\section{seqaligndisplay}
\label{module_seqaligndisplay}
This module only contains factory methods

\subsection{seqaligndisplay factory methods}
\subsubsection{write_pretty_str_align}
\begin{description}
\item[External C] {\tt Wise2_write_pretty_str_align (alb,qname,query,tname,target,name,main,ofp)}
\item[Perl] {\tt &Wise2::write_pretty_str_align (alb,qname,query,tname,target,name,main,ofp)}

\end{description}
Arguments
\begin{description}
\item[alb] [UNKN ] alignment structure [AlnBlock *]
\item[qname] [UNKN ] name of first sequence [char *]
\item[query] [UNKN ] first sequence [char *]
\item[tname] [UNKN ] name of second sequence [char *]
\item[target] [UNKN ] second sequence [char *]
\item[name] [UNKN ] length of the name block [int]
\item[main] [UNKN ] length of the main block [int]
\item[ofp] [UNKN ] output file [FILE *]
\item[returns] [UNKN ] Undocumented return value [boolean]
\end{description}
This gives an interface into the alignment
display using strings and files.


\subsubsection{write_pretty_seq_align}
\begin{description}
\item[External C] {\tt Wise2_write_pretty_seq_align (alb,q,t,name,main,ofp)}
\item[Perl] {\tt &Wise2::write_pretty_seq_align (alb,q,t,name,main,ofp)}

\end{description}
Arguments
\begin{description}
\item[alb] [UNKN ] alignment structure [AlnBlock *]
\item[q] [UNKN ] first sequence [Sequence *]
\item[t] [UNKN ] second sequence  [Sequence *]
\item[name] [UNKN ] length of the name block [int]
\item[main] [UNKN ] length of the main block [int]
\item[ofp] [UNKN ] output file [FILE *]
\item[returns] [UNKN ] Undocumented return value [boolean]
\end{description}
This gives an interface into the alignment
display using sequences and files. A more
generic function is write_pretty_str_align


\subsubsection{write_pretty_Protein_align}
\begin{description}
\item[External C] {\tt Wise2_write_pretty_Protein_align (alb,q,t,name,main,ofp)}
\item[Perl] {\tt &Wise2::write_pretty_Protein_align (alb,q,t,name,main,ofp)}

\end{description}
Arguments
\begin{description}
\item[alb] [UNKN ] alignment structure [AlnBlock *]
\item[q] [UNKN ] first sequence [Protein *]
\item[t] [UNKN ] second sequence  [Protein *]
\item[name] [UNKN ] length of the name block [int]
\item[main] [UNKN ] length of the main block [int]
\item[ofp] [UNKN ] output file [FILE *]
\item[returns] [UNKN ] Undocumented return value [boolean]
\end{description}
This gives an interface into the
alignment display using Protein
objects




