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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.patch38
1 files changed, 0 insertions, 38 deletions
diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch
deleted file mode 100644
index 827ce4cdfa7..00000000000
--- a/sci-biology/wise/files/wise-api.tex.patch
+++ /dev/null
@@ -1,38 +0,0 @@
---- 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}