\section{matchsum}
\label{module_matchsum}
This module contains the following objects

\begin{itemize}
\item \ref{object_MatchSummarySet} MatchSummarySet

\item \ref{object_MatchSummary} MatchSummary

\end{itemize}
\subsection{Object MatchSummarySet}

\label{object_MatchSummarySet}

The MatchSummarySet object has the following fields. To see how to access them refer to \ref{accessing_fields}
\begin{description}
\item{ms} Type [MatchSummary ** : List] No documentation

\end{description}
This holds a set of MatchSummaries,




Member functions of MatchSummarySet

\subsubsection{MatchSummarySet_from_AlnBlock_estwise}

\begin{description}
\item[External C] {\tt Wise2_MatchSummarySet_from_AlnBlock_estwise (alb,qname,offset,target)}
\item[Perl] {\tt &Wise2::MatchSummarySet::MatchSummarySet_from_AlnBlock_estwise (alb,qname,offset,target)}

\item[Perl-OOP call] {\tt $obj->MatchSummarySet_from_AlnBlock_estwise(qname,offset,target)}

\end{description}
Arguments
\begin{description}
\item[alb] [UNKN ] Undocumented argument [AlnBlock *]
\item[qname] [UNKN ] Undocumented argument [char *]
\item[offset] [UNKN ] Undocumented argument [int]
\item[target] [UNKN ] Undocumented argument [Sequence *]
\item[returns] [UNKN ] Undocumented return value [MatchSummarySet *]
\end{description}
Builds a MatchSummarySet from a
EstWise alignment. this makes
alot of assumptions about the labels
setc in alb, so make sure it was a 
estwise alignment  - however as you
can notice this is exactly the same 
labels as found in genewise set


\subsubsection{MatchSummarySet_from_AlnBlock_genewise}

\begin{description}
\item[External C] {\tt Wise2_MatchSummarySet_from_AlnBlock_genewise (alb,qname,protoff,target)}
\item[Perl] {\tt &Wise2::MatchSummarySet::MatchSummarySet_from_AlnBlock_genewise (alb,qname,protoff,target)}

\item[Perl-OOP call] {\tt $obj->MatchSummarySet_from_AlnBlock_genewise(qname,protoff,target)}

\end{description}
Arguments
\begin{description}
\item[alb] [UNKN ] Undocumented argument [AlnBlock *]
\item[qname] [UNKN ] Undocumented argument [char *]
\item[protoff] [UNKN ] Undocumented argument [int]
\item[target] [UNKN ] Undocumented argument [Sequence *]
\item[returns] [UNKN ] Undocumented return value [MatchSummarySet *]
\end{description}
Builds a MatchSummarySet from a
GeneWise alignment. this makes
alot of assumptions about the labels
setc in alb, so make sure it was a 
genewise alignment 


\subsection{Object MatchSummary}

\label{object_MatchSummary}

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

\item{qname} Type [char * : Scalar] No documentation

\item{tname} Type [char * : Scalar] No documentation

\item{qstart} Type [int : Scalar] No documentation

\item{qend} Type [int : Scalar] No documentation

\item{tstart} Type [int : Scalar] No documentation

\item{tend} Type [int : Scalar] No documentation

\item{qintron} Type [int : Scalar] No documentation

\item{qframeshift} Type [int : Scalar] No documentation

\item{tintron} Type [int : Scalar] No documentation

\item{tframeshift} Type [int : Scalar] No documentation

\end{description}
A Match Summary has summary statistics
for a single alignment, with the
two start/end ranges and the number of
introns and frameshifts for each
sequence (obviously, if one is a protein
then neither are valid!)




Member functions of MatchSummary

