c3d86d7}{V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}~32\-U
  65 \item
  66 \#define \hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{M\-I\-N2}(A, B)~((A) $<$ (B) ? (A) \-: (B))
  67 \item
  68 \#define \hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{M\-A\-X2}(A, B)~((A) $>$ (B) ? (A) \-: (B))
  69 \item
  70 \#define \hyperlink{utils_8h_a721b8d5f3abef17f10293f1f7f8c958e}{M\-I\-N3}(A, B, C)~(\hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{M\-I\-N2}(  (\hyperlink{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{M\-I\-N2}((A),(B))) ,(C)))
  71 \item
  72 \#define \hyperlink{utils_8h_a8d577123d2e66d2b7d0bf9af6e172b93}{M\-A\-X3}(A, B, C)~(\hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{M\-A\-X2}(  (\hyperlink{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{M\-A\-X2}((A),(B))) ,(C)))
  73 \item
  74 \#define \hyperlink{utils_8h_a03943706e48069237cd57f2d35ca987e}{X\-S\-T\-R}(s)~\hyperlink{utils_8h_a6388870e639eee9c0a69446876f1f8cc}{S\-T\-R}(s)
  75 \item
  76 \#define \hyperlink{utils_8h_a6388870e639eee9c0a69446876f1f8cc}{S\-T\-R}(s)~\#s
  77 \item
  78 \#define \hyperlink{utils_8h_afb228174279df9486a5cb56ac0bc79a3}{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H}~80
  79 \begin{DoxyCompactList}\small\item\em Maximum length of filenames that are generated by our programs. \end{DoxyCompactList}\item
  80 \#define \hyperlink{utils_8h_a33c3b1826b8e2739f09f111ec719ded5}{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H}~42
  81 \begin{DoxyCompactList}\small\item\em Maximum length of id taken from fasta header for filename generation. \end{DoxyCompactList}\end{DoxyCompactItemize}
  82 \subsection*{Functions}
  83 \begin{DoxyCompactItemize}
  84 \item
  85 void $\ast$ \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space} (unsigned size)
  86 \begin{DoxyCompactList}\small\item\em Allocate space safely. \end{DoxyCompactList}\item
  87 void $\ast$ \hyperlink{utils_8h_a9037ada838835b1b9db41581a021b0c8}{xrealloc} (void $\ast$p, unsigned size)
  88 \begin{DoxyCompactList}\small\item\em Reallocate space safely. \end{DoxyCompactList}\item
  89 void \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror} (const char message\mbox{[}$\,$\mbox{]})
  90 \begin{DoxyCompactList}\small\item\em Die with an error message. \end{DoxyCompactList}\item
  91 void \hyperlink{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{warn\-\_\-user} (const char message\mbox{[}$\,$\mbox{]})
  92 \begin{DoxyCompactList}\small\item\em Print a warning message. \end{DoxyCompactList}\item
  93 \hypertarget{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{void \hyperlink{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}{init\-\_\-rand} (void)}\label{utils_8h_a8aaa6d9be6f803f496d9b97375c371f3}
  94
  95 \begin{DoxyCompactList}\small\item\em Make random number seeds. \end{DoxyCompactList}\item
  96 double \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn} (void)
  97 \begin{DoxyCompactList}\small\item\em get a random number from \mbox{[}0..1\mbox{]} \end{DoxyCompactList}\item
  98 int \hyperlink{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{int\-\_\-urn} (int from, int to)
  99 \begin{DoxyCompactList}\small\item\em Generates a pseudo random integer in a specified range. \end{DoxyCompactList}\item
 100 char $\ast$ \hyperlink{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{time\-\_\-stamp} (void)
 101 \begin{DoxyCompactList}\small\item\em Get a timestamp. \end{DoxyCompactList}\item
 102 char $\ast$ \hyperlink{utils_8h_a1b95eac365a021572e1c37e5993a89be}{random\-\_\-string} (int l, const char symbols\mbox{[}$\,$\mbox{]})
 103 \begin{DoxyCompactList}\small\item\em Create a random string using characters from a specified symbol set. \end{DoxyCompactList}\item
 104 int \hyperlink{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{hamming} (const char $\ast$s1, const char $\ast$s2)
 105 \begin{DoxyCompactList}\small\item\em Calculate hamming distance between two sequences. \end{DoxyCompactList}\item
 106 int \hyperlink{utils_8h_a96d3c36717d624514055ce201cab1542}{hamming\-\_\-bound} (const char $\ast$s1, const char $\ast$s2, int n)
 107 \begin{DoxyCompactList}\small\item\em Calculate hamming distance between two sequences up to a specified length. \end{DoxyCompactList}\item
 108 char $\ast$ \hyperlink{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{get\-\_\-line} (F\-I\-L\-E $\ast$fp)
 109 \begin{DoxyCompactList}\small\item\em Read a line of arbitrary length from a stream. \end{DoxyCompactList}\item
 110 unsigned int \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line} (char $\ast$$\ast$string, unsigned int options)
 111 \item
 112 unsigned int \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record} (char $\ast$$\ast$header, char $\ast$$\ast$sequence, char $\ast$$\ast$$\ast$rest, unsigned int options)
 113 \begin{DoxyCompactList}\small\item\em Get a data record from stdin. \end{DoxyCompactList}\item
 114 char $\ast$ \hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\-\_\-structure} (const char $\ast$struc)
 115 \begin{DoxyCompactList}\small\item\em Pack secondary secondary structure, 5\-:1 compression using base 3 encoding. \end{DoxyCompactList}\item
 116 char $\ast$ \hyperlink{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{unpack\-\_\-structure} (const char $\ast$packed)
 117 \begin{DoxyCompactList}\small\item\em Unpack secondary structure previously packed with \hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\-\_\-structure()} \end{DoxyCompactList}\item
 118 short $\ast$ \hyperlink{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{make\-\_\-pair\-\_\-table} (const char $\ast$structure)
 119 \begin{DoxyCompactList}\small\item\em Create a pair table of a secondary structure. \end{DoxyCompactList}\item
 120 short $\ast$ \hyperlink{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{copy\-\_\-pair\-\_\-table} (const short $\ast$pt)
 121 \begin{DoxyCompactList}\small\item\em Get an exact copy of a pair table. \end{DoxyCompactList}\item
 122 short $\ast$ \hyperlink{utils_8h_a3c81b3967056c3888b8472b65fbb16f5}{alimake\-\_\-pair\-\_\-table} (const char $\ast$structure)
 123 \item
 124 short $\ast$ \hyperlink{utils_8h_a9aa3bf3b4346bb7fb88efc154dd07a79}{make\-\_\-pair\-\_\-table\-\_\-snoop} (const char $\ast$structure)
 125 \item
 126 int $\ast$ \hyperlink{utils_8h_a4358e89f64cc87a563b7ef3855f75bed}{make\-\_\-loop\-\_\-index\-\_\-pt} (short $\ast$pt)
 127 \begin{DoxyCompactList}\small\item\em Compute the \char`\"{}base pair\char`\"{} distance between two secondary structures s1 and s2. \end{DoxyCompactList}\item
 128 void \hyperlink{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{print\-\_\-tty\-\_\-input\-\_\-seq} (void)
 129 \begin{DoxyCompactList}\small\item\em Print a line to {\itshape stdout} that asks for an input sequence. \end{DoxyCompactList}\item
 130 void \hyperlink{utils_8h_ae4ef89b662a3e9b5b5f0781d9757aba0}{print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str} (const char $\ast$s)
 131 \begin{DoxyCompactList}\small\item\em Print a line with a user defined string and a ruler to stdout. \end{DoxyCompactList}\item
 132 \hypertarget{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{void \hyperlink{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}{print\-\_\-tty\-\_\-constraint\-\_\-full} (void)}\label{utils_8h_ae8ae8a34962b9959be3f6c40f0a80ac1}
 133
 134 \begin{DoxyCompactList}\small\item\em Print structure constraint characters to stdout (full constraint support) \end{DoxyCompactList}\item
 135 void \hyperlink{utils_8h_a4d167deb70bb51723e44374dc981deb2}{print\-\_\-tty\-\_\-constraint} (unsigned int option)
 136 \begin{DoxyCompactList}\small\item\em Print structure constraint characters to stdout. (constraint support is specified by option parameter) \end{DoxyCompactList}\item
 137 void \hyperlink{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{str\-\_\-\-D\-N\-A2\-R\-N\-A} (char $\ast$sequence)
 138 \begin{DoxyCompactList}\small\item\em Convert a D\-N\-A input sequence to R\-N\-A alphabet. \end{DoxyCompactList}\item
 139 void \hyperlink{utils_8h_a17b796b806f96b70382077fb5bc519bb}{str\-\_\-uppercase} (char $\ast$sequence)
 140 \begin{DoxyCompactList}\small\item\em Convert an input sequence to uppercase. \end{DoxyCompactList}\item
 141 int $\ast$ \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx} (unsigned int length)
 142 \begin{DoxyCompactList}\small\item\em Get an index mapper array (iindx) for accessing the energy matrices, e.\-g. in partition function related functions. \end{DoxyCompactList}\item
 143 int $\ast$ \hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\-\_\-indx} (unsigned int length)
 144 \begin{DoxyCompactList}\small\item\em Get an index mapper array (indx) for accessing the energy matrices, e.\-g. in M\-F\-E related functions. \end{DoxyCompactList}\item
 145 void \hyperlink{utils_8h_a36c3a6c3218b041f992052767bc74549}{constrain\-\_\-ptypes} (const char $\ast$constraint, unsigned int length, char $\ast$ptype, int $\ast$B\-P, int min\-\_\-loop\-\_\-size, unsigned int idx\-\_\-type)
 146 \begin{DoxyCompactList}\small\item\em Insert constraining pair types according to constraint structure string. \end{DoxyCompactList}\end{DoxyCompactItemize}
 147 \subsection*{Variables}
 148 \begin{DoxyCompactItemize}
 149 \item
 150 unsigned short \hyperlink{utils_8h_af9a866c8417afda7368bbac939ab3c47}{xsubi} \mbox{[}3\mbox{]}
 151 \begin{DoxyCompactList}\small\item\em Current 48 bit random number. \end{DoxyCompactList}\end{DoxyCompactItemize}
