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[jabaws.git] / binaries / src / ViennaRNA / doc / latex / profiledist_8h.tex

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+\hypertarget{profiledist_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/profiledist.h File Reference}
+\label{profiledist_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/profiledist.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/profiledist.\-h}}
+}
+Include dependency graph for profiledist.\-h\-:
+\nopagebreak
+\begin{figure}[H]
+\begin{center}
+\leavevmode
+\includegraphics[width=250pt]{profiledist_8h__incl}
+\end{center}
+\end{figure}
+\subsection*{Functions}
+\begin{DoxyCompactItemize}
+\item 
+float \hyperlink{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{profile\-\_\-edit\-\_\-distance} (const float $\ast$T1, const float $\ast$T2)
+\begin{DoxyCompactList}\small\item\em Align the 2 probability profiles T1, T2\par
+. \end{DoxyCompactList}\item 
+float $\ast$ \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\-\_\-bp\-\_\-profile\-\_\-bppm} (double $\ast$bppm, int length)
+\begin{DoxyCompactList}\small\item\em condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired. \end{DoxyCompactList}\item 
+\hypertarget{profiledist_8h_a8e0b4fe3698b3502945116ecc0ba6160}{void \hyperlink{profiledist_8h_a8e0b4fe3698b3502945116ecc0ba6160}{print\-\_\-bppm} (const float $\ast$T)}\label{profiledist_8h_a8e0b4fe3698b3502945116ecc0ba6160}
+
+\begin{DoxyCompactList}\small\item\em print string representation of probability profile \end{DoxyCompactList}\item 
+void \hyperlink{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{free\-\_\-profile} (float $\ast$T)
+\begin{DoxyCompactList}\small\item\em free space allocated in Make\-\_\-bp\-\_\-profile \end{DoxyCompactList}\item 
+float $\ast$ \hyperlink{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{Make\-\_\-bp\-\_\-profile} (int length)
+\end{DoxyCompactItemize}
+
+
+\subsection{Function Documentation}
+\hypertarget{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{\index{profiledist.\-h@{profiledist.\-h}!profile\-\_\-edit\-\_\-distance@{profile\-\_\-edit\-\_\-distance}}
+\index{profile\-\_\-edit\-\_\-distance@{profile\-\_\-edit\-\_\-distance}!profiledist.h@{profiledist.\-h}}
+\subsubsection[{profile\-\_\-edit\-\_\-distance}]{\setlength{\rightskip}{0pt plus 5cm}float profile\-\_\-edit\-\_\-distance (
+\begin{DoxyParamCaption}
+\item[{const float $\ast$}]{T1, }
+\item[{const float $\ast$}]{T2}
+\end{DoxyParamCaption}
+)}}\label{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}
+
+
+Align the 2 probability profiles T1, T2\par
+. 
+
+This is like a Needleman-\/\-Wunsch alignment, we should really use affine gap-\/costs ala Gotoh \hypertarget{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{\index{profiledist.\-h@{profiledist.\-h}!Make\-\_\-bp\-\_\-profile\-\_\-bppm@{Make\-\_\-bp\-\_\-profile\-\_\-bppm}}
+\index{Make\-\_\-bp\-\_\-profile\-\_\-bppm@{Make\-\_\-bp\-\_\-profile\-\_\-bppm}!profiledist.h@{profiledist.\-h}}
+\subsubsection[{Make\-\_\-bp\-\_\-profile\-\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}float$\ast$ Make\-\_\-bp\-\_\-profile\-\_\-bppm (
+\begin{DoxyParamCaption}
+\item[{double $\ast$}]{bppm, }
+\item[{int}]{length}
+\end{DoxyParamCaption}
+)}}\label{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}
+
+
+condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired. 
+
+This resulting probability profile is used as input for profile\-\_\-edit\-\_\-distance
+
+
+\begin{DoxyParams}{Parameters}
+{\em bppm} & A pointer to the base pair probability matrix \\
+\hline
+{\em length} & The length of the sequence \\
+\hline
+\end{DoxyParams}
+\begin{DoxyReturn}{Returns}
+The bp profile 
+\end{DoxyReturn}
+\hypertarget{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{\index{profiledist.\-h@{profiledist.\-h}!free\-\_\-profile@{free\-\_\-profile}}
+\index{free\-\_\-profile@{free\-\_\-profile}!profiledist.h@{profiledist.\-h}}
+\subsubsection[{free\-\_\-profile}]{\setlength{\rightskip}{0pt plus 5cm}void free\-\_\-profile (
+\begin{DoxyParamCaption}
+\item[{float $\ast$}]{T}
+\end{DoxyParamCaption}
+)}}\label{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}
+
+
+free space allocated in Make\-\_\-bp\-\_\-profile 
+
+Backward compatibility only. You can just use plain free() \hypertarget{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{\index{profiledist.\-h@{profiledist.\-h}!Make\-\_\-bp\-\_\-profile@{Make\-\_\-bp\-\_\-profile}}
+\index{Make\-\_\-bp\-\_\-profile@{Make\-\_\-bp\-\_\-profile}!profiledist.h@{profiledist.\-h}}
+\subsubsection[{Make\-\_\-bp\-\_\-profile}]{\setlength{\rightskip}{0pt plus 5cm}float$\ast$ Make\-\_\-bp\-\_\-profile (
+\begin{DoxyParamCaption}
+\item[{int}]{length}
+\end{DoxyParamCaption}
+)}}\label{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}
+\begin{DoxyNote}{Note}
+This function is N\-O\-T threadsafe
+\end{DoxyNote}
+\begin{DoxySeeAlso}{See Also}
+\hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\-\_\-bp\-\_\-profile\-\_\-bppm()}
+\end{DoxySeeAlso}
+\begin{DoxyRefDesc}{Deprecated}
+\item[\hyperlink{deprecated__deprecated000018}{Deprecated}]This function is deprecated and will be removed soon! See \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\-\_\-bp\-\_\-profile\-\_\-bppm()} for a replacement\end{DoxyRefDesc}