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\section{genomicdb}
\label{module_genomicdb}
This module contains the following objects
\begin{itemize}
\item \ref{object_GenomicDB} GenomicDB
\item This module also contains some factory methods
\end{itemize}
\subsection{genomicdb factory methods}
\subsubsection{new_GenomicDB_from_single_seq}
\begin{description}
\item[External C] {\tt Wise2_new_GenomicDB_from_single_seq (gen,cses,score_in_repeat_coding)}
\item[Perl] {\tt &Wise2::new_GenomicDB_from_single_seq (gen,cses,score_in_repeat_coding)}
\end{description}
Arguments
\begin{description}
\item[gen] [UNKN ] sequence which as placed into GenomicDB structure. [Genomic *]
\item[cses] [UNKN ] Undocumented argument [ComplexSequenceEvalSet *]
\item[score_in_repeat_coding] [UNKN ] Undocumented argument [int]
\item[returns] [UNKN ] Undocumented return value [GenomicDB *]
\end{description}
To make a new genomic database
from a single Genomic Sequence with a eval system
\subsubsection{new_GenomicDB}
\begin{description}
\item[External C] {\tt Wise2_new_GenomicDB (seqdb,cses,length_of_N,repeat_in_cds_score)}
\item[Perl] {\tt &Wise2::new_GenomicDB (seqdb,cses,length_of_N,repeat_in_cds_score)}
\end{description}
Arguments
\begin{description}
\item[seqdb] [UNKN ] sequence database [SequenceDB *]
\item[cses] [UNKN ] protein evaluation set [ComplexSequenceEvalSet *]
\item[length_of_N] [UNKN ] Undocumented argument [int]
\item[repeat_in_cds_score] [UNKN ] Undocumented argument [int]
\item[returns] [UNKN ] Undocumented return value [GenomicDB *]
\end{description}
To make a new genomic database
\subsection{Object GenomicDB}
\label{object_GenomicDB}
The GenomicDB 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{done_forward} Type [boolean : Scalar] No documentation
\item{forw} Type [ComplexSequence * : Scalar] No documentation
\item{rev} Type [ComplexSequence * : Scalar] No documentation
\item{sdb} Type [SequenceDB * : Scalar] No documentation
\item{current} Type [Genomic * : Scalar] No documentation
\item{cses} Type [ComplexSequenceEvalSet * : Scalar] No documentation
\item{error_handling} Type [GenDBErrorType : Scalar] No documentation
\item{single} Type [Genomic * : Scalar] for single sequence cases, so we can 'index' on it
\item{revsingle} Type [Genomic * : Scalar] No documentation
\item{length_of_N} Type [int : Scalar] No documentation
\item{repeat_in_cds_score} Type [int : Scalar] No documentation
\end{description}
This object hold a database of
genomic sequences.
You will probably use it in one of
two ways
1 A sequence formatted database, which
is provided by a /SequenceDB object
is used to provide the raw sequences
2 A single Genomic sequence is used.
In each case this database provides
both the forward and reverse strands
into the system.
Notice that what is exported are
/ComplexSequence objects, not genomic dna,
as this is what is generally needed.
These are things with splice sites calculated
etc. This is why for initialisation this needs
a /ComplexSequenceEvalSet of the correct type.
Member functions of GenomicDB
\subsubsection{get_Genomic_from_GenomicDB}
\begin{description}
\item[External C] {\tt Wise2_get_Genomic_from_GenomicDB (gendb,de)}
\item[Perl] {\tt &Wise2::GenomicDB::get_Genomic_from_GenomicDB (gendb,de)}
\item[Perl-OOP call] {\tt $obj->get_Genomic_from_GenomicDB(de)}
\end{description}
Arguments
\begin{description}
\item[gendb] [UNKN ] Undocumented argument [GenomicDB *]
\item[de] [UNKN ] Undocumented argument [DataEntry *]
\item[returns] [UNKN ] Undocumented return value [Genomic *]
\end{description}
Gets Genomic sequence out from
the GenomicDB using the information stored in
dataentry
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