-\hypertarget{group__consensus__fold}{\section{Predicting Consensus Structures from Alignment(s)}
+\hypertarget{group__consensus__fold}{
+\section{Predicting Consensus Structures from Alignment(s)}
\label{group__consensus__fold}\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
}
-compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments
+compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
-Collaboration diagram for Predicting Consensus Structures from Alignment(s)\-:
-\nopagebreak
+Collaboration diagram for Predicting Consensus Structures from Alignment(s):\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=350pt]{group__consensus__fold}
+\includegraphics[width=420pt]{group__consensus__fold}
\end{center}
\end{figure}
\subsection*{Modules}
\begin{DoxyCompactItemize}
\item
-\hyperlink{group__consensus__mfe__fold}{M\-F\-E Consensus Structures for Sequence Alignment(s)}
+\hyperlink{group__consensus__mfe__fold}{MFE Consensus Structures for Sequence Alignment(s)}
\item
\hyperlink{group__consensus__pf__fold}{Partition Function and Base Pair Probabilities for Sequence Alignment(s)}
\item
\hyperlink{group__consensus__stochbt}{Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)}
\item
-\hyperlink{group__local__consensus__fold}{Local M\-F\-E consensus structures for Sequence Alignments}
+\hyperlink{group__local__consensus__fold}{Local MFE consensus structures for Sequence Alignments}
\end{DoxyCompactItemize}
-\subsection*{Files}
-\begin{DoxyCompactItemize}
-\item
-file \hyperlink{alifold_8h}{alifold.\-h}
-\begin{DoxyCompactList}\small\item\em compute various properties (consensus M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments \end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Functions}
\begin{DoxyCompactItemize}
\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) \end{DoxyCompactList}\item
-\hypertarget{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{float $\ast$$\ast$ \hyperlink{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}{readribosum} (char $\ast$name)}\label{group__consensus__fold_ga5e125c9586fcd4e2e1559fe76f7289cc}
-
-\begin{DoxyCompactList}\small\item\em Read a ribosum or other user-\/defined scoring matrix. \end{DoxyCompactList}\item
-float \hyperlink{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{energy\-\_\-of\-\_\-alistruct} (const char $\ast$$\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. \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. \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$$\ast$Ss, int \hyperlink{fold__vars_8h_af9202a1a09f5828dc731e2d9a10fa111}{circ})
-\begin{DoxyCompactList}\small\item\em Allocate memory for sequence array used to deal with aligned sequences. \end{DoxyCompactList}\item
-void \hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free\-\_\-sequence\-\_\-arrays} (unsigned int n\-\_\-seq, short $\ast$$\ast$$\ast$S, short $\ast$$\ast$$\ast$S5, short $\ast$$\ast$$\ast$S3, unsigned short $\ast$$\ast$$\ast$a2s, char $\ast$$\ast$$\ast$Ss)
-\begin{DoxyCompactList}\small\item\em Free the memory of the sequence arrays used to deal with aligned sequences. \end{DoxyCompactList}\item
-int \hyperlink{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}{get\-\_\-alipf\-\_\-arrays} (short $\ast$$\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)
-\begin{DoxyCompactList}\small\item\em Get pointers to (almost) all relavant arrays used in alifold's partition function computation. \end{DoxyCompactList}\end{DoxyCompactItemize}
+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$$\ast$Ss)
+\begin{DoxyCompactList}\small\item\em Free the memory of the sequence arrays used to deal with aligned sequences. \item\end{DoxyCompactList}\item
+int \hyperlink{group__consensus__fold_ga5349960075b1847720a2e9df021e2675}{get\_\-alipf\_\-arrays} (short $\ast$$\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. \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. \end{DoxyCompactList}\end{DoxyCompactItemize}
+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 M\-F\-E structures, partition function, Boltzmann distributed stochastic samples, ...) for R\-N\-A sequence alignments Consensus structures can be predicted by a modified version of the \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} algorithm that takes a set of aligned sequences instead of a single sequence. The energy function consists of the mean energy averaged over the sequences, plus a covariance term that favors pairs with consistent and compensatory mutations and penalizes pairs that cannot be formed by all structures. For details see\cite{hofacker:2002} and \cite{bernhart:2008}.
+compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments Consensus structures can be predicted by a modified version of the \hyperlink{group__mfe__fold_gaadafcb0f140795ae62e5ca027e335a9b}{fold()} algorithm that takes a set of aligned sequences instead of a single sequence. The energy function consists of the mean energy averaged over the sequences, plus a covariance term that favors pairs with consistent and compensatory mutations and penalizes pairs that cannot be formed by all structures. For details see hofacker:2002 and bernhart:2008.
\subsection{Function Documentation}
-\hypertarget{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!get\-\_\-mpi@{get\-\_\-mpi}}
-\index{get\-\_\-mpi@{get\-\_\-mpi}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
-\subsubsection[{get\-\_\-mpi}]{\setlength{\rightskip}{0pt plus 5cm}int get\-\_\-mpi (
-\begin{DoxyParamCaption}
-\item[{char $\ast$}]{Alseq\mbox{[}$\,$\mbox{]}, }
-\item[{int}]{n\-\_\-seq, }
-\item[{int}]{length, }
-\item[{int $\ast$}]{mini}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}
-
-
-Get the mean pairwise identity in steps from ?to?(ident)
+\hypertarget{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}{
+\index{consensus\_\-fold@{consensus\_\-fold}!get\_\-mpi@{get\_\-mpi}}
+\index{get\_\-mpi@{get\_\-mpi}!consensus_fold@{consensus\_\-fold}}
+\subsubsection[{get\_\-mpi}]{\setlength{\rightskip}{0pt plus 5cm}int get\_\-mpi (char $\ast$ {\em Alseq}\mbox{[}$\,$\mbox{]}, \/ int {\em n\_\-seq}, \/ int {\em length}, \/ int $\ast$ {\em mini})}}
+\label{group__consensus__fold_gaa2d600be90844094ec145ea14a314d2f}
+Get the mean pairwise identity in steps from ?to?(ident).
\begin{DoxyParams}{Parameters}
-{\em Alseq} & \\
-\hline
-{\em n\-\_\-seq} & The number of sequences in the alignment \\
-\hline
-{\em length} & The length of the alignment \\
-\hline
-{\em mini} & \\
-\hline
-\end{DoxyParams}
+\item[{\em Alseq}]\item[{\em n\_\-seq}]The number of sequences in the alignment \item[{\em length}]The length of the alignment \item[{\em mini}]\end{DoxyParams}
\begin{DoxyReturn}{Returns}
The mean pairwise identity
\end{DoxyReturn}
-\hypertarget{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!energy\-\_\-of\-\_\-alistruct@{energy\-\_\-of\-\_\-alistruct}}
-\index{energy\-\_\-of\-\_\-alistruct@{energy\-\_\-of\-\_\-alistruct}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
-\subsubsection[{energy\-\_\-of\-\_\-alistruct}]{\setlength{\rightskip}{0pt plus 5cm}float energy\-\_\-of\-\_\-alistruct (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$$\ast$}]{sequences, }
-\item[{const char $\ast$}]{structure, }
-\item[{int}]{n\-\_\-seq, }
-\item[{float $\ast$}]{energy}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}
+\hypertarget{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}{
+\index{consensus\_\-fold@{consensus\_\-fold}!energy\_\-of\_\-alistruct@{energy\_\-of\_\-alistruct}}
+\index{energy\_\-of\_\-alistruct@{energy\_\-of\_\-alistruct}!consensus_fold@{consensus\_\-fold}}
+\subsubsection[{energy\_\-of\_\-alistruct}]{\setlength{\rightskip}{0pt plus 5cm}float energy\_\-of\_\-alistruct (const char $\ast$$\ast$ {\em sequences}, \/ const char $\ast$ {\em structure}, \/ int {\em n\_\-seq}, \/ float $\ast$ {\em energy})}}
+\label{group__consensus__fold_ga1c48869c03b49a342bf4cbdd61900081}
Calculate the free energy of a consensus structure given a set of aligned sequences.
