-\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}}
+\hypertarget{profiledist_8h}{
+\section{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/profiledist.h File Reference}
+\label{profiledist_8h}\index{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/profiledist.h@{/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/profiledist.h}}
}
-Include dependency graph for profiledist.\-h\-:
-\nopagebreak
+Include dependency graph for profiledist.h:\nopagebreak
\begin{figure}[H]
\begin{center}
\leavevmode
-\includegraphics[width=250pt]{profiledist_8h__incl}
+\includegraphics[width=216pt]{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)
+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}
+. \item\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. \item\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)
+\begin{DoxyCompactList}\small\item\em print string representation of probability profile \item\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 \item\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}
+\subsection{Detailed Description}
-Align the 2 probability profiles T1, T2\par
-.
+\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 (const float $\ast$ {\em T1}, \/ const float $\ast$ {\em T2})}}
+\label{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}
-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}
+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 (double $\ast$ {\em bppm}, \/ int {\em length})}}
+\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
+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}
+\item[{\em bppm}]A pointer to the base pair probability matrix \item[{\em length}]The length of the sequence \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}
-
+\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 (float $\ast$ {\em T})}}
+\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}
+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 (int {\em length})}}
+\label{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}
\begin{DoxyNote}{Note}
-This function is N\-O\-T threadsafe
+This function is NOT threadsafe
\end{DoxyNote}
-\begin{DoxySeeAlso}{See Also}
-\hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\-\_\-bp\-\_\-profile\-\_\-bppm()}
+\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}
+\begin{Desc}
+\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{Desc}
git://source.jalview.org / jabaws.git / blobdiff