 152
 153
 154 \subsection{Detailed Description}
 155 Various utility-\/ and helper-\/functions used throughout the Vienna R\-N\-A package.
 156
 157 \subsection{Macro Definition Documentation}
 158 \hypertarget{utils_8h_ad403c9ea58f1836689404c2931419c8c}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R}}
 159 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R}!utils.h@{utils.\-h}}
 160 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R~1\-U}}\label{utils_8h_ad403c9ea58f1836689404c2931419c8c}
 161 Output flag of \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-: \char`\"{}\-An E\-R\-R\-O\-R has occured, maybe E\-O\-F\char`\"{} \hypertarget{utils_8h_a72f3c6ca5c83d2b9baed2922d19c403d}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T}}
 162 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T}!utils.h@{utils.\-h}}
 163 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T~2\-U}}\label{utils_8h_a72f3c6ca5c83d2b9baed2922d19c403d}
 164 Output flag of \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-: \char`\"{}the user requested quitting the program\char`\"{} \hypertarget{utils_8h_a8e3241b321c9c1a78a69e59e2e019a71}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C}}
 165 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C}!utils.h@{utils.\-h}}
 166 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C~4\-U}}\label{utils_8h_a8e3241b321c9c1a78a69e59e2e019a71}
 167 Output flag of \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-: \char`\"{}something was read\char`\"{} \hypertarget{utils_8h_a2f0d8069e93d3ac54d9320d6bdb8e7e7}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R}}
 168 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R}!utils.h@{utils.\-h}}
 169 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R~8\-U}}\label{utils_8h_a2f0d8069e93d3ac54d9320d6bdb8e7e7}
 170 Input/\-Output flag of \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-:\par
 171  if used as input option this tells \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()} that the data to be read should comply with the F\-A\-S\-T\-A format
 172
 173 the function will return this flag if a fasta header was read \hypertarget{utils_8h_a8566d6787972100e68b5a2a159b4cf45}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E}}
 174 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E}!utils.h@{utils.\-h}}
 175 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-S\-E\-Q\-U\-E\-N\-C\-E~16\-U}}\label{utils_8h_a8566d6787972100e68b5a2a159b4cf45}
 176 Input flag for \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-:\par
 177  Tell \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()} that we assume to read a nucleotide sequence \hypertarget{utils_8h_ac08a9df45b9721b97a47dbfe7a6e5f85}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T}}
 178 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T}!utils.h@{utils.\-h}}
 179 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T~32\-U}}\label{utils_8h_ac08a9df45b9721b97a47dbfe7a6e5f85}
 180 Input flag for \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-:\par
 181  Tell \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()} that we assume to read a structure constraint \hypertarget{utils_8h_a086742158293217a46ae2f71bb296937}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N}}
 182 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N}!utils.h@{utils.\-h}}
 183 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-T\-R\-U\-N\-C\-A\-T\-I\-O\-N~256\-U}}\label{utils_8h_a086742158293217a46ae2f71bb296937}
 184 Input switch for \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-: \char`\"{}do not trunkate the line by eliminating white spaces at end of line\char`\"{} \hypertarget{utils_8h_a7a2e8c50a0c7ce82e60da1016e1367fd}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T}}
 185 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T}!utils.h@{utils.\-h}}
 186 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T~512\-U}}\label{utils_8h_a7a2e8c50a0c7ce82e60da1016e1367fd}
 187 Input switch for \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}\-: \char`\"{}do fill rest array\char`\"{} \hypertarget{utils_8h_a0de536599b881c787b0943a2671da476}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N}}
 188 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N}!utils.h@{utils.\-h}}
 189 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N~1024\-U}}\label{utils_8h_a0de536599b881c787b0943a2671da476}
 190 Input switch for \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}\-: \char`\"{}never allow data to span more than one line\char`\"{} \hypertarget{utils_8h_ab4db885222b3b69608310d7c7e63e286}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S}}
 191 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S}!utils.h@{utils.\-h}}
 192 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S~2048\-U}}\label{utils_8h_ab4db885222b3b69608310d7c7e63e286}
 193 Input switch for \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}\-: \char`\"{}do not skip empty lines\char`\"{} \hypertarget{utils_8h_a305474b93ccb79ae4c7754016a8ddd84}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E}}
 194 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E}!utils.h@{utils.\-h}}
 195 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E~4096\-U}}\label{utils_8h_a305474b93ccb79ae4c7754016a8ddd84}
 196 Output flag for \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}\-: \char`\"{}read an empty line\char`\"{} \hypertarget{utils_8h_a0f6311f11bed1842e3a527ab27b294c6}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S}}
 197 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S}!utils.h@{utils.\-h}}
 198 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S~128\-U}}\label{utils_8h_a0f6311f11bed1842e3a527ab27b294c6}
 199 Input switch for \hyperlink{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{get\-\_\-input\-\_\-line()}\-: \char`\"{}do not skip comment lines\char`\"{} \hypertarget{utils_8h_af2062e0eeefffd3ed639af460b3d4fab}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T}}
 200 \index{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T@{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T}!utils.h@{utils.\-h}}
 201 \subsubsection[{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T~8192\-U}}\label{utils_8h_af2062e0eeefffd3ed639af460b3d4fab}
 202 Output flag for \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}\-: \char`\"{}read a comment\char`\"{} \hypertarget{utils_8h_a4e8d7120619b21df0309af425acbc9a2}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E}}
 203 \index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E}!utils.h@{utils.\-h}}
 204 \subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E~1\-U}}\label{utils_8h_a4e8d7120619b21df0309af425acbc9a2}
 205 pipe sign '$|$' switch for structure constraints (paired with another base) \hypertarget{utils_8h_a55e1d16fd693ae9ec8e987b0750da804}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T}}
 206 \index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T}!utils.h@{utils.\-h}}
 207 \subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T~2\-U}}\label{utils_8h_a55e1d16fd693ae9ec8e987b0750da804}
