\hypertarget{alifold_8h}{
\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h File Reference}
\label{alifold_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/alifold.h}}
}


compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments  
Include dependency graph for alifold.h:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
\includegraphics[width=208pt]{alifold_8h__incl}
\end{center}
\end{figure}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\item 
void \hyperlink{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{update\_\-alifold\_\-params} (void)
\begin{DoxyCompactList}\small\item\em Update the energy parameters for alifold function. \item\end{DoxyCompactList}\item 
float \hyperlink{group__consensus__mfe__fold_ga4cf00f0659e5f0480335d69e797f05b1}{alifold} (const char $\ast$$\ast$strings, char $\ast$structure)
\begin{DoxyCompactList}\small\item\em Compute MFE and according consensus structure of an alignment of sequences. \item\end{DoxyCompactList}\item 
float \hyperlink{group__consensus__mfe__fold_gadbd3b0b1c144cbfb4efe704b2b260f96}{circalifold} (const char $\ast$$\ast$strings, char $\ast$structure)
\begin{DoxyCompactList}\small\item\em Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear. \item\end{DoxyCompactList}\item 
\hypertarget{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{
void \hyperlink{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}{free\_\-alifold\_\-arrays} (void)}
\label{group__consensus__mfe__fold_ga72095e4554b5d577250ea14c42acc49e}

\begin{DoxyCompactList}\small\item\em Free the memory occupied by MFE alifold functions. \item\end{DoxyCompactList}\item 
int \hyperlink{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{get\_\-mpi} (char $\ast$Alseq\mbox{[}$\,$\mbox{]}, int n\_\-seq, int length, int $\ast$mini)
\begin{DoxyCompactList}\small\item\em Get the mean pairwise identity in steps from ?to?(ident). \item\end{DoxyCompactList}\item 
\hypertarget{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{
float $\ast$$\ast$ \hyperlink{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{readribosum} (char $\ast$name)}
\label{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}

\begin{DoxyCompactList}\small\item\em Read a ribosum or other user-\/defined scoring matrix. \item\end{DoxyCompactList}\item 
float \hyperlink{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{energy\_\-of\_\-alistruct} (const char $\ast$$\ast$sequences, const char $\ast$structure, int n\_\-seq, float $\ast$energy)
\begin{DoxyCompactList}\small\item\em Calculate the free energy of a consensus structure given a set of aligned sequences. \item\end{DoxyCompactList}\item 
void \hyperlink{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{encode\_\-ali\_\-sequence} (const char $\ast$sequence, short $\ast$S, short $\ast$s5, short $\ast$s3, char $\ast$ss, unsigned short $\ast$as, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ})
\begin{DoxyCompactList}\small\item\em Get arrays with encoded sequence of the alignment. \item\end{DoxyCompactList}\item 
void \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\_\-sequence\_\-arrays} (const char $\ast$$\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})
\begin{DoxyCompactList}\small\item\em Allocate memory for sequence array used to deal with aligned sequences. \item\end{DoxyCompactList}\item 
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)
\begin{DoxyCompactList}\small\item\em Free the memory of the sequence arrays used to deal with aligned sequences. \item\end{DoxyCompactList}\item 
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)
\item 
float \hyperlink{group__consensus__pf__fold_gad32ded7d753ccaf211ab35782d1f42a9}{alipf\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
\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 
float \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\_\-circ\_\-fold} (const char $\ast$$\ast$sequences, char $\ast$structure, \hyperlink{structplist}{plist} $\ast$$\ast$pl)
\item 
FLT\_\-OR\_\-DBL $\ast$ \hyperlink{group__consensus__pf__fold_ga11b6ab8bd9be1821fea352b190a01cab}{export\_\-ali\_\-bppm} (void)
\begin{DoxyCompactList}\small\item\em Get a pointer to the base pair probability array. \item\end{DoxyCompactList}\item 
char $\ast$ \hyperlink{group__consensus__stochbt_ga0df40248788f0fb17ebdc59d74116d1c}{alipbacktrack} (double $\ast$prob)
\begin{DoxyCompactList}\small\item\em Sample a consensus secondary structure from the Boltzmann ensemble according its probability\par
. \item\end{DoxyCompactList}\item 
int \hyperlink{group__consensus__fold_ga5349960075b1847720a2e9df021e2675}{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, FLT\_\-OR\_\-DBL $\ast$$\ast$qb\_\-p, FLT\_\-OR\_\-DBL $\ast$$\ast$qm\_\-p, FLT\_\-OR\_\-DBL $\ast$$\ast$q1k\_\-p, FLT\_\-OR\_\-DBL $\ast$$\ast$qln\_\-p, short $\ast$$\ast$pscore)
\begin{DoxyCompactList}\small\item\em Get pointers to (almost) all relavant arrays used in alifold's partition function computation. \item\end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Variables}
\begin{DoxyCompactItemize}
\item 
double \hyperlink{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{cv\_\-fact}
\begin{DoxyCompactList}\small\item\em This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. \item\end{DoxyCompactList}\item 
double \hyperlink{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{nc\_\-fact}
\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. \item\end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Detailed Description}
compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments 

\subsection{Function Documentation}
\hypertarget{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}{
\index{alifold.h@{alifold.h}!update\_\-alifold\_\-params@{update\_\-alifold\_\-params}}
\index{update\_\-alifold\_\-params@{update\_\-alifold\_\-params}!alifold.h@{alifold.h}}
\subsubsection[{update\_\-alifold\_\-params}]{\setlength{\rightskip}{0pt plus 5cm}void update\_\-alifold\_\-params (void)}}
\label{alifold_8h_ac484c6bd429bafbd353b91044508d8e9}


Update the energy parameters for alifold function. Call this to recalculate the pair matrix and energy parameters after a change in folding parameters like \hyperlink{fold__vars_8h_ab4b11c8d9c758430960896bc3fe82ead}{temperature} 