binaries/src/ViennaRNA/doc/latex/profiledist_8h.tex

   1 \hypertarget{profiledist_8h}{\section{/home/asherstnev/\-Projects/\-Java.projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/profiledist.h File Reference}
   2 \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}}
   3 }
   4 Include dependency graph for profiledist.\-h\-:
   5 \nopagebreak
   6 \begin{figure}[H]
   7 \begin{center}
   8 \leavevmode
   9 \includegraphics[width=250pt]{profiledist_8h__incl}
  10 \end{center}
  11 \end{figure}
  12 \subsection*{Functions}
  13 \begin{DoxyCompactItemize}
  14 \item
  15 float \hyperlink{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{profile\-\_\-edit\-\_\-distance} (const float $\ast$T1, const float $\ast$T2)
  16 \begin{DoxyCompactList}\small\item\em Align the 2 probability profiles T1, T2\par
  17 . \end{DoxyCompactList}\item
  18 float $\ast$ \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\-\_\-bp\-\_\-profile\-\_\-bppm} (double $\ast$bppm, int length)
  19 \begin{DoxyCompactList}\small\item\em condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired. \end{DoxyCompactList}\item
  20 \hypertarget{profiledist_8h_a8e0b4fe3698b3502945116ecc0ba6160}{void \hyperlink{profiledist_8h_a8e0b4fe3698b3502945116ecc0ba6160}{print\-\_\-bppm} (const float $\ast$T)}\label{profiledist_8h_a8e0b4fe3698b3502945116ecc0ba6160}
  21
  22 \begin{DoxyCompactList}\small\item\em print string representation of probability profile \end{DoxyCompactList}\item
  23 void \hyperlink{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{free\-\_\-profile} (float $\ast$T)
  24 \begin{DoxyCompactList}\small\item\em free space allocated in Make\-\_\-bp\-\_\-profile \end{DoxyCompactList}\item
  25 float $\ast$ \hyperlink{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{Make\-\_\-bp\-\_\-profile} (int length)
  26 \end{DoxyCompactItemize}
  27
  28
  29 \subsection{Function Documentation}
  30 \hypertarget{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}{\index{profiledist.\-h@{profiledist.\-h}!profile\-\_\-edit\-\_\-distance@{profile\-\_\-edit\-\_\-distance}}
  31 \index{profile\-\_\-edit\-\_\-distance@{profile\-\_\-edit\-\_\-distance}!profiledist.h@{profiledist.\-h}}
  32 \subsubsection[{profile\-\_\-edit\-\_\-distance}]{\setlength{\rightskip}{0pt plus 5cm}float profile\-\_\-edit\-\_\-distance (
  33 \begin{DoxyParamCaption}
  34 \item[{const float $\ast$}]{T1, }
  35 \item[{const float $\ast$}]{T2}
  36 \end{DoxyParamCaption}
  37 )}}\label{profiledist_8h_abe75e90e00a1e5dd8862944ed53dad5d}
  38
  39
  40 Align the 2 probability profiles T1, T2\par
  41 .
  42
  43 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}}
  44 \index{Make\-\_\-bp\-\_\-profile\-\_\-bppm@{Make\-\_\-bp\-\_\-profile\-\_\-bppm}!profiledist.h@{profiledist.\-h}}
  45 \subsubsection[{Make\-\_\-bp\-\_\-profile\-\_\-bppm}]{\setlength{\rightskip}{0pt plus 5cm}float$\ast$ Make\-\_\-bp\-\_\-profile\-\_\-bppm (
  46 \begin{DoxyParamCaption}
  47 \item[{double $\ast$}]{bppm, }
  48 \item[{int}]{length}
  49 \end{DoxyParamCaption}
  50 )}}\label{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}
  51
  52
  53 condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired.
  54
  55 This resulting probability profile is used as input for profile\-\_\-edit\-\_\-distance
  56
  57
  58 \begin{DoxyParams}{Parameters}
  59 {\em bppm} & A pointer to the base pair probability matrix \\
  60 \hline
  61 {\em length} & The length of the sequence \\
  62 \hline
  63 \end{DoxyParams}
  64 \begin{DoxyReturn}{Returns}
  65 The bp profile
  66 \end{DoxyReturn}
  67 \hypertarget{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}{\index{profiledist.\-h@{profiledist.\-h}!free\-\_\-profile@{free\-\_\-profile}}
  68 \index{free\-\_\-profile@{free\-\_\-profile}!profiledist.h@{profiledist.\-h}}
  69 \subsubsection[{free\-\_\-profile}]{\setlength{\rightskip}{0pt plus 5cm}void free\-\_\-profile (
  70 \begin{DoxyParamCaption}
  71 \item[{float $\ast$}]{T}
  72 \end{DoxyParamCaption}
  73 )}}\label{profiledist_8h_a9b0b84a5a45761bf42d7c835dcdb3b85}
  74
  75
  76 free space allocated in Make\-\_\-bp\-\_\-profile
  77
  78 Backward compatibility only. You can just use plain free() \hypertarget{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{\index{profiledist.\-h@{profiledist.\-h}!Make\-\_\-bp\-\_\-profile@{Make\-\_\-bp\-\_\-profile}}
  79 \index{Make\-\_\-bp\-\_\-profile@{Make\-\_\-bp\-\_\-profile}!profiledist.h@{profiledist.\-h}}
  80 \subsubsection[{Make\-\_\-bp\-\_\-profile}]{\setlength{\rightskip}{0pt plus 5cm}float$\ast$ Make\-\_\-bp\-\_\-profile (
  81 \begin{DoxyParamCaption}
  82 \item[{int}]{length}
  83 \end{DoxyParamCaption}
  84 )}}\label{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}
  85 \begin{DoxyNote}{Note}
  86 This function is N\-O\-T threadsafe
  87 \end{DoxyNote}
  88 \begin{DoxySeeAlso}{See Also}
  89 \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\-\_\-bp\-\_\-profile\-\_\-bppm()}
  90 \end{DoxySeeAlso}
  91 \begin{DoxyRefDesc}{Deprecated}
  92 \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}