 208 dot '.' switch for structure constraints (no constraint at all) \hypertarget{utils_8h_a077c56550c915d4516d84a5ed8d051f4}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X}}
 209 \index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X}!utils.h@{utils.\-h}}
 210 \subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X~4\-U}}\label{utils_8h_a077c56550c915d4516d84a5ed8d051f4}
 211 'x' switch for structure constraint (base must not pair) \hypertarget{utils_8h_a0512d790f738742cbdcf3f7c87b46f48}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K}}
 212 \index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K}!utils.h@{utils.\-h}}
 213 \subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K~8\-U}}\label{utils_8h_a0512d790f738742cbdcf3f7c87b46f48}
 214 angle brackets '$<$', '$>$' switch for structure constraint (paired downstream/upstream) \hypertarget{utils_8h_aa20bfca4bb2903c8548000a33d7bbb53}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K}}
 215 \index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K}!utils.h@{utils.\-h}}
 216 \subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K~16\-U}}\label{utils_8h_aa20bfca4bb2903c8548000a33d7bbb53}
 217 round brackets '(',')' switch for structure constraint (base i pairs base j) \hypertarget{utils_8h_a7d725ef525b29891abef3f1ed42599a4}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}}
 218 \index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}!utils.h@{utils.\-h}}
 219 \subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E~32\-U}}\label{utils_8h_a7d725ef525b29891abef3f1ed42599a4}
 220 constraint may span over several lines \hypertarget{utils_8h_a08d12a9a846ea593b7171d277c9f033f}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R}}
 221 \index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R}!utils.h@{utils.\-h}}
 222 \subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-N\-O\-\_\-\-H\-E\-A\-D\-E\-R~64\-U}}\label{utils_8h_a08d12a9a846ea593b7171d277c9f033f}
 223 do not print the header information line \hypertarget{utils_8h_a0a697f77a6fbb10f34e16fa68ed9e655}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L}}
 224 \index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L}!utils.h@{utils.\-h}}
 225 \subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-L\-L~128\-U}}\label{utils_8h_a0a697f77a6fbb10f34e16fa68ed9e655}
 226 placeholder for all constraining characters \hypertarget{utils_8h_a99dc6b23dc4080a76e2ed1a81c20e94d}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G}}
 227 \index{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G@{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G}!utils.h@{utils.\-h}}
 228 \subsubsection[{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-G~256\-U}}\label{utils_8h_a99dc6b23dc4080a76e2ed1a81c20e94d}
 229 '+' switch for structure constraint (base is involved in a gquad) \hypertarget{utils_8h_abec89c09874528c6cb73140a4c3d86d7}{\index{utils.\-h@{utils.\-h}!V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}}
 230 \index{V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E@{V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}!utils.h@{utils.\-h}}
 231 \subsubsection[{V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E}]{\setlength{\rightskip}{0pt plus 5cm}\#define V\-R\-N\-A\-\_\-\-O\-P\-T\-I\-O\-N\-\_\-\-M\-U\-L\-T\-I\-L\-I\-N\-E~32\-U}}\label{utils_8h_abec89c09874528c6cb73140a4c3d86d7}
 232 Tell a function that an input is assumed to span several lines if used as input-\/option A function might also be returning this state telling that it has read data from multiple lines.
 233
 234 \begin{DoxySeeAlso}{See Also}
 235 extract\-\_\-record\-\_\-rest\-\_\-structure(), \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()}, get\-Constraint()
 236 \end{DoxySeeAlso}
 237 \hypertarget{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}{\index{utils.\-h@{utils.\-h}!M\-I\-N2@{M\-I\-N2}}
 238 \index{M\-I\-N2@{M\-I\-N2}!utils.h@{utils.\-h}}
 239 \subsubsection[{M\-I\-N2}]{\setlength{\rightskip}{0pt plus 5cm}\#define M\-I\-N2(
 240 \begin{DoxyParamCaption}
 241 \item[{}]{A, }
 242 \item[{}]{B}
 243 \end{DoxyParamCaption}
 244 )~((A) $<$ (B) ? (A) \-: (B))}}\label{utils_8h_ae0b9cd0ce090bd69b951aa73e8fa4f7d}
 245 Get the minimum of two comparable values \hypertarget{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}{\index{utils.\-h@{utils.\-h}!M\-A\-X2@{M\-A\-X2}}
 246 \index{M\-A\-X2@{M\-A\-X2}!utils.h@{utils.\-h}}
 247 \subsubsection[{M\-A\-X2}]{\setlength{\rightskip}{0pt plus 5cm}\#define M\-A\-X2(
 248 \begin{DoxyParamCaption}
 249 \item[{}]{A, }
 250 \item[{}]{B}
 251 \end{DoxyParamCaption}
 252 )~((A) $>$ (B) ? (A) \-: (B))}}\label{utils_8h_a33297b3679c713b0c4d897cd0fe3b122}
 253 Get the maximum of two comparable values \hypertarget{utils_8h_a721b8d5f3abef17f10293f1f7f8c958e}{\index{utils.\-h@{utils.\-h}!M\-I\-N3@{M\-I\-N3}}
 254 \index{M\-I\-N3@{M\-I\-N3}!utils.h@{utils.\-h}}
 255 \subsubsection[{M\-I\-N3}]{\setlength{\rightskip}{0pt plus 5cm}\#define M\-I\-N3(
 256 \begin{DoxyParamCaption}
 257 \item[{}]{A, }
 258 \item[{}]{B, }
 259 \item[{}]{C}
 260 \end{DoxyParamCaption}
 261 )~({\bf M\-I\-N2}(  ({\bf M\-I\-N2}((A),(B))) ,(C)))}}\label{utils_8h_a721b8d5f3abef17f10293f1f7f8c958e}
 262 Get the minimum of three comparable values \hypertarget{utils_8h_a8d577123d2e66d2b7d0bf9af6e172b93}{\index{utils.\-h@{utils.\-h}!M\-A\-X3@{M\-A\-X3}}
 263 \index{M\-A\-X3@{M\-A\-X3}!utils.h@{utils.\-h}}
 264 \subsubsection[{M\-A\-X3}]{\setlength{\rightskip}{0pt plus 5cm}\#define M\-A\-X3(
 265 \begin{DoxyParamCaption}
 266 \item[{}]{A, }
 267 \item[{}]{B, }
 268 \item[{}]{C}
 269 \end{DoxyParamCaption}
 270 )~({\bf M\-A\-X2}(  ({\bf M\-A\-X2}((A),(B))) ,(C)))}}\label{utils_8h_a8d577123d2e66d2b7d0bf9af6e172b93}
 271 Get the maximum of three comparable values \hypertarget{utils_8h_a03943706e48069237cd57f2d35ca987e}{\index{utils.\-h@{utils.\-h}!X\-S\-T\-R@{X\-S\-T\-R}}
 272 \index{X\-S\-T\-R@{X\-S\-T\-R}!utils.h@{utils.\-h}}
 273 \subsubsection[{X\-S\-T\-R}]{\setlength{\rightskip}{0pt plus 5cm}\#define X\-S\-T\-R(
 274 \begin{DoxyParamCaption}
 275 \item[{}]{s}
 276 \end{DoxyParamCaption}
 277 )~{\bf S\-T\-R}(s)}}\label{utils_8h_a03943706e48069237cd57f2d35ca987e}
 278 Stringify a macro after expansion \hypertarget{utils_8h_a6388870e639eee9c0a69446876f1f8cc}{\index{utils.\-h@{utils.\-h}!S\-T\-R@{S\-T\-R}}
 279 \index{S\-T\-R@{S\-T\-R}!utils.h@{utils.\-h}}
 280 \subsubsection[{S\-T\-R}]{\setlength{\rightskip}{0pt plus 5cm}\#define S\-T\-R(
 281 \begin{DoxyParamCaption}
 282 \item[{}]{s}
 283 \end{DoxyParamCaption}
 284 )~\#s}}\label{utils_8h_a6388870e639eee9c0a69446876f1f8cc}
 285 Stringify a macro argument \hypertarget{utils_8h_afb228174279df9486a5cb56ac0bc79a3}{\index{utils.\-h@{utils.\-h}!F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H@{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H}}
 286 \index{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H@{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H}!utils.h@{utils.\-h}}
 287 \subsubsection[{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H}]{\setlength{\rightskip}{0pt plus 5cm}\#define F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H~80}}\label{utils_8h_afb228174279df9486a5cb56ac0bc79a3}