-
-
\begin{DoxyParams}{Parameters}
-{\em sequences} & The N\-U\-L\-L terminated array of sequences \\
-\hline
-{\em structure} & The consensus structure \\
-\hline
-{\em n\-\_\-seq} & The number of sequences in the alignment \\
-\hline
-{\em energy} & A pointer to an array of at least two floats that will hold the free energies (energy\mbox{[}0\mbox{]} will contain the free energy, energy\mbox{[}1\mbox{]} will be filled with the covariance energy term) \\
-\hline
-\end{DoxyParams}
+\item[{\em sequences}]The NULL terminated array of sequences \item[{\em structure}]The consensus structure \item[{\em n\_\-seq}]The number of sequences in the alignment \item[{\em energy}]A pointer to an array of at least two floats that will hold the free energies (energy\mbox{[}0\mbox{]} will contain the free energy, energy\mbox{[}1\mbox{]} will be filled with the covariance energy term) \end{DoxyParams}
\begin{DoxyReturn}{Returns}
free energy in kcal/mol
\end{DoxyReturn}
-\hypertarget{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!encode\-\_\-ali\-\_\-sequence@{encode\-\_\-ali\-\_\-sequence}}
-\index{encode\-\_\-ali\-\_\-sequence@{encode\-\_\-ali\-\_\-sequence}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
-\subsubsection[{encode\-\_\-ali\-\_\-sequence}]{\setlength{\rightskip}{0pt plus 5cm}void encode\-\_\-ali\-\_\-sequence (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$}]{sequence, }
-\item[{short $\ast$}]{S, }
-\item[{short $\ast$}]{s5, }
-\item[{short $\ast$}]{s3, }
-\item[{char $\ast$}]{ss, }
-\item[{unsigned short $\ast$}]{as, }
-\item[{int}]{circ}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}
-
+\hypertarget{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}{
+\index{consensus\_\-fold@{consensus\_\-fold}!encode\_\-ali\_\-sequence@{encode\_\-ali\_\-sequence}}
+\index{encode\_\-ali\_\-sequence@{encode\_\-ali\_\-sequence}!consensus_fold@{consensus\_\-fold}}
+\subsubsection[{encode\_\-ali\_\-sequence}]{\setlength{\rightskip}{0pt plus 5cm}void encode\_\-ali\_\-sequence (const char $\ast$ {\em sequence}, \/ short $\ast$ {\em S}, \/ short $\ast$ {\em s5}, \/ short $\ast$ {\em s3}, \/ char $\ast$ {\em ss}, \/ unsigned short $\ast$ {\em as}, \/ int {\em circ})}}
+\label{group__consensus__fold_gaa3e40277c837d6f7603afe319884c786}
-Get arrays with encoded sequence of the alignment.
