binaries/src/ViennaRNA/doc/latex/alifold_8h.tex

   1 \hypertarget{alifold_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/alifold.h File Reference}
   2 \label{alifold_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/alifold.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/alifold.\-h}}
   3 }
   4
   5
   6 compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments
   7
   8
   9 Include dependency graph for alifold.\-h\-:
  10 \nopagebreak
  11 \begin{figure}[H]
  12 \begin{center}
  13 \leavevmode
  14 \includegraphics[width=250pt]{alifold_8h__incl}
  15 \end{center}
  16 \end{figure}
  17 \subsection*{Functions}
  18 \begin{DoxyCompactItemize}
  19 \item
  20 void \hyperlink{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{update\-\_\-alifold\-\_\-params} (void)
  21 \begin{DoxyCompactList}\small\item\em Update the energy parameters for alifold function. \end{DoxyCompactList}\item
  22 float \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold} (const char $\ast$$\ast$strings, char $\ast$structure)
  23 \begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according consensus structure of an alignment of sequences. \end{DoxyCompactList}\item
  24 float \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold} (const char $\ast$$\ast$strings, char $\ast$structure)
  25 \begin{DoxyCompactList}\small\item\em Compute M\-F\-E and according structure of an alignment of sequences assuming the sequences are circular instead of linear. \end{DoxyCompactList}\item
  26 \hypertarget{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{void \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free\-\_\-alifold\-\_\-arrays} (void)}\label{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}
  27
  28 \begin{DoxyCompactList}\small\item\em Free the memory occupied by M\-F\-E alifold functions. \end{DoxyCompactList}\item
  29 int \hyperlink{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{get\-\_\-mpi} (char $\ast$Alseq\mbox{[}$\,$\mbox{]}, int n\-\_\-seq, int length, int $\ast$mini)
  30 \begin{DoxyCompactList}\small\item\em Get the mean pairwise identity in steps from ?to?(ident) \end{DoxyCompactList}\item
  31 \hypertarget{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{float $\ast$$\ast$ \hyperlink{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{readribosum} (char $\ast$name)}\label{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}
  32
  33 \begin{DoxyCompactList}\small\item\em Read a ribosum or other user-\/defined scoring matrix. \end{DoxyCompactList}\item
  34 float \hyperlink{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{energy\-\_\-of\-\_\-alistruct} (const char $\ast$$\ast$sequences, const char $\ast$structure, int n\-\_\-seq, float $\ast$energy)
  35 \begin{DoxyCompactList}\small\item\em Calculate the free energy of a consensus structure given a set of aligned sequences. \end{DoxyCompactList}\item
  36 void \hyperlink{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{encode\-\_\-ali\-\_\-sequence} (const char $\ast$sequence, short $\ast$S, short $\ast$s5, short $\ast$s3, char $\ast$ss, unsigned short $\ast$as, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ})
  37 \begin{DoxyCompactList}\small\item\em Get arrays with encoded sequence of the alignment. \end{DoxyCompactList}\item
  38 void \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\-\_\-sequence\-\_\-arrays} (const char $\ast$$\ast$sequences, short $\ast$$\ast$$\ast$S, short $\ast$$\ast$$\ast$S5, short $\ast$$\ast$$\ast$S3, unsigned short $\ast$$\ast$$\ast$a2s, char $\ast$$\ast$$\ast$Ss, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ})
  39 \begin{DoxyCompactList}\small\item\em Allocate memory for sequence array used to deal with aligned sequences. \end{DoxyCompactList}\item
