\section{proteindb}
\label{module_proteindb}
This module contains the following objects

\begin{itemize}
\item \ref{object_ProteinDB} ProteinDB

\item This module also contains some factory methods
\end{itemize}
\subsection{proteindb factory methods}
\subsubsection{new_ProteinDB_from_single_seq}
\begin{description}
\item[External C] {\tt Wise2_new_ProteinDB_from_single_seq (seq)}
\item[Perl] {\tt &Wise2::new_ProteinDB_from_single_seq (seq)}

\end{description}
Arguments
\begin{description}
\item[seq] [UNKN ] sequence which as placed into ProteinDB structure. [Sequence *]
\item[returns] [UNKN ] Undocumented return value [ProteinDB *]
\end{description}
To make a new protein database
from a single Sequence with default amino acid mapping


\subsubsection{single_fasta_ProteinDB}
\begin{description}
\item[External C] {\tt Wise2_single_fasta_ProteinDB (filename)}
\item[Perl] {\tt &Wise2::single_fasta_ProteinDB (filename)}

\end{description}
Arguments
\begin{description}
\item[filename] [UNKN ] name of fasta file [char *]
\item[returns] [UNKN ] Undocumented return value [ProteinDB *]
\end{description}
pre-packed single fasta protein database




\subsubsection{new_ProteinDB}
\begin{description}
\item[External C] {\tt Wise2_new_ProteinDB (seqdb,cses)}
\item[Perl] {\tt &Wise2::new_ProteinDB (seqdb,cses)}

\end{description}
Arguments
\begin{description}
\item[seqdb] [UNKN ] sequence database [SequenceDB *]
\item[cses] [UNKN ] protein evaluation set [ComplexSequenceEvalSet *]
\item[returns] [UNKN ] Undocumented return value [ProteinDB *]
\end{description}
To make a new protein database




\subsection{Object ProteinDB}

\label{object_ProteinDB}

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

\item{is_random_db} Type [boolean : Scalar] No documentation

\item{single} Type [ComplexSequence * : Scalar] No documentation

\item{sdb} Type [SequenceDB * : Scalar] No documentation

\item{cses} Type [ComplexSequenceEvalSet * : Scalar] No documentation

\item{rnd} Type [RandomProteinDB * : Scalar] No documentation

\item{test_dna} Type [boolean : Scalar] No documentation

\end{description}
A database of proteins. This takes
either a single sequence or a 
sequence database and allows a
method expecting protein complexsequences
to loop over it.


It also provides generic database indexing
for this




Horrible physical dependency in this
generated by the random protein db
requiring histogram and randommodel
stuff. Yuk!




Member functions of ProteinDB