-this function assumes that in S, S5, s3, ss and as enough space is already allocated (size must be at least sequence length+2)
+Get arrays with encoded sequence of the alignment. this function assumes that in S, S5, s3, ss and as enough space is already allocated (size must be at least sequence length+2)
\begin{DoxyParams}{Parameters}
-{\em sequence} & The gapped sequence from the alignment \\
-\hline
-{\em S} & pointer to an array that holds encoded sequence \\
-\hline
-{\em s5} & pointer to an array that holds the next base 5' of alignment position i \\
-\hline
-{\em s3} & pointer to an array that holds the next base 3' of alignment position i \\
-\hline
-{\em ss} & \\
-\hline
-{\em as} & \\
-\hline
-{\em circ} & assume the molecules to be circular instead of linear (circ=0) \\
-\hline
-\end{DoxyParams}
-\hypertarget{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!alloc\-\_\-sequence\-\_\-arrays@{alloc\-\_\-sequence\-\_\-arrays}}
-\index{alloc\-\_\-sequence\-\_\-arrays@{alloc\-\_\-sequence\-\_\-arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
-\subsubsection[{alloc\-\_\-sequence\-\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void alloc\-\_\-sequence\-\_\-arrays (
-\begin{DoxyParamCaption}
-\item[{const char $\ast$$\ast$}]{sequences, }
-\item[{short $\ast$$\ast$$\ast$}]{S, }
-\item[{short $\ast$$\ast$$\ast$}]{S5, }
-\item[{short $\ast$$\ast$$\ast$}]{S3, }
-\item[{unsigned short $\ast$$\ast$$\ast$}]{a2s, }
-\item[{char $\ast$$\ast$$\ast$}]{Ss, }
-\item[{int}]{circ}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}
-
-
-Allocate memory for sequence array used to deal with aligned sequences.
-
-Note that these arrays will also be initialized according to the sequence alignment given
-
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free\-\_\-sequence\-\_\-arrays()}
+\item[{\em sequence}]The gapped sequence from the alignment \item[{\em S}]pointer to an array that holds encoded sequence \item[{\em s5}]pointer to an array that holds the next base 5' of alignment position i \item[{\em s3}]pointer to an array that holds the next base 3' of alignment position i \item[{\em ss}]\item[{\em as}]\item[{\em circ}]assume the molecules to be circular instead of linear (circ=0) \end{DoxyParams}
+\hypertarget{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{
+\index{consensus\_\-fold@{consensus\_\-fold}!alloc\_\-sequence\_\-arrays@{alloc\_\-sequence\_\-arrays}}
+\index{alloc\_\-sequence\_\-arrays@{alloc\_\-sequence\_\-arrays}!consensus_fold@{consensus\_\-fold}}
+\subsubsection[{alloc\_\-sequence\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void alloc\_\-sequence\_\-arrays (const char $\ast$$\ast$ {\em sequences}, \/ short $\ast$$\ast$$\ast$ {\em S}, \/ short $\ast$$\ast$$\ast$ {\em S5}, \/ short $\ast$$\ast$$\ast$ {\em S3}, \/ unsigned short $\ast$$\ast$$\ast$ {\em a2s}, \/ char $\ast$$\ast$$\ast$ {\em Ss}, \/ int {\em circ})}}
+\label{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}
+
+
+Allocate memory for sequence array used to deal with aligned sequences. Note that these arrays will also be initialized according to the sequence alignment given
+
+\begin{DoxySeeAlso}{See also}
+\hyperlink{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{free\_\-sequence\_\-arrays()}
\end{DoxySeeAlso}
\begin{DoxyParams}{Parameters}
-{\em sequences} & The aligned sequences \\
-\hline
-{\em S} & A pointer to the array of encoded sequences \\
-\hline
-{\em S5} & A pointer to the array that contains the next 5' nucleotide of a sequence position \\
-\hline
-{\em S3} & A pointer to the array that contains the next 3' nucleotide of a sequence position \\
-\hline
-{\em a2s} & A pointer to the array that contains the alignment to sequence position mapping \\
-\hline
-{\em Ss} & A pointer to the array that contains the ungapped sequence \\
-\hline
-{\em circ} & assume the molecules to be circular instead of linear (circ=0) \\
-\hline
-\end{DoxyParams}
-\hypertarget{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!free\-\_\-sequence\-\_\-arrays@{free\-\_\-sequence\-\_\-arrays}}
-\index{free\-\_\-sequence\-\_\-arrays@{free\-\_\-sequence\-\_\-arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
-\subsubsection[{free\-\_\-sequence\-\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void free\-\_\-sequence\-\_\-arrays (
-\begin{DoxyParamCaption}
-\item[{unsigned int}]{n\-\_\-seq, }
-\item[{short $\ast$$\ast$$\ast$}]{S, }
-\item[{short $\ast$$\ast$$\ast$}]{S5, }
-\item[{short $\ast$$\ast$$\ast$}]{S3, }
-\item[{unsigned short $\ast$$\ast$$\ast$}]{a2s, }
-\item[{char $\ast$$\ast$$\ast$}]{Ss}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}
-
-
-Free the memory of the sequence arrays used to deal with aligned sequences.
