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Diffstat (limited to 'sci-biology/wise/files/wise-api.tex.patch')
| -rw-r--r-- | sci-biology/wise/files/wise-api.tex.patch | 38 |
1 files changed, 38 insertions, 0 deletions
diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch new file mode 100644 index 000000000000..d6d56888dfb3 --- /dev/null +++ b/sci-biology/wise/files/wise-api.tex.patch @@ -0,0 +1,38 @@ +--- a/api.tex.old ++++ b/api.tex +@@ -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} |