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

   1 \hypertarget{group__consensus__pf__fold}{
   2 \section{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}
   3 \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)}}
   4 }
   5
   6
   7 Collaboration diagram for Partition Function and Base Pair Probabilities for Sequence Alignment(s):\nopagebreak
   8 \begin{figure}[H]
   9 \begin{center}
  10 \leavevmode
  11 \includegraphics[width=334pt]{group__consensus__pf__fold}
  12 \end{center}
  13 \end{figure}
  14 \subsection*{Functions}
  15 \begin{DoxyCompactItemize}
  16 \item
  17 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\_\-paramT} $\ast$parameters, int calculate\_\-bppm, int is\_\-constrained, int is\_\-circular)
  18 \item
  19 float \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
  20 \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. \item\end{DoxyCompactList}\item
  21 float \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\_\-circ\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
  22 \item
  23 FLT\_\-OR\_\-DBL $\ast$ \hyperlink{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}{export\_\-ali\_\-bppm} (void)
  24 \begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
  25
  26
  27 \subsection{Function Documentation}
  28 \hypertarget{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{
  29 \index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!alipf\_\-fold\_\-par@{alipf\_\-fold\_\-par}}
  30 \index{alipf\_\-fold\_\-par@{alipf\_\-fold\_\-par}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
  31 \subsubsection[{alipf\_\-fold\_\-par}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-fold\_\-par (const char $\ast$$\ast$ {\em sequences}, \/  char $\ast$ {\em structure}, \/  {\bf plist} $\ast$$\ast$ {\em pl}, \/  {\bf pf\_\-paramT} $\ast$ {\em parameters}, \/  int {\em calculate\_\-bppm}, \/  int {\em is\_\-constrained}, \/  int {\em is\_\-circular})}}
  32 \label{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}
  33
  34 \begin{DoxyParams}{Parameters}
  35 \item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\item[{\em parameters}]\item[{\em calculate\_\-bppm}]\item[{\em is\_\-constrained}]\item[{\em is\_\-circular}]\end{DoxyParams}
  36 \begin{DoxyReturn}{Returns}
  37
  38 \end{DoxyReturn}
  39 \hypertarget{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{
  40 \index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!alipf\_\-fold@{alipf\_\-fold}}
  41 \index{alipf\_\-fold@{alipf\_\-fold}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
  42 \subsubsection[{alipf\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-fold (const char $\ast$$\ast$ {\em sequences}, \/  char $\ast$ {\em structure}, \/  {\bf plist} $\ast$$\ast$ {\em pl})}}
  43 \label{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}
  44
  45
  46 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.
  47 \begin{DoxyParams}{Parameters}
  48 \item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\end{DoxyParams}
  49 \begin{DoxyReturn}{Returns}
  50
  51 \end{DoxyReturn}
  52 \hypertarget{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{
  53 \index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!alipf\_\-circ\_\-fold@{alipf\_\-circ\_\-fold}}
  54 \index{alipf\_\-circ\_\-fold@{alipf\_\-circ\_\-fold}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
  55 \subsubsection[{alipf\_\-circ\_\-fold}]{\setlength{\rightskip}{0pt plus 5cm}float alipf\_\-circ\_\-fold (const char $\ast$$\ast$ {\em sequences}, \/  char $\ast$ {\em structure}, \/  {\bf plist} $\ast$$\ast$ {\em pl})}}
  56 \label{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}
  57
  58 \begin{DoxyParams}{Parameters}
  59 \item[{\em sequences}]\item[{\em structure}]\item[{\em pl}]\end{DoxyParams}
  60 \begin{DoxyReturn}{Returns}
  61
  62 \end{DoxyReturn}
  63 \hypertarget{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}{
  64 \index{consensus\_\-pf\_\-fold@{consensus\_\-pf\_\-fold}!export\_\-ali\_\-bppm@{export\_\-ali\_\-bppm}}
  65 \index{export\_\-ali\_\-bppm@{export\_\-ali\_\-bppm}!consensus_pf_fold@{consensus\_\-pf\_\-fold}}
  66 \subsubsection[{export\_\-ali\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}FLT\_\-OR\_\-DBL$\ast$ export\_\-ali\_\-bppm (void)}}
  67 \label{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}
  68
  69
  70 Get a pointer to the base pair probability array. 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}
  71
  72
  73 \begin{DoxySeeAlso}{See also}
  74 \hyperlink{utils_8h_a55c0f6b3b07b6adf2ee235ba901fe397}{get\_\-iindx()}
  75 \end{DoxySeeAlso}
  76 \begin{DoxyReturn}{Returns}
  77 A pointer to the base pair probability array
  78 \end{DoxyReturn}