-
-This function frees the memory previously allocated with \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\-\_\-sequence\-\_\-arrays()}
-
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\-\_\-sequence\-\_\-arrays()}
+\item[{\em sequences}]The aligned sequences \item[{\em S}]A pointer to the array of encoded sequences \item[{\em S5}]A pointer to the array that contains the next 5' nucleotide of a sequence position \item[{\em S3}]A pointer to the array that contains the next 3' nucleotide of a sequence position \item[{\em a2s}]A pointer to the array that contains the alignment to sequence position mapping \item[{\em Ss}]A pointer to the array that contains the ungapped sequence \item[{\em circ}]assume the molecules to be circular instead of linear (circ=0) \end{DoxyParams}
+\hypertarget{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}{
+\index{consensus\_\-fold@{consensus\_\-fold}!free\_\-sequence\_\-arrays@{free\_\-sequence\_\-arrays}}
+\index{free\_\-sequence\_\-arrays@{free\_\-sequence\_\-arrays}!consensus_fold@{consensus\_\-fold}}
+\subsubsection[{free\_\-sequence\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}void free\_\-sequence\_\-arrays (unsigned int {\em n\_\-seq}, \/ short $\ast$$\ast$$\ast$ {\em S}, \/ short $\ast$$\ast$$\ast$ {\em S5}, \/ short $\ast$$\ast$$\ast$ {\em S3}, \/ unsigned short $\ast$$\ast$$\ast$ {\em a2s}, \/ char $\ast$$\ast$$\ast$ {\em Ss})}}
+\label{group__consensus__fold_ga298a420a8c879202e2617b3f724fde38}
+
+
+Free the memory of the sequence arrays used to deal with aligned sequences. This function frees the memory previously allocated with \hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\_\-sequence\_\-arrays()}
+
+\begin{DoxySeeAlso}{See also}
+\hyperlink{group__consensus__fold_ga8a560930f7f2582cc3967723a86cfdfa}{alloc\_\-sequence\_\-arrays()}
\end{DoxySeeAlso}
\begin{DoxyParams}{Parameters}
-{\em n\-\_\-seq} & The number of aligned sequences \\
-\hline
-{\em S} & A pointer to the array of encoded sequences \\
-\hline
-{\em S5} & A pointer to the array that contains the next 5' nucleotide of a sequence position \\
-\hline
-{\em S3} & A pointer to the array that contains the next 3' nucleotide of a sequence position \\
-\hline
-{\em a2s} & A pointer to the array that contains the alignment to sequence position mapping \\
-\hline
-{\em Ss} & A pointer to the array that contains the ungapped sequence \\
-\hline
-\end{DoxyParams}
-\hypertarget{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!get\-\_\-alipf\-\_\-arrays@{get\-\_\-alipf\-\_\-arrays}}
-\index{get\-\_\-alipf\-\_\-arrays@{get\-\_\-alipf\-\_\-arrays}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
-\subsubsection[{get\-\_\-alipf\-\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}int get\-\_\-alipf\-\_\-arrays (
-\begin{DoxyParamCaption}
-\item[{short $\ast$$\ast$$\ast$}]{S\-\_\-p, }
-\item[{short $\ast$$\ast$$\ast$}]{S5\-\_\-p, }
-\item[{short $\ast$$\ast$$\ast$}]{S3\-\_\-p, }
-\item[{unsigned short $\ast$$\ast$$\ast$}]{a2s\-\_\-p, }
-\item[{char $\ast$$\ast$$\ast$}]{Ss\-\_\-p, }
-\item[{double $\ast$$\ast$}]{qb\-\_\-p, }
-\item[{double $\ast$$\ast$}]{qm\-\_\-p, }
-\item[{double $\ast$$\ast$}]{q1k\-\_\-p, }
-\item[{double $\ast$$\ast$}]{qln\-\_\-p, }
-\item[{short $\ast$$\ast$}]{pscore}
-\end{DoxyParamCaption}
-)}}\label{group__consensus__fold_ga0cc49457fd79eeb04d4a7f97c868b09b}
-
-
-Get pointers to (almost) all relavant arrays used in alifold's partition function computation.