 288
 289
 290 Maximum length of filenames that are generated by our programs.
 291
 292 This definition should be used throughout the complete Vienna\-R\-N\-A package wherever a static array holding filenames of output files is declared. \hypertarget{utils_8h_a33c3b1826b8e2739f09f111ec719ded5}{\index{utils.\-h@{utils.\-h}!F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H@{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H}}
 293 \index{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H@{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H}!utils.h@{utils.\-h}}
 294 \subsubsection[{F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H}]{\setlength{\rightskip}{0pt plus 5cm}\#define F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-I\-D\-\_\-\-L\-E\-N\-G\-T\-H~42}}\label{utils_8h_a33c3b1826b8e2739f09f111ec719ded5}
 295
 296
 297 Maximum length of id taken from fasta header for filename generation.
 298
 299 this has to be smaller than F\-I\-L\-E\-N\-A\-M\-E\-\_\-\-M\-A\-X\-\_\-\-L\-E\-N\-G\-T\-H since in most cases, some suffix will be appended to the I\-D
 300
 301 \subsection{Function Documentation}
 302 \hypertarget{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{\index{utils.\-h@{utils.\-h}!space@{space}}
 303 \index{space@{space}!utils.h@{utils.\-h}}
 304 \subsubsection[{space}]{\setlength{\rightskip}{0pt plus 5cm}void$\ast$ space (
 305 \begin{DoxyParamCaption}
 306 \item[{unsigned}]{size}
 307 \end{DoxyParamCaption}
 308 )}}\label{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}
 309
 310
 311 Allocate space safely.
 312
 313
 314 \begin{DoxyParams}{Parameters}
 315 {\em size} & The size of the memory to be allocated in bytes \\
 316 \hline
 317 \end{DoxyParams}
 318 \begin{DoxyReturn}{Returns}
 319 A pointer to the allocated memory
 320 \end{DoxyReturn}
 321 \hypertarget{utils_8h_a9037ada838835b1b9db41581a021b0c8}{\index{utils.\-h@{utils.\-h}!xrealloc@{xrealloc}}
 322 \index{xrealloc@{xrealloc}!utils.h@{utils.\-h}}
 323 \subsubsection[{xrealloc}]{\setlength{\rightskip}{0pt plus 5cm}void$\ast$ xrealloc (
 324 \begin{DoxyParamCaption}
 325 \item[{void $\ast$}]{p, }
 326 \item[{unsigned}]{size}
 327 \end{DoxyParamCaption}
 328 )}}\label{utils_8h_a9037ada838835b1b9db41581a021b0c8}
 329
 330
 331 Reallocate space safely.
 332
 333
 334 \begin{DoxyParams}{Parameters}
 335 {\em p} & A pointer to the memory region to be reallocated \\
 336 \hline
 337 {\em size} & The size of the memory to be allocated in bytes \\
 338 \hline
 339 \end{DoxyParams}
 340 \begin{DoxyReturn}{Returns}
 341 A pointer to the newly allocated memory
 342 \end{DoxyReturn}
 343 \hypertarget{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{\index{utils.\-h@{utils.\-h}!nrerror@{nrerror}}
 344 \index{nrerror@{nrerror}!utils.h@{utils.\-h}}
 345 \subsubsection[{nrerror}]{\setlength{\rightskip}{0pt plus 5cm}void nrerror (
 346 \begin{DoxyParamCaption}
 347 \item[{const char}]{message\mbox{[}$\,$\mbox{]}}
 348 \end{DoxyParamCaption}
 349 )}}\label{utils_8h_a127ce946e56b5a5773781cabe68e38c5}
 350
 351
 352 Die with an error message.
 353
 354 \begin{DoxySeeAlso}{See Also}
 355 \hyperlink{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{warn\-\_\-user()}
 356 \end{DoxySeeAlso}
 357
 358 \begin{DoxyParams}{Parameters}
 359 {\em message} & The error message to be printed before exiting with 'F\-A\-I\-L\-U\-R\-E' \\
 360 \hline
 361 \end{DoxyParams}
 362 \hypertarget{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}{\index{utils.\-h@{utils.\-h}!warn\-\_\-user@{warn\-\_\-user}}
 363 \index{warn\-\_\-user@{warn\-\_\-user}!utils.h@{utils.\-h}}
 364 \subsubsection[{warn\-\_\-user}]{\setlength{\rightskip}{0pt plus 5cm}void warn\-\_\-user (
 365 \begin{DoxyParamCaption}
 366 \item[{const char}]{message\mbox{[}$\,$\mbox{]}}
 367 \end{DoxyParamCaption}
 368 )}}\label{utils_8h_af2355fa8746f2f30fbe71db65dea3d51}
 369
 370
 371 Print a warning message.
 372
 373 Print a warning message to {\itshape stderr}
 374
 375
 376 \begin{DoxyParams}{Parameters}
 377 {\em message} & The warning message \\
 378 \hline
 379 \end{DoxyParams}
 380 \hypertarget{utils_8h_aaa328491c84996e445d027fde9800f2e}{\index{utils.\-h@{utils.\-h}!urn@{urn}}
 381 \index{urn@{urn}!utils.h@{utils.\-h}}
 382 \subsubsection[{urn}]{\setlength{\rightskip}{0pt plus 5cm}double urn (
 383 \begin{DoxyParamCaption}
 384 \item[{void}]{}
 385 \end{DoxyParamCaption}
 386 )}}\label{utils_8h_aaa328491c84996e445d027fde9800f2e}
 387
 388
 389 get a random number from \mbox{[}0..1\mbox{]}
 390
 391 \begin{DoxyNote}{Note}
 392 Usually implemented by calling {\itshape erand48()}.
 393 \end{DoxyNote}
 394 \begin{DoxyReturn}{Returns}
 395 A random number in range \mbox{[}0..1\mbox{]}
 396 \end{DoxyReturn}
 397 \hypertarget{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}{\index{utils.\-h@{utils.\-h}!int\-\_\-urn@{int\-\_\-urn}}
 398 \index{int\-\_\-urn@{int\-\_\-urn}!utils.h@{utils.\-h}}
 399 \subsubsection[{int\-\_\-urn}]{\setlength{\rightskip}{0pt plus 5cm}int int\-\_\-urn (
 400 \begin{DoxyParamCaption}
 401 \item[{int}]{from, }
 402 \item[{int}]{to}
 403 \end{DoxyParamCaption}
 404 )}}\label{utils_8h_a68ff0849d44f62fe491800378a5ffcb4}
 405
 406
 407 Generates a pseudo random integer in a specified range.
 408
 409
 410 \begin{DoxyParams}{Parameters}
 411 {\em from} & The first number in range \\
 412 \hline
 413 {\em to} & The last number in range \\
 414 \hline
 415 \end{DoxyParams}
 416 \begin{DoxyReturn}{Returns}
 417 A pseudo random number in range \mbox{[}from, to\mbox{]}
 418 \end{DoxyReturn}
 419 \hypertarget{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}{\index{utils.\-h@{utils.\-h}!time\-\_\-stamp@{time\-\_\-stamp}}
 420 \index{time\-\_\-stamp@{time\-\_\-stamp}!utils.h@{utils.\-h}}
 421 \subsubsection[{time\-\_\-stamp}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ time\-\_\-stamp (
 422 \begin{DoxyParamCaption}
 423 \item[{void}]{}
 424 \end{DoxyParamCaption}
 425 )}}\label{utils_8h_a7afeb906cb36e9d77379eabc6907ac46}
 426
 427
 428 Get a timestamp.
 429
 430 Returns a string containing the current date in the format \begin{DoxyVerb}Fri Mar 19 21:10:57 1993\end{DoxyVerb}
 431
 432
 433 \begin{DoxyReturn}{Returns}
 434 A string containing the timestamp
 435 \end{DoxyReturn}
 436 \hypertarget{utils_8h_a1b95eac365a021572e1c37e5993a89be}{\index{utils.\-h@{utils.\-h}!random\-\_\-string@{random\-\_\-string}}
 437 \index{random\-\_\-string@{random\-\_\-string}!utils.h@{utils.\-h}}
 438 \subsubsection[{random\-\_\-string}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ random\-\_\-string (