  40 void \hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free\-\_\-sequence\-\_\-arrays} (unsigned int n\-\_\-seq, short $\ast$$\ast$$\ast$S, short $\ast$$\ast$$\ast$S5, short $\ast$$\ast$$\ast$S3, unsigned short $\ast$$\ast$$\ast$a2s, char $\ast$$\ast$$\ast$Ss)
  41 \begin{DoxyCompactList}\small\item\em Free the memory of the sequence arrays used to deal with aligned sequences. \end{DoxyCompactList}\item
  42 float \hyperlink{group__consensus__pf__fold_ga4d2ff54d8210fc7cceeeff389d4dbd1d}{alipf\-\_\-fold\-\_\-par} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl, \hyperlink{structpf__paramT}{pf\-\_\-param\-T} $\ast$parameters, int calculate\-\_\-bppm, int is\-\_\-constrained, int is\-\_\-circular)
  43 \item
  44 float \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
  45 \begin{DoxyCompactList}\small\item\em The partition function version of \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold()} works in analogy to \hyperlink{group__pf__fold_gadc3db3d98742427e7001a7fd36ef28c2}{pf\-\_\-fold()}. Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of \hyperlink{structpair__info}{pair\-\_\-info} structs. The list is terminated by the first entry with pi.\-i = 0. \end{DoxyCompactList}\item
  46 float \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\-\_\-circ\-\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
  47 \item
  48 double $\ast$ \hyperlink{group__consensus__pf__fold_gadaaf83394216413505e48d913dbc1b4e}{export\-\_\-ali\-\_\-bppm} (void)
  49 \begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \end{DoxyCompactList}\item
  50 char $\ast$ \hyperlink{group__consensus__stochbt_ga0df40248788f0fb17ebdc59d74116d1c}{alipbacktrack} (double $\ast$prob)
  51 \begin{DoxyCompactList}\small\item\em Sample a consensus secondary structure from the Boltzmann ensemble according its probability\par
  52 . \end{DoxyCompactList}\item
  53 int \hyperlink{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}{get\-\_\-alipf\-\_\-arrays} (short $\ast$$\ast$$\ast$S\-\_\-p, short $\ast$$\ast$$\ast$S5\-\_\-p, short $\ast$$\ast$$\ast$S3\-\_\-p, unsigned short $\ast$$\ast$$\ast$a2s\-\_\-p, char $\ast$$\ast$$\ast$Ss\-\_\-p, double $\ast$$\ast$qb\-\_\-p, double $\ast$$\ast$qm\-\_\-p, double $\ast$$\ast$q1k\-\_\-p, double $\ast$$\ast$qln\-\_\-p, short $\ast$$\ast$pscore)
  54 \begin{DoxyCompactList}\small\item\em Get pointers to (almost) all relavant arrays used in alifold's partition function computation. \end{DoxyCompactList}\end{DoxyCompactItemize}
  55 \subsection*{Variables}
  56 \begin{DoxyCompactItemize}
  57 \item
  58 double \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv\-\_\-fact}
  59 \begin{DoxyCompactList}\small\item\em This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. \end{DoxyCompactList}\item
  60 double \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc\-\_\-fact}
  61 \begin{DoxyCompactList}\small\item\em This variable controls the magnitude of the penalty for non-\/compatible sequences in the covariance term of alignment folding algorithms. \end{DoxyCompactList}\end{DoxyCompactItemize}
  62
  63
  64 \subsection{Detailed Description}
  65 compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments
  66
  67 \subsection{Function Documentation}
  68 \hypertarget{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{\index{alifold.\-h@{alifold.\-h}!update\-\_\-alifold\-\_\-params@{update\-\_\-alifold\-\_\-params}}
  69 \index{update\-\_\-alifold\-\_\-params@{update\-\_\-alifold\-\_\-params}!alifold.h@{alifold.\-h}}
  70 \subsubsection[{update\-\_\-alifold\-\_\-params}]{\setlength{\rightskip}{0pt plus 5cm}void update\-\_\-alifold\-\_\-params (
  71 \begin{DoxyParamCaption}
  72 \item[{void}]{}
  73 \end{DoxyParamCaption}
  74 )}}\label{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}
  75
  76
  77 Update the energy parameters for alifold function.
  78
  79 Call this to recalculate the pair matrix and energy parameters after a change in folding parameters like \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature}