\section{packaln}
\label{module_packaln}
This module contains the following objects

\begin{itemize}
\item \ref{object_PackAln} PackAln

\item \ref{object_PackAlnUnit} PackAlnUnit

\end{itemize}
\subsection{Object PackAln}

\label{object_PackAln}

The PackAln object has the following fields. To see how to access them refer to \ref{accessing_fields}
\begin{description}
\item{pau} Type [PackAlnUnit ** : List]  list of PackAlnUnits from start to end

\item{score} Type [int : Scalar]  score over the entire alignment

\end{description}
This is the lowest-level of representation
of a DP alignment, being the list of 
(i,j,state) triples taken through the
DP matrix. The score for the transition to
this point is held as well.


This object is very low level and often a
much better choice for representation is
in /AlnBlock objects 




Member functions of PackAln

\subsubsection{show_simple_PackAln}

\begin{description}
\item[External C] {\tt Wise2_show_simple_PackAln (pal,ofp)}
\item[Perl] {\tt &Wise2::PackAln::show_simple_PackAln (pal,ofp)}

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

\end{description}
Arguments
\begin{description}
\item[pal] [UNKN ] Undocumented argument [PackAln *]
\item[ofp] [UNKN ] Undocumented argument [FILE *]
\item[returns] Nothing - no return value
\end{description}
shows packaln with a pretty verbose debugging 
format


\subsubsection{show_bits_and_cumlative_PackAln}

\begin{description}
\item[External C] {\tt Wise2_show_bits_and_cumlative_PackAln (pal,ofp)}
\item[Perl] {\tt &Wise2::PackAln::show_bits_and_cumlative_PackAln (pal,ofp)}

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

\end{description}
Arguments
\begin{description}
\item[pal] [UNKN ] Undocumented argument [PackAln *]
\item[ofp] [UNKN ] Undocumented argument [FILE *]
\item[returns] Nothing - no return value
\end{description}
Shows packaln as: 


i,j,state,score,bits,cumlative-score,cumlative-bits


cumlative score and cumlative bits are useful sometimes


\subsection{Object PackAlnUnit}

\label{object_PackAlnUnit}

The PackAlnUnit object has the following fields. To see how to access them refer to \ref{accessing_fields}
\begin{description}
\item{i} Type [int : Scalar]  position in query 

\item{j} Type [int : Scalar]  position in target

\item{state} Type [int : Scalar]  state in FSM

\item{score} Type [int : Scalar]  score of the transition that reached this state

\end{description}
Internal object for /PackAln:
A single position of an alignment
as the (i,j,state) triple




Member functions of PackAlnUnit

