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--- api.tex.old 2005-03-06 11:31:59.862760952 -0500
+++ api.tex 2005-03-06 11:42:31.375756384 -0500
@@ -204,7 +204,7 @@
\item Build two Sequence objects, from a file or strings (\ref{object_Sequence})
\item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins
\item Read in the comparison matrix using CompMat (\ref{object_CompMat})
-\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap})
+\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap})
\item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay})
\end{itemize}
@@ -213,7 +213,7 @@
\item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence})
\item Make a protein database from the single protein object (\ref{object_ProteinDB})
\item Make a protein database from a single fasta file (\ref{object_ProteinDB})
-\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap})
+\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap})
\item Show the Hscore object using a show function (\ref{object_Hscore})
\item Retrieve individual protein objects from the database by taking out the
DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object
@@ -232,7 +232,7 @@
\item Read in a codon table (\ref{object_CodonTable})
\item Make a random DNA model (\ref{object_RandomModelDNA})
\item Make an algorithm type (\ref{module_gwrap})
-\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap})
+\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap})
\item Run the actual algorithm (\ref{module_gwrap})
\item show the alignment using genedisplay (\ref{module_gwrap})
\end{itemize}
@@ -5055,7 +5055,7 @@
Member functions of RandomModel
\section{sequence\_codon}
-\label{module_sequence\_codon}
+\label{module_sequence_codon}
This module only contains factory methods
\subsection{sequence\_codon factory methods}
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