\section{dnaalign}
\label{module_dnaalign}
This module contains the following objects

\begin{itemize}
\item \ref{object_DnaStartEnd} DnaStartEnd

\item This module also contains some factory methods
\end{itemize}
\subsection{dnaalign factory methods}
\subsubsection{make_align_dnaalign}
\begin{description}
\item[External C] {\tt Wise2_make_align_dnaalign (one,two,mat,se,qgap,qext,tgap,text,dpri)}
\item[Perl] {\tt &Wise2::make_align_dnaalign (one,two,mat,se,qgap,qext,tgap,text,dpri)}

\end{description}
Arguments
\begin{description}
\item[one] [READ ] first sequence to align [Sequence *]
\item[two] [READ ] second sequence to align [Sequence *]
\item[mat] [READ ] DnaMatrix for the matching [DnaMatrix *]
\item[se] [READ ] DnaStartEnd policy [DnaStartEnd *]
\item[qgap] [READ ] gap open penalty in query (one) coordinate [int]
\item[qext] [READ ] gap extension penalty in query (one) coordinate [int]
\item[tgap] [READ ] gap open penalty in target (two) coordinate [int]
\item[text] [READ ] gap extension penalty in target (two) coordinate [int]
\item[dpri] [READ ] DPRunImpl structure [DPRunImpl *]
\item[returns] [UNKN ] an alb structure of the alignment [AlnBlock *]
\end{description}
Makes an alignment out of two DNA sequences


\subsubsection{DnaStartEnd_from_policy}
\begin{description}
\item[External C] {\tt Wise2_DnaStartEnd_from_policy (policy)}
\item[Perl] {\tt &Wise2::DnaStartEnd_from_policy (policy)}

\end{description}
Arguments
\begin{description}
\item[policy] [UNKN ] Undocumented argument [char *]
\item[returns] [UNKN ] Undocumented return value [DnaStartEnd *]
\end{description}
Makes a DnaStartEnd from a particular string.
Possible strings are:


local - fully local
global - fully global
edge - aligns only to edges




\subsection{Object DnaStartEnd}

\label{object_DnaStartEnd}

The DnaStartEnd object has the following fields. To see how to access them refer to \ref{accessing_fields}
\begin{description}
\item{trans[DSE_NUMBER]} Type [int : Scalar]  start/end points possibilities

\end{description}
No documentation for DnaStartEnd

Member functions of DnaStartEnd