 439 \begin{DoxyParamCaption}
 440 \item[{int}]{l, }
 441 \item[{const char}]{symbols\mbox{[}$\,$\mbox{]}}
 442 \end{DoxyParamCaption}
 443 )}}\label{utils_8h_a1b95eac365a021572e1c37e5993a89be}
 444
 445
 446 Create a random string using characters from a specified symbol set.
 447
 448
 449 \begin{DoxyParams}{Parameters}
 450 {\em l} & The length of the sequence \\
 451 \hline
 452 {\em symbols} & The symbol set \\
 453 \hline
 454 \end{DoxyParams}
 455 \begin{DoxyReturn}{Returns}
 456 A random string of length 'l' containing characters from the symbolset
 457 \end{DoxyReturn}
 458 \hypertarget{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{\index{utils.\-h@{utils.\-h}!hamming@{hamming}}
 459 \index{hamming@{hamming}!utils.h@{utils.\-h}}
 460 \subsubsection[{hamming}]{\setlength{\rightskip}{0pt plus 5cm}int hamming (
 461 \begin{DoxyParamCaption}
 462 \item[{const char $\ast$}]{s1, }
 463 \item[{const char $\ast$}]{s2}
 464 \end{DoxyParamCaption}
 465 )}}\label{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}
 466
 467
 468 Calculate hamming distance between two sequences.
 469
 470 Calculate the number of positions in which
 471 \begin{DoxyParams}{Parameters}
 472 {\em s1} & The first sequence \\
 473 \hline
 474 {\em s2} & The second sequence \\
 475 \hline
 476 \end{DoxyParams}
 477 \begin{DoxyReturn}{Returns}
 478 The hamming distance between s1 and s2
 479 \end{DoxyReturn}
 480 \hypertarget{utils_8h_a96d3c36717d624514055ce201cab1542}{\index{utils.\-h@{utils.\-h}!hamming\-\_\-bound@{hamming\-\_\-bound}}
 481 \index{hamming\-\_\-bound@{hamming\-\_\-bound}!utils.h@{utils.\-h}}
 482 \subsubsection[{hamming\-\_\-bound}]{\setlength{\rightskip}{0pt plus 5cm}int hamming\-\_\-bound (
 483 \begin{DoxyParamCaption}
 484 \item[{const char $\ast$}]{s1, }
 485 \item[{const char $\ast$}]{s2, }
 486 \item[{int}]{n}
 487 \end{DoxyParamCaption}
 488 )}}\label{utils_8h_a96d3c36717d624514055ce201cab1542}
 489
 490
 491 Calculate hamming distance between two sequences up to a specified length.
 492
 493 This function is similar to \hyperlink{utils_8h_ad9dc7bfc9aa664dc6698f17ce07fc7e7}{hamming()} but instead of comparing both sequences up to their actual length only the first 'n' characters are taken into account
 494 \begin{DoxyParams}{Parameters}
 495 {\em s1} & The first sequence \\
 496 \hline
 497 {\em s2} & The second sequence \\
 498 \hline
 499 \end{DoxyParams}
 500 \begin{DoxyReturn}{Returns}
 501 The hamming distance between s1 and s2
 502 \end{DoxyReturn}
 503 \hypertarget{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}{\index{utils.\-h@{utils.\-h}!get\-\_\-line@{get\-\_\-line}}
 504 \index{get\-\_\-line@{get\-\_\-line}!utils.h@{utils.\-h}}
 505 \subsubsection[{get\-\_\-line}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ get\-\_\-line (
 506 \begin{DoxyParamCaption}
 507 \item[{F\-I\-L\-E $\ast$}]{fp}
 508 \end{DoxyParamCaption}
 509 )}}\label{utils_8h_abe51806d14cff0789a8c1df7dbc45b71}
 510
 511
 512 Read a line of arbitrary length from a stream.
 513
 514 Returns a pointer to the resulting string. The necessary memory is allocated and should be released using {\itshape free()} when the string is no longer needed.
 515
 516
 517 \begin{DoxyParams}{Parameters}
 518 {\em fp} & A file pointer to the stream where the function should read from \\
 519 \hline
 520 \end{DoxyParams}
 521 \begin{DoxyReturn}{Returns}
 522 A pointer to the resulting string
 523 \end{DoxyReturn}
 524 \hypertarget{utils_8h_a8ef1835eb83f542396f59f0b205965e5}{\index{utils.\-h@{utils.\-h}!get\-\_\-input\-\_\-line@{get\-\_\-input\-\_\-line}}
 525 \index{get\-\_\-input\-\_\-line@{get\-\_\-input\-\_\-line}!utils.h@{utils.\-h}}
 526 \subsubsection[{get\-\_\-input\-\_\-line}]{\setlength{\rightskip}{0pt plus 5cm}unsigned int get\-\_\-input\-\_\-line (
 527 \begin{DoxyParamCaption}
 528 \item[{char $\ast$$\ast$}]{string, }
 529 \item[{unsigned int}]{options}
 530 \end{DoxyParamCaption}
 531 )}}\label{utils_8h_a8ef1835eb83f542396f59f0b205965e5}
 532 Retrieve a line from 'stdin' savely while skipping comment characters and other features This function returns the type of input it has read if recognized. An option argument allows to switch between different reading modes.\par
 533  Currently available options are\-:\par
 534  \#\-V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-P\-R\-I\-N\-T\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S, \hyperlink{utils_8h_a0f6311f11bed1842e3a527ab27b294c6}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S}, \#\-V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-E\-L\-I\-M\-\_\-\-W\-S\-\_\-\-S\-U\-F\-F\-I\-X
 535
 536 pass a collection of options as one value like this\-: \begin{DoxyVerb}get_input_line(string, option_1 | option_2 | option_n) \end{DoxyVerb}
 537
 538
 539 If the function recognizes the type of input, it will report it in the return value. It also reports if a user defined 'quit' command (@-\/sign on 'stdin') was given. Possible return values are\-:\par
 540  \hyperlink{utils_8h_a2f0d8069e93d3ac54d9320d6bdb8e7e7}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-F\-A\-S\-T\-A\-\_\-\-H\-E\-A\-D\-E\-R}, \hyperlink{utils_8h_ad403c9ea58f1836689404c2931419c8c}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-E\-R\-R\-O\-R}, \hyperlink{utils_8h_a8e3241b321c9c1a78a69e59e2e019a71}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-M\-I\-S\-C}, \hyperlink{utils_8h_a72f3c6ca5c83d2b9baed2922d19c403d}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-Q\-U\-I\-T}
 541
 542
 543 \begin{DoxyParams}{Parameters}
 544 {\em string} & A pointer to the character array that contains the line read \\
 545 \hline
 546 {\em options} & A collection of options for switching the functions behavior \\
 547 \hline
 548 \end{DoxyParams}
 549 \begin{DoxyReturn}{Returns}
 550 A flag with information about what has been read
 551 \end{DoxyReturn}
 552 \hypertarget{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{\index{utils.\-h@{utils.\-h}!read\-\_\-record@{read\-\_\-record}}
 553 \index{read\-\_\-record@{read\-\_\-record}!utils.h@{utils.\-h}}
 554 \subsubsection[{read\-\_\-record}]{\setlength{\rightskip}{0pt plus 5cm}unsigned int read\-\_\-record (
