\hypertarget{profiledist_8h}{
\section{H/profiledist.h File Reference}
\label{profiledist_8h}\index{H/profiledist.h@{H/profiledist.h}}
}
Include dependency graph for profiledist.h:\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
. \item\end{DoxyCompactList}\item 
float $\ast$ \hyperlink{profiledist_8h_a3dff26e707a2a2e65a0f759caabde6e7}{Make\_\-bp\_\-profile\_\-bppm} (FLT\_\-OR\_\-DBL $\ast$bppm, int length)
\begin{DoxyCompactList}\small\item\em condense pair probability matrix into a vector containing probabilities for upstream paired, downstream paired and unpaired. \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 \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{Detailed Description}


\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}


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_a3dff26e707a2a2e65a0f759caabde6e7}{
\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 (FLT\_\-OR\_\-DBL $\ast$ {\em bppm}, \/  int {\em length})}}
\label{profiledist_8h_a3dff26e707a2a2e65a0f759caabde6e7}


condense pair probability matrix into a vector containing probabilities for upstream paired, downstream paired and unpaired. This resulting probability profile is used as input for profile\_\-edit\_\-distance


\begin{DoxyParams}{Parameters}
\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 (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 (int {\em length})}}
\label{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}
\begin{DoxyNote}{Note}
This function is NOT threadsafe
\end{DoxyNote}
\begin{DoxySeeAlso}{See also}
\hyperlink{profiledist_8h_a3dff26e707a2a2e65a0f759caabde6e7}{Make\_\-bp\_\-profile\_\-bppm()}
\end{DoxySeeAlso}
\begin{Desc}
\item[\hyperlink{deprecated__deprecated000018}{Deprecated}]This function is deprecated and will be removed soon! See \hyperlink{profiledist_8h_a3dff26e707a2a2e65a0f759caabde6e7}{Make\_\-bp\_\-profile\_\-bppm()} for a replacement\end{Desc}
