\section{dnamatrix}
\label{module_dnamatrix}
This module contains the following objects

\begin{itemize}
\item \ref{object_DnaMatrix} DnaMatrix

\item \ref{object_DnaProbMatrix} DnaProbMatrix

\item This module also contains some factory methods
\end{itemize}
\subsection{dnamatrix factory methods}
\subsubsection{identity_DnaMatrix}
\begin{description}
\item[External C] {\tt Wise2_identity_DnaMatrix (id_score,mismatch)}
\item[Perl] {\tt &Wise2::identity_DnaMatrix (id_score,mismatch)}

\end{description}
Arguments
\begin{description}
\item[id_score] [UNKN ] score of idenities [Score]
\item[mismatch] [UNKN ] score of mistmatches [Score]
\item[returns] [UNKN ] Undocumented return value [DnaMatrix *]
\end{description}
makes an idenity matrix wth id_score on the leading
diagonal and mismatch elsewhere.




\subsubsection{DnaProbMatrix_from_match}
\begin{description}
\item[External C] {\tt Wise2_DnaProbMatrix_from_match (match,nmask_type)}
\item[Perl] {\tt &Wise2::DnaProbMatrix_from_match (match,nmask_type)}

\end{description}
Arguments
\begin{description}
\item[match] [UNKN ] Undocumented argument [Probability]
\item[nmask_type] [UNKN ] Undocumented argument [int]
\item[returns] [UNKN ] Undocumented return value [DnaProbMatrix *]
\end{description}
Makes a probability matrix from simple match/mismatch 
probabilities.




\subsubsection{DnaMatrix_from_DnaProbMatrix}
\begin{description}
\item[External C] {\tt Wise2_DnaMatrix_from_DnaProbMatrix (dpm)}
\item[Perl] {\tt &Wise2::DnaMatrix_from_DnaProbMatrix (dpm)}

\end{description}
Arguments
\begin{description}
\item[dpm] [UNKN ] Undocumented argument [DnaProbMatrix *]
\item[returns] [UNKN ] Undocumented return value [DnaMatrix *]
\end{description}
Maps probabilities to scores




\subsection{Object DnaMatrix}

\label{object_DnaMatrix}

The DnaMatrix object has the following fields. To see how to access them refer to \ref{accessing_fields}
\begin{description}
\item{score[5][5]} Type [Score : Scalar] No documentation

\end{description}
No documentation for DnaMatrix

Member functions of DnaMatrix

\subsection{Object DnaProbMatrix}

\label{object_DnaProbMatrix}

The DnaProbMatrix object has the following fields. To see how to access them refer to \ref{accessing_fields}
\begin{description}
\item{prob[5][5]} Type [Probability : Scalar] No documentation

\end{description}
No documentation for DnaProbMatrix

Member functions of DnaProbMatrix

\subsubsection{flat_null_DnaProbMatrix}

\begin{description}
\item[External C] {\tt Wise2_flat_null_DnaProbMatrix (dpm)}
\item[Perl] {\tt &Wise2::DnaProbMatrix::flat_null_DnaProbMatrix (dpm)}

\item[Perl-OOP call] {\tt $obj->flat_null_DnaProbMatrix()}

\end{description}
Arguments
\begin{description}
\item[dpm] [UNKN ] Undocumented argument [DnaProbMatrix *]
\item[returns] Nothing - no return value
\end{description}
makes a odds of dpm via a 0.25 factor 
into each base.