-
-\begin{DoxyNote}{Note}
-To obtain meaningful pointers, call alipf\-\_\-fold first!
+\item[{\em n\_\-seq}]The number of aligned sequences \item[{\em S}]A pointer to the array of encoded sequences \item[{\em S5}]A pointer to the array that contains the next 5' nucleotide of a sequence position \item[{\em S3}]A pointer to the array that contains the next 3' nucleotide of a sequence position \item[{\em a2s}]A pointer to the array that contains the alignment to sequence position mapping \item[{\em Ss}]A pointer to the array that contains the ungapped sequence \end{DoxyParams}
+\hypertarget{group__consensus__fold_ga5349960075b1847720a2e9df021e2675}{
+\index{consensus\_\-fold@{consensus\_\-fold}!get\_\-alipf\_\-arrays@{get\_\-alipf\_\-arrays}}
+\index{get\_\-alipf\_\-arrays@{get\_\-alipf\_\-arrays}!consensus_fold@{consensus\_\-fold}}
+\subsubsection[{get\_\-alipf\_\-arrays}]{\setlength{\rightskip}{0pt plus 5cm}int get\_\-alipf\_\-arrays (short $\ast$$\ast$$\ast$ {\em S\_\-p}, \/ short $\ast$$\ast$$\ast$ {\em S5\_\-p}, \/ short $\ast$$\ast$$\ast$ {\em S3\_\-p}, \/ unsigned short $\ast$$\ast$$\ast$ {\em a2s\_\-p}, \/ char $\ast$$\ast$$\ast$ {\em Ss\_\-p}, \/ FLT\_\-OR\_\-DBL $\ast$$\ast$ {\em qb\_\-p}, \/ FLT\_\-OR\_\-DBL $\ast$$\ast$ {\em qm\_\-p}, \/ FLT\_\-OR\_\-DBL $\ast$$\ast$ {\em q1k\_\-p}, \/ FLT\_\-OR\_\-DBL $\ast$$\ast$ {\em qln\_\-p}, \/ short $\ast$$\ast$ {\em pscore})}}
+\label{group__consensus__fold_ga5349960075b1847720a2e9df021e2675}
+
+
+Get pointers to (almost) all relavant arrays used in alifold's partition function computation. \begin{DoxyNote}{Note}
+To obtain meaningful pointers, call alipf\_\-fold first!