 555 \begin{DoxyParamCaption}
 556 \item[{char $\ast$$\ast$}]{header, }
 557 \item[{char $\ast$$\ast$}]{sequence, }
 558 \item[{char $\ast$$\ast$$\ast$}]{rest, }
 559 \item[{unsigned int}]{options}
 560 \end{DoxyParamCaption}
 561 )}}\label{utils_8h_afd194a69af9d92b5b0412a7627ac1595}
 562
 563
 564 Get a data record from stdin.
 565
 566 \begin{DoxyVerb}This function may be used to obtain complete datasets from stdin. A dataset is always
 567 defined to contain at least a sequence. If data on stdin starts with a fasta header,
 568 i.e. a line like
 569 \end{DoxyVerb}
 570  \begin{DoxyVerb}>some header info \end{DoxyVerb}
 571  then \hyperlink{utils_8h_afd194a69af9d92b5b0412a7627ac1595}{read\-\_\-record()} will assume that the sequence that follows the header may span over several lines. To disable this behavior and to assign a single line to the argument 'sequence' one can pass V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-S\-P\-A\-N in the 'options' argument. If no fasta header is read in the beginning of a data block, a sequence must not span over multiple lines!\par
 572  Unless the options \hyperlink{utils_8h_a0f6311f11bed1842e3a527ab27b294c6}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-C\-O\-M\-M\-E\-N\-T\-S} or \hyperlink{utils_8h_ab4db885222b3b69608310d7c7e63e286}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-S\-K\-I\-P\-\_\-\-B\-L\-A\-N\-K\-\_\-\-L\-I\-N\-E\-S} are passed, a sequence may be interrupted by lines starting with a comment character or empty lines.\par
 573  A sequence is regarded as completely read if it was either assumed to not span over multiple lines, a secondary structure or structure constraint follows the sequence on the next line or a new header marks the beginning of a new sequence...\par
 574  All lines following the sequence (this includes comments) and not initiating a new dataset are available through the line-\/array 'rest'. Here one can usually find the structure constraint or other information belonging to the current dataset. Filling of 'rest' may be prevented by passing \hyperlink{utils_8h_a7a2e8c50a0c7ce82e60da1016e1367fd}{V\-R\-N\-A\-\_\-\-I\-N\-P\-U\-T\-\_\-\-N\-O\-\_\-\-R\-E\-S\-T} to the options argument.\par
 575
 576
 577 \begin{DoxyNote}{Note}
 578 This function will exit any program with an error message if no sequence could be read! \begin{DoxyVerb}The main purpose of this function is to be able to easily parse blocks of data from stdin
 579 in the header of a loop where all calculations for the appropriate data is done inside the
 580 loop. The loop may be then left on certain return values, e.g.:
 581 \end{DoxyVerb}
 582  \begin{DoxyVerb}char *id, *seq, **rest;
 583 int  i;
 584 while(!(read_record(&id, &seq, &rest, 0) & (VRNA_INPUT_ERROR | VRNA_INPUT_QUIT))){
 585   if(id) printf("%s\n", id);
 586   printf("%s\n", seq);
 587   if(rest)
 588     for(i=0;rest[i];i++)
 589       printf("%s\n", rest[i]);
 590 } \end{DoxyVerb}
 591  \begin{DoxyVerb}In the example above, the while loop will be terminated when read_record() returns either an
 592 error or a user initiated quit request.\n
 593 As long as data is read from stdin, the id is printed if it is available for the current block
 594 of data. The sequence will be printed in any case and if some more lines belong to the current
 595 block of data each line will be printed as well.
 596 \end{DoxyVerb}
 597
 598
 599 Do not forget to free the memory occupied by header, sequence and rest!
 600 \end{DoxyNote}
 601
 602 \begin{DoxyParams}{Parameters}
 603 {\em header} & A pointer which will be set such that it points to the header of the record \\
 604 \hline
 605 {\em sequence} & A pointer which will be set such that it points to the sequence of the record \\
 606 \hline
 607 {\em rest} & A pointer which will be set such that it points to an array of lines which also belong to the record \\
 608 \hline
 609 {\em options} & Some options which may be passed to alter the behavior of the function, use 0 for no options \\
 610 \hline
 611 \end{DoxyParams}
 612 \begin{DoxyReturn}{Returns}
 613 A flag with information about what the function actually did read
 614 \end{DoxyReturn}
 615 \hypertarget{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{\index{utils.\-h@{utils.\-h}!pack\-\_\-structure@{pack\-\_\-structure}}
 616 \index{pack\-\_\-structure@{pack\-\_\-structure}!utils.h@{utils.\-h}}
 617 \subsubsection[{pack\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ pack\-\_\-structure (
 618 \begin{DoxyParamCaption}
 619 \item[{const char $\ast$}]{struc}
 620 \end{DoxyParamCaption}
 621 )}}\label{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}
 622
 623
 624 Pack secondary secondary structure, 5\-:1 compression using base 3 encoding.
 625
 626 Returns a binary string encoding of the secondary structure using a 5\-:1 compression scheme. The string is N\-U\-L\-L terminated and can therefore be used with standard string functions such as strcmp(). Useful for programs that need to keep many structures in memory.
 627
 628
 629 \begin{DoxyParams}{Parameters}
 630 {\em struc} & The secondary structure in dot-\/bracket notation \\
 631 \hline
 632 \end{DoxyParams}
 633 \begin{DoxyReturn}{Returns}
 634 The binary encoded structure
 635 \end{DoxyReturn}
 636 \hypertarget{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}{\index{utils.\-h@{utils.\-h}!unpack\-\_\-structure@{unpack\-\_\-structure}}
 637 \index{unpack\-\_\-structure@{unpack\-\_\-structure}!utils.h@{utils.\-h}}
 638 \subsubsection[{unpack\-\_\-structure}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ unpack\-\_\-structure (
 639 \begin{DoxyParamCaption}
 640 \item[{const char $\ast$}]{packed}
 641 \end{DoxyParamCaption}
 642 )}}\label{utils_8h_a071c6921efe1eb974f115ee6fefa3c39}
 643
 644
 645 Unpack secondary structure previously packed with \hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\-\_\-structure()}
 646
 647 Translate a compressed binary string produced by \hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\-\_\-structure()} back into the familiar dot-\/bracket notation.
 648
 649
 650 \begin{DoxyParams}{Parameters}
 651 {\em packed} & The binary encoded packed secondary structure \\
 652 \hline
 653 \end{DoxyParams}
 654 \begin{DoxyReturn}{Returns}
 655 The unpacked secondary structure in dot-\/bracket notation
 656 \end{DoxyReturn}
 657 \hypertarget{utils_8h_a89c32307ee50a0026f4a3131fac0845a}{\index{utils.\-h@{utils.\-h}!make\-\_\-pair\-\_\-table@{make\-\_\-pair\-\_\-table}}
 658 \index{make\-\_\-pair\-\_\-table@{make\-\_\-pair\-\_\-table}!utils.h@{utils.\-h}}
 659 \subsubsection[{make\-\_\-pair\-\_\-table}]{\setlength{\rightskip}{0pt plus 5cm}short$\ast$ make\-\_\-pair\-\_\-table (
 660 \begin{DoxyParamCaption}
 661 \item[{const char $\ast$}]{structure}
 662 \end{DoxyParamCaption}
 663 )}}\label{utils_8h_a89c32307ee50a0026f4a3131fac0845a}
 664
 665
 666 Create a pair table of a secondary structure.
 667
 668 Returns a newly allocated table, such that table\mbox{[}i\mbox{]}=j if (i.\-j) pair or 0 if i is unpaired, table\mbox{[}0\mbox{]} contains the length of the structure.
 669
 670
 671 \begin{DoxyParams}{Parameters}
 672 {\em structure} & The secondary structure in dot-\/bracket notation \\
 673 \hline
 674 \end{DoxyParams}
 675 \begin{DoxyReturn}{Returns}
 676 A pointer to the created pair\-\_\-table
 677 \end{DoxyReturn}
 678 \hypertarget{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}{\index{utils.\-h@{utils.\-h}!copy\-\_\-pair\-\_\-table@{copy\-\_\-pair\-\_\-table}}
 679 \index{copy\-\_\-pair\-\_\-table@{copy\-\_\-pair\-\_\-table}!utils.h@{utils.\-h}}
 680 \subsubsection[{copy\-\_\-pair\-\_\-table}]{\setlength{\rightskip}{0pt plus 5cm}short$\ast$ copy\-\_\-pair\-\_\-table (
