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

   1 \hypertarget{group__consensus__pf__fold}{\section{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}
   2 \label{group__consensus__pf__fold}\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
   3 }
   4 Collaboration diagram for Partition Function and Base Pair Probabilities for Sequence Alignment(s)\-:
   5 \nopagebreak
   6 \begin{figure}[H]
   7 \begin{center}
   8 \leavevmode
   9 \includegraphics[width=350pt]{group__consensus__pf__fold}
  10 \end{center}
  11 \end{figure}
  12 \subsection*{Functions}
  13 \begin{DoxyCompactItemize}
  14 \item
  15 float \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf\-\_\-fold\-\_\-par} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters, int calculate\-\_\-bppm, int is\-\_\-constrained, int is\-\_\-circular)
  16 \item
  17 float \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
  18 \begin{DoxyCompactList}\small\item\em The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\-\_\-info} structs. The list is terminated by the first entry with pi.\-i = 0. \end{DoxyCompactList}\item
  19 float \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\-\_\-circ\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
  20 \item
  21 double $\ast$ \hyperlink{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{export\-\_\-ali\-\_\-bppm} (void)
  22 \begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \end{DoxyCompactList}\end{DoxyCompactItemize}
  23
  24
  25 \subsection{Detailed Description}
  26
  27
  28 \subsection{Function Documentation}
  29 \hypertarget{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\-\_\-fold\-\_\-par@{alipf\-\_\-fold\-\_\-par}}
  30 \index{alipf\-\_\-fold\-\_\-par@{alipf\-\_\-fold\-\_\-par}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
  31 \subsubsection[{alipf\-\_\-fold\-\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-fold\-\_\-par (
  32 \begin{DoxyParamCaption}
  33 \item[{const char $\ast$$\ast$}]{sequences, }
  34 \item[{char $\ast$}]{structure, }
  35 \item[{{\bf plist} $\ast$$\ast$}]{pl, }
  36 \item[{{\bf pf\-\_\-param\-T} $\ast$}]{parameters, }
  37 \item[{int}]{calculate\-\_\-bppm, }
  38 \item[{int}]{is\-\_\-constrained, }
  39 \item[{int}]{is\-\_\-circular}
  40 \end{DoxyParamCaption}
  41 )}}\label{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}
  42
  43 \begin{DoxyParams}{Parameters}
  44 {\em sequences} & \\
  45 \hline
  46 {\em structure} & \\
  47 \hline
  48 {\em pl} & \\
  49 \hline
  50 {\em parameters} & \\
  51 \hline
  52 {\em calculate\-\_\-bppm} & \\
  53 \hline
  54 {\em is\-\_\-constrained} & \\
  55 \hline
  56 {\em is\-\_\-circular} & \\
  57 \hline
  58 \end{DoxyParams}
  59 \begin{DoxyReturn}{Returns}
  60
  61 \end{DoxyReturn}
  62 \hypertarget{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\-\_\-fold@{alipf\-\_\-fold}}
  63 \index{alipf\-\_\-fold@{alipf\-\_\-fold}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
  64 \subsubsection[{alipf\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-fold (
  65 \begin{DoxyParamCaption}
  66 \item[{const char $\ast$$\ast$}]{sequences, }
  67 \item[{char $\ast$}]{structure, }
  68 \item[{{\bf plist} $\ast$$\ast$}]{pl}
  69 \end{DoxyParamCaption}
  70 )}}\label{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}
  71
  72
  73 The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\-\_\-info} structs. The list is terminated by the first entry with pi.\-i = 0.
  74
  75
  76 \begin{DoxyParams}{Parameters}
  77 {\em sequences} & \\
  78 \hline
  79 {\em structure} & \\
  80 \hline
  81 {\em pl} & \\
  82 \hline
  83 \end{DoxyParams}
  84 \begin{DoxyReturn}{Returns}
  85
  86 \end{DoxyReturn}
  87 \hypertarget{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!alipf\-\_\-circ\-\_\-fold@{alipf\-\_\-circ\-\_\-fold}}
  88 \index{alipf\-\_\-circ\-\_\-fold@{alipf\-\_\-circ\-\_\-fold}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
  89 \subsubsection[{alipf\-\_\-circ\-\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\-\_\-circ\-\_\-fold (
  90 \begin{DoxyParamCaption}
  91 \item[{const char $\ast$$\ast$}]{sequences, }
  92 \item[{char $\ast$}]{structure, }
  93 \item[{{\bf plist} $\ast$$\ast$}]{pl}
  94 \end{DoxyParamCaption}
  95 )}}\label{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}
  96
  97 \begin{DoxyParams}{Parameters}
  98 {\em sequences} & \\
  99 \hline
 100 {\em structure} & \\
 101 \hline
 102 {\em pl} & \\
 103 \hline
 104 \end{DoxyParams}
 105 \begin{DoxyReturn}{Returns}
 106
 107 \end{DoxyReturn}
 108 \hypertarget{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{\index{Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}!export\-\_\-ali\-\_\-bppm@{export\-\_\-ali\-\_\-bppm}}
 109 \index{export\-\_\-ali\-\_\-bppm@{export\-\_\-ali\-\_\-bppm}!Partition Function and Base Pair Probabilities for Sequence Alignment(s)@{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}}
 110 \subsubsection[{export\-\_\-ali\-\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}double$\ast$ export\-\_\-ali\-\_\-bppm (
 111 \begin{DoxyParamCaption}
 112 \item[{void}]{}
 113 \end{DoxyParamCaption}
 114 )}}\label{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}
 115
 116
 117 Get a pointer to the base pair probability array.
 118
 119 Accessing the base pair probabilities for a pair (i,j) is achieved by \begin{DoxyVerb}FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; \end{DoxyVerb}
 120
 121
 122 \begin{DoxySeeAlso}{See Also}
 123 \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\-\_\-iindx()}
 124 \end{DoxySeeAlso}
 125 \begin{DoxyReturn}{Returns}
 126 A pointer to the base pair probability array
 127 \end{DoxyReturn}