\end{DoxyNote}
-\begin{DoxySeeAlso}{See Also}
-pf\-\_\-alifold(), \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\-\_\-circ\-\_\-fold()}
+\begin{DoxySeeAlso}{See also}
+pf\_\-alifold(), \hyperlink{group__consensus__pf__fold_ga6b4dde1d43b79ab3753508c46cf50363}{alipf\_\-circ\_\-fold()}
\end{DoxySeeAlso}
\begin{DoxyParams}{Parameters}
-{\em S\-\_\-p} & A pointer to the 'S' array (integer representation of nucleotides) \\
-\hline
-{\em S5\-\_\-p} & A pointer to the 'S5' array \\
-\hline
-{\em S3\-\_\-p} & A pointer to the 'S3' array \\
-\hline
-{\em a2s\-\_\-p} & A pointer to the pair type matrix \\
-\hline
-{\em Ss\-\_\-p} & A pointer to the 'Ss' array \\
-\hline
-{\em qb\-\_\-p} & A pointer to the Q$^{\mbox{B}}$ matrix \\
-\hline
-{\em qm\-\_\-p} & A pointer to the Q$^{\mbox{M}}$ matrix \\
-\hline
-{\em q1k\-\_\-p} & A pointer to the 5' slice of the Q matrix ( $q1k(k) = Q(1, k)$) \\
-\hline
-{\em qln\-\_\-p} & A pointer to the 3' slice of the Q matrix ( $qln(l) = Q(l, n)$) \\
-\hline
-\end{DoxyParams}
+\item[{\em S\_\-p}]A pointer to the 'S' array (integer representation of nucleotides) \item[{\em S5\_\-p}]A pointer to the 'S5' array \item[{\em S3\_\-p}]A pointer to the 'S3' array \item[{\em a2s\_\-p}]A pointer to the pair type matrix \item[{\em Ss\_\-p}]A pointer to the 'Ss' array \item[{\em qb\_\-p}]A pointer to the Q$^{\mbox{B}}$ matrix \item[{\em qm\_\-p}]A pointer to the Q$^{\mbox{M}}$ matrix \item[{\em q1k\_\-p}]A pointer to the 5' slice of the Q matrix ($q1k(k) = Q(1, k)$) \item[{\em qln\_\-p}]A pointer to the 3' slice of the Q matrix ($qln(l) = Q(l, n)$) \end{DoxyParams}
\begin{DoxyReturn}{Returns}
Non Zero if everything went fine, 0 otherwise
\end{DoxyReturn}
\subsection{Variable Documentation}
-\hypertarget{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!cv\-\_\-fact@{cv\-\_\-fact}}
-\index{cv\-\_\-fact@{cv\-\_\-fact}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
-\subsubsection[{cv\-\_\-fact}]{\setlength{\rightskip}{0pt plus 5cm}double cv\-\_\-fact}}\label{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}
-
-
-This variable controls the weight of the covariance term in the energy function of alignment folding algorithms.
+\hypertarget{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}{
+\index{consensus\_\-fold@{consensus\_\-fold}!cv\_\-fact@{cv\_\-fact}}
+\index{cv\_\-fact@{cv\_\-fact}!consensus_fold@{consensus\_\-fold}}
+\subsubsection[{cv\_\-fact}]{\setlength{\rightskip}{0pt plus 5cm}double {\bf cv\_\-fact}}}
+\label{group__consensus__fold_gaf3cbac6ff5d706d6e414677841ddf94c}
-Default is 1. \hypertarget{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{\index{Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}!nc\-\_\-fact@{nc\-\_\-fact}}
-\index{nc\-\_\-fact@{nc\-\_\-fact}!Predicting Consensus Structures from Alignment(s)@{Predicting Consensus Structures from Alignment(s)}}
-\subsubsection[{nc\-\_\-fact}]{\setlength{\rightskip}{0pt plus 5cm}double nc\-\_\-fact}}\label{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}
+This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. Default is 1. \hypertarget{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}{
+\index{consensus\_\-fold@{consensus\_\-fold}!nc\_\-fact@{nc\_\-fact}}
+\index{nc\_\-fact@{nc\_\-fact}!consensus_fold@{consensus\_\-fold}}
+\subsubsection[{nc\_\-fact}]{\setlength{\rightskip}{0pt plus 5cm}double {\bf nc\_\-fact}}}
+\label{group__consensus__fold_ga502948a122a2af5b914355b1f3ea2f61}
-This variable controls the magnitude of the penalty for non-\/compatible sequences in the covariance term of alignment folding algorithms.
-Default is 1.
\ No newline at end of file
+This variable controls the magnitude of the penalty for non-\/compatible sequences in the covariance term of alignment folding algorithms. Default is 1.
\ No newline at end of file
git://source.jalview.org / jabaws.git / blobdiff