 681 \begin{DoxyParamCaption}
 682 \item[{const short $\ast$}]{pt}
 683 \end{DoxyParamCaption}
 684 )}}\label{utils_8h_afeaa6d68eef3a99d0a7aa08aa91c6601}
 685
 686
 687 Get an exact copy of a pair table.
 688
 689
 690 \begin{DoxyParams}{Parameters}
 691 {\em pt} & The pair table to be copied \\
 692 \hline
 693 \end{DoxyParams}
 694 \begin{DoxyReturn}{Returns}
 695 A pointer to the copy of 'pt'
 696 \end{DoxyReturn}
 697 \hypertarget{utils_8h_a3c81b3967056c3888b8472b65fbb16f5}{\index{utils.\-h@{utils.\-h}!alimake\-\_\-pair\-\_\-table@{alimake\-\_\-pair\-\_\-table}}
 698 \index{alimake\-\_\-pair\-\_\-table@{alimake\-\_\-pair\-\_\-table}!utils.h@{utils.\-h}}
 699 \subsubsection[{alimake\-\_\-pair\-\_\-table}]{\setlength{\rightskip}{0pt plus 5cm}short$\ast$ alimake\-\_\-pair\-\_\-table (
 700 \begin{DoxyParamCaption}
 701 \item[{const char $\ast$}]{structure}
 702 \end{DoxyParamCaption}
 703 )}}\label{utils_8h_a3c81b3967056c3888b8472b65fbb16f5}
 704 $\ast$$\ast$$\ast$\-Pair table for snoop align \hypertarget{utils_8h_a9aa3bf3b4346bb7fb88efc154dd07a79}{\index{utils.\-h@{utils.\-h}!make\-\_\-pair\-\_\-table\-\_\-snoop@{make\-\_\-pair\-\_\-table\-\_\-snoop}}
 705 \index{make\-\_\-pair\-\_\-table\-\_\-snoop@{make\-\_\-pair\-\_\-table\-\_\-snoop}!utils.h@{utils.\-h}}
 706 \subsubsection[{make\-\_\-pair\-\_\-table\-\_\-snoop}]{\setlength{\rightskip}{0pt plus 5cm}short$\ast$ make\-\_\-pair\-\_\-table\-\_\-snoop (
 707 \begin{DoxyParamCaption}
 708 \item[{const char $\ast$}]{structure}
 709 \end{DoxyParamCaption}
 710 )}}\label{utils_8h_a9aa3bf3b4346bb7fb88efc154dd07a79}
 711 returns a newly allocated table, such that\-: table\mbox{[}i\mbox{]}=j if (i.\-j) pair or 0 if i is unpaired, table\mbox{[}0\mbox{]} contains the length of the structure. The special pseudoknotted H/\-A\-C\-A-\/m\-R\-N\-A structure is taken into account. \hypertarget{utils_8h_a4358e89f64cc87a563b7ef3855f75bed}{\index{utils.\-h@{utils.\-h}!make\-\_\-loop\-\_\-index\-\_\-pt@{make\-\_\-loop\-\_\-index\-\_\-pt}}
 712 \index{make\-\_\-loop\-\_\-index\-\_\-pt@{make\-\_\-loop\-\_\-index\-\_\-pt}!utils.h@{utils.\-h}}
 713 \subsubsection[{make\-\_\-loop\-\_\-index\-\_\-pt}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ make\-\_\-loop\-\_\-index\-\_\-pt (
 714 \begin{DoxyParamCaption}
 715 \item[{short $\ast$}]{pt}
 716 \end{DoxyParamCaption}
 717 )}}\label{utils_8h_a4358e89f64cc87a563b7ef3855f75bed}
 718
 719
 720 Compute the \char`\"{}base pair\char`\"{} distance between two secondary structures s1 and s2.
 721
 722 The sequences should have the same length. dist = number of base pairs in one structure but not in the other same as edit distance with open-\/pair close-\/pair as move-\/set
 723
 724
 725 \begin{DoxyParams}{Parameters}
 726 {\em str1} & First structure in dot-\/bracket notation \\
 727 \hline
 728 {\em str2} & Second structure in dot-\/bracket notation \\
 729 \hline
 730 \end{DoxyParams}
 731 \begin{DoxyReturn}{Returns}
 732 The base pair distance between str1 and str2
 733 \end{DoxyReturn}
 734 \hypertarget{utils_8h_a6bf778117d31b7fd90db435323f4ef74}{\index{utils.\-h@{utils.\-h}!print\-\_\-tty\-\_\-input\-\_\-seq@{print\-\_\-tty\-\_\-input\-\_\-seq}}
 735 \index{print\-\_\-tty\-\_\-input\-\_\-seq@{print\-\_\-tty\-\_\-input\-\_\-seq}!utils.h@{utils.\-h}}
 736 \subsubsection[{print\-\_\-tty\-\_\-input\-\_\-seq}]{\setlength{\rightskip}{0pt plus 5cm}void print\-\_\-tty\-\_\-input\-\_\-seq (
 737 \begin{DoxyParamCaption}
 738 \item[{void}]{}
 739 \end{DoxyParamCaption}
 740 )}}\label{utils_8h_a6bf778117d31b7fd90db435323f4ef74}
 741
 742
 743 Print a line to {\itshape stdout} that asks for an input sequence.
 744
 745 There will also be a ruler (scale line) printed that helps orientation of the sequence positions \hypertarget{utils_8h_ae4ef89b662a3e9b5b5f0781d9757aba0}{\index{utils.\-h@{utils.\-h}!print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str@{print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str}}
 746 \index{print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str@{print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str}!utils.h@{utils.\-h}}
 747 \subsubsection[{print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str}]{\setlength{\rightskip}{0pt plus 5cm}void print\-\_\-tty\-\_\-input\-\_\-seq\-\_\-str (
 748 \begin{DoxyParamCaption}
 749 \item[{const char $\ast$}]{s}
 750 \end{DoxyParamCaption}
 751 )}}\label{utils_8h_ae4ef89b662a3e9b5b5f0781d9757aba0}
 752
 753
 754 Print a line with a user defined string and a ruler to stdout.
 755
 756 (usually this is used to ask for user input) There will also be a ruler (scale line) printed that helps orientation of the sequence positions
 757
 758
 759 \begin{DoxyParams}{Parameters}
 760 {\em s} & A user defined string that will be printed to stdout \\
 761 \hline
 762 \end{DoxyParams}
 763 \hypertarget{utils_8h_a4d167deb70bb51723e44374dc981deb2}{\index{utils.\-h@{utils.\-h}!print\-\_\-tty\-\_\-constraint@{print\-\_\-tty\-\_\-constraint}}
 764 \index{print\-\_\-tty\-\_\-constraint@{print\-\_\-tty\-\_\-constraint}!utils.h@{utils.\-h}}
 765 \subsubsection[{print\-\_\-tty\-\_\-constraint}]{\setlength{\rightskip}{0pt plus 5cm}void print\-\_\-tty\-\_\-constraint (
 766 \begin{DoxyParamCaption}
 767 \item[{unsigned int}]{option}
 768 \end{DoxyParamCaption}
 769 )}}\label{utils_8h_a4d167deb70bb51723e44374dc981deb2}
 770
 771
 772 Print structure constraint characters to stdout. (constraint support is specified by option parameter)
 773
 774 Currently available options are\-:\par
 775  \hyperlink{utils_8h_a4e8d7120619b21df0309af425acbc9a2}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-P\-I\-P\-E} (paired with another base)\par
 776  \hyperlink{utils_8h_a55e1d16fd693ae9ec8e987b0750da804}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-D\-O\-T} (no constraint at all)\par
 777  \hyperlink{utils_8h_a077c56550c915d4516d84a5ed8d051f4}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-X} (base must not pair)\par
 778  \hyperlink{utils_8h_a0512d790f738742cbdcf3f7c87b46f48}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-A\-N\-G\-\_\-\-B\-R\-A\-C\-K} (paired downstream/upstream)\par
 779  \hyperlink{utils_8h_aa20bfca4bb2903c8548000a33d7bbb53}{V\-R\-N\-A\-\_\-\-C\-O\-N\-S\-T\-R\-A\-I\-N\-T\-\_\-\-R\-N\-D\-\_\-\-B\-R\-A\-C\-K} (base i pairs base j)\par
 780
 781
 782 pass a collection of options as one value like this\-: \begin{DoxyVerb}print_tty_constraint(option_1 | option_2 | option_n) \end{DoxyVerb}
 783
 784
 785
 786 \begin{DoxyParams}{Parameters}
 787 {\em option} & Option switch that tells which constraint help will be printed \\
 788 \hline
 789 \end{DoxyParams}
 790 \hypertarget{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}{\index{utils.\-h@{utils.\-h}!str\-\_\-\-D\-N\-A2\-R\-N\-A@{str\-\_\-\-D\-N\-A2\-R\-N\-A}}
 791 \index{str\-\_\-\-D\-N\-A2\-R\-N\-A@{str\-\_\-\-D\-N\-A2\-R\-N\-A}!utils.h@{utils.\-h}}
 792 \subsubsection[{str\-\_\-\-D\-N\-A2\-R\-N\-A}]{\setlength{\rightskip}{0pt plus 5cm}void str\-\_\-\-D\-N\-A2\-R\-N\-A (
 793 \begin{DoxyParamCaption}
 794 \item[{char $\ast$}]{sequence}
 795 \end{DoxyParamCaption}
 796 )}}\label{utils_8h_ad3f18dd83f958f18b2f26ecb99305208}
 797
 798
 799 Convert a D\-N\-A input sequence to R\-N\-A alphabet.
 800
 801 This function substitudes {\itshape T} and {\itshape t} with {\itshape U} and {\itshape u}, respectively
 802
 803
 804 \begin{DoxyParams}{Parameters}
 805 {\em sequence} & The sequence to be converted \\
 806 \hline
 807 \end{DoxyParams}
 808 \hypertarget{utils_8h_a17b796b806f96b70382077fb5bc519bb}{\index{utils.\-h@{utils.\-h}!str\-\_\-uppercase@{str\-\_\-uppercase}}
 809 \index{str\-\_\-uppercase@{str\-\_\-uppercase}!utils.h@{utils.\-h}}
 810 \subsubsection[{str\-\_\-uppercase}]{\setlength{\rightskip}{0pt plus 5cm}void str\-\_\-uppercase (
 811 \begin{DoxyParamCaption}
 812 \item[{char $\ast$}]{sequence}
 813 \end{DoxyParamCaption}
 814 )}}\label{utils_8h_a17b796b806f96b70382077fb5bc519bb}
 815
 816
 817 Convert an input sequence to uppercase.
 818
 819
 820 \begin{DoxyParams}{Parameters}
 821 {\em sequence} & The sequence to be converted \\
 822 \hline
 823 \end{DoxyParams}
 824 \hypertarget{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{\index{utils.\-h@{utils.\-h}!get\-\_\-iindx@{get\-\_\-iindx}}
 825 \index{get\-\_\-iindx@{get\-\_\-iindx}!utils.h@{utils.\-h}}
 826 \subsubsection[{get\-\_\-iindx}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ get\-\_\-iindx (
 827 \begin{DoxyParamCaption}
 828 \item[{unsigned int}]{length}
 829 \end{DoxyParamCaption}
 830 )}}\label{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}
 831
 832
 833 Get an index mapper array (iindx) for accessing the energy matrices, e.\-g. in partition function related functions.
 834
 835 Access of a position \char`\"{}(i,j)\char`\"{} is then accomplished by using\begin{DoxyVerb}(i,j) ~ iindx[i]-j \end{DoxyVerb}
 836  This function is necessary as most of the two-\/dimensional energy matrices are actually one-\/dimensional arrays throughout the Vienna\-R\-N\-A\-Package
 837
 838 Consult the implemented code to find out about the mapping formula ;)
 839
 840 \begin{DoxySeeAlso}{See Also}
 841 \hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\-\_\-indx()}
 842 \end{DoxySeeAlso}
 843
 844 \begin{DoxyParams}{Parameters}
 845 {\em length} & The length of the R\-N\-A sequence \\
 846 \hline
 847 \end{DoxyParams}
 848 \begin{DoxyReturn}{Returns}
 849 The mapper array
 850 \end{DoxyReturn}
 851 \hypertarget{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{\index{utils.\-h@{utils.\-h}!get\-\_\-indx@{get\-\_\-indx}}
 852 \index{get\-\_\-indx@{get\-\_\-indx}!utils.h@{utils.\-h}}
 853 \subsubsection[{get\-\_\-indx}]{\setlength{\rightskip}{0pt plus 5cm}int$\ast$ get\-\_\-indx (
 854 \begin{DoxyParamCaption}
 855 \item[{unsigned int}]{length}
 856 \end{DoxyParamCaption}
 857 )}}\label{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}
 858
 859
 860 Get an index mapper array (indx) for accessing the energy matrices, e.\-g. in M\-F\-E related functions.
 861
 862 Access of a position \char`\"{}(i,j)\char`\"{} is then accomplished by using\begin{DoxyVerb}(i,j) ~ indx[j]+i \end{DoxyVerb}
 863  This function is necessary as most of the two-\/dimensional energy matrices are actually one-\/dimensional arrays throughout the Vienna\-R\-N\-A\-Package
 864
 865 Consult the implemented code to find out about the mapping formula ;)
 866
 867 \begin{DoxySeeAlso}{See Also}
 868 \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx()}
 869 \end{DoxySeeAlso}
 870
 871 \begin{DoxyParams}{Parameters}
 872 {\em length} & The length of the R\-N\-A sequence \\
 873 \hline
 874 \end{DoxyParams}
 875 \begin{DoxyReturn}{Returns}
 876 The mapper array
 877 \end{DoxyReturn}
 878 \hypertarget{utils_8h_a36c3a6c3218b041f992052767bc74549}{\index{utils.\-h@{utils.\-h}!constrain\-\_\-ptypes@{constrain\-\_\-ptypes}}
 879 \index{constrain\-\_\-ptypes@{constrain\-\_\-ptypes}!utils.h@{utils.\-h}}
 880 \subsubsection[{constrain\-\_\-ptypes}]{\setlength{\rightskip}{0pt plus 5cm}void constrain\-\_\-ptypes (
 881 \begin{DoxyParamCaption}
 882 \item[{const char $\ast$}]{constraint, }
 883 \item[{unsigned int}]{length, }
 884 \item[{char $\ast$}]{ptype, }
 885 \item[{int $\ast$}]{B\-P, }
 886 \item[{int}]{min\-\_\-loop\-\_\-size, }
 887 \item[{unsigned int}]{idx\-\_\-type}
 888 \end{DoxyParamCaption}
 889 )}}\label{utils_8h_a36c3a6c3218b041f992052767bc74549}
 890
 891
 892 Insert constraining pair types according to constraint structure string.
 893
 894 \begin{DoxySeeAlso}{See Also}
 895 \hyperlink{utils_8h_a4d9ee1572c1bfcd02d3d3f2db8a6530f}{get\-\_\-indx()}, \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx()}
 896 \end{DoxySeeAlso}
 897
 898 \begin{DoxyParams}{Parameters}
 899 {\em constraint} & The structure constraint string \\
 900 \hline
 901 {\em length} & The actual length of the sequence (constraint may be shorter) \\
 902 \hline
 903 {\em ptype} & A pointer to the basepair type array \\
 904 \hline
 905 {\em min\-\_\-loop\-\_\-size} & The minimal loop size (usually \hyperlink{energy__const_8h_ae646250fd59311356c7e5722a81c3a96}{T\-U\-R\-N} ) \\
 906 \hline
 907 {\em idx\-\_\-type} & Define the access type for base pair type array (0 = indx, 1 = iindx) \\
 908 \hline
 909 \end{DoxyParams}
 910
 911
 912 \subsection{Variable Documentation}
 913 \hypertarget{utils_8h_af9a866c8417afda7368bbac939ab3c47}{\index{utils.\-h@{utils.\-h}!xsubi@{xsubi}}
 914 \index{xsubi@{xsubi}!utils.h@{utils.\-h}}
 915 \subsubsection[{xsubi}]{\setlength{\rightskip}{0pt plus 5cm}unsigned short xsubi\mbox{[}3\mbox{]}}}\label{utils_8h_af9a866c8417afda7368bbac939ab3c47}
 916
 917
 918 Current 48 bit random number.
 919
 920 This variable is used by \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn()}. These should be set to some random number seeds before the first call to \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn()}.
 921
 922 \begin{DoxySeeAlso}{See Also}
 923 \hyperlink{utils_8h_aaa328491c84996e445d027fde9800f2e}{urn()}
 924 \end{DoxySeeAlso}