diff --git a/doc/Presentation_24-02-11_HumGen_Mutalyzer2/leftover.txt b/doc/Presentation_24-02-11_HumGen_Mutalyzer2/leftover.txt
deleted file mode 100644
index 49b03543e0630be0f42bc3c4e800d90505ecb4a7..0000000000000000000000000000000000000000
--- a/doc/Presentation_24-02-11_HumGen_Mutalyzer2/leftover.txt
+++ /dev/null
@@ -1,271 +0,0 @@
-% - Mutalyzer 1.0.4
-\begin{slide}
- \slideheading{Mutalyzer 1.0.4}
-
- \begin{itemize}
- \item Developed in over four years by multiple people.
- \item Originally a command line program.
- \item Web interface added later.
- \end{itemize}
- \vfill
-\end{slide}
-
-% - Design flaws:
-% - Nomenclature rules interwoven with the code.
-% - No modularity (reuse of code is very hard).
-% - Reference sequence parsing not abstracted.
-% - HTML output interwoven with the code.
-\begin{slide}
- \slideheading{Mutalyzer 1.0.4}
-
- Design flaws:
-
- \begin{itemize}
- \item Nomenclature rules interwoven with the code.
- \item HTML output interwoven with the code.
- \item No modularity (reuse of code is very hard).
- \item Reference sequence parsing not abstracted.
- \end{itemize}
- \vfill
-\end{slide}
-
-% - Implementation flaws:
-% - Inheritance of types (del on DNA -> del on PROT).
-% - Disambiguation not general.
-% - Support up/downstream exons.
-% - Speed
-\begin{slide}
- \slideheading{Mutalyzer 1.0.4}
-
- Implementation flaws:
-
- \begin{itemize}
- \item Inheritance of types (del on DNA -> del on PROT).
- \item Disambiguation not general.
- \item Support up/downstream exons.
- \item Nothing was ever redesigned, only wrapped in loops.
- \begin{itemize}
- \item Debugging, altering code made impossible.
- \item Speed drastically deminished.
- \end{itemize}
- \end{itemize}
- \vfill
-\end{slide}
-
-% - Programming flaws:
-% - Excessive usage of exceptions.
-% - Incomprehensible error messages.
-% - Poor documentation.
-\begin{slide}
- \slideheading{Mutalyzer 1.0.4}
-
- Programming flaws:
-
- \begin{itemize}
- \item Excessive usage of exceptions.
- \item Incomprehensible error messages.
- \item Poor documentation.
- \end{itemize}
- \vfill
-\end{slide}
-
-% - Feature requests:
-% - Extension of HGVS nomenclature rules.
-% - Support for other reference files (LRG)
-% - Programmatic access to internal functions.
-% - Solving all problems mentioned above.
-% - Since the nomenclature has changed, a rewrite was in order.
-%
-
-\begin{slide}
- \slideheading{Mutalyzer 1.0.4}
-
- Feature requests:
-
- \begin{itemize}
- \item Solving all problems mentioned above.
- \item Support for other reference files (LRG).
- \item Programmatic access to internal functions.
- \end{itemize}
- Since the HGVS nomenclature rules were changed in the mean time, and the
- language was no longer regular (but context free), the only possible couse of
- action was a complete redesign.
- \vfill
-\end{slide}
-
-% - Preparations for version 2.0
-% - Gathering and archiving all old versions (for comparison).
-% - Setting up a version control repository.
-% - Talking for months.
-% - Figuring out what the HGVS language is.
-% - Formalising that language (BNF).
-% - Semantic rules.
-% - Chopping everything up in functional modules.
-% - Designing interfaces (web, webservice, command line, etc.)
-\begin{slide}
- \slideheading{Preparing for a new version}
-
-
- \begin{itemize}
- \item Setting up a version control repository.
- \item Gathering all old versions and putting then under version control.
- \begin{itemize}
- \item Critical bugfixes until there is a new version.
- \item Easy to search and track changes.
- \item Point of reference for the new version.
- \end{itemize}
- \item Talking for months.
- \begin{itemize}
- \item Figuring out what the HGVS language is.
- \item Formalising that language (BNF).
- \item Semantic rules.
- \end{itemize}
- \item Chopping everything up in functional modules.
- \item Designing interfaces (web, webservice, command line, etc.).
- \end{itemize}
- \vfill
-\end{slide}
-
-%
-% - Then finally, after months of talking and drawing with pencil and paper..
-% - Implementing the modules.
-% - Implementing the interfaces.
-\begin{slide}
- \slideheading{Mutalyzer 2.0}
-
- Then finally, after months of talking and drawing with pencil and paper..
-
- \begin{itemize}
- \item Implementing the modules.
- \item Implementing the interfaces.
- \end{itemize}
-
- \vfill
-\end{slide}
-
-%
-% - Mutalyzer 2.0
-% - Core functionalities.
-% - Webservices.
-% - ...
-
-
-\begin{slide}
- \slideheading{TAL}
-
- \begin{lstlisting}[language = HTML, caption = {TAL example}]
- <table class = "raTable">
- <tr>
- <td>Number</td>
- <td>Start (g.)</td>
- <td>Stop (g.)</td>
- <td>Start (c.)</td>
- <td>Stop (c.)</td>
- </tr>
- <tr tal:repeat = "i exonInfo">
- <td tal:content = "repeat/i/number"></td>
- <td tal:repeat = "j i" tal:content = "j"></td>
- </tr>
- </table>
- \end{lstlisting}
-
- When we give a list of exon coordinates, a table is generated.
- \vfill
-\end{slide}
-
-\begin{slide}
- \slideheading{BNF}
-
- \begin{lstlisting}[language = BNF, caption = {Abstract HGVS nomenclature}]
- TransVar -> `_v' Number
- ProtIso -> `_i' Number
- GeneSymbol -> `(' Name (TransVar | ProtIso)? `)'
- \end{lstlisting}
-
- \begin{lstlisting}[caption = {HGVS nomenclature in Python}]
- TransVar = Suppress("_v") + Number("TransVar")
- ProtIso = Suppress("_i") + Number("ProtIso")
- GeneSymbol = Suppress('(') + Group(Name("GeneSymbol") + \
- Optional(TransVar ^ ProtIso))("Gene") + Suppress(')')
- \end{lstlisting}
-
- \bt{(CDKN2A\_v001)}
- \begin{lstlisting}[caption = {Python object}]
- Gene.GeneSymbol = CDKN2A
- Gene.TransVar = 001
- \end{lstlisting}
-
- \bt{(CDKN2A\_i002)}
- \begin{lstlisting}[caption = {Python object}]
- Gene.GeneSymbol = CDKN2A
- Gene.ProtIso = 002
- \end{lstlisting}
- \vfill
-\end{slide}
-
-\begin{slide}
- \slideheading{Comparison to the old version (1.0.4)}
-
- \renewcommand{\arraystretch}{0.99}
- \begin{tabular}{l|c|c}
- & Mutalyzer 1.0.4 & Mutalyzer 2.0\\
- \hline
- Disambiguation & $\pm$ & $++$\\
- Complex variants & $--$ & $++$\\
- Protein description & $\pm$ & $+$\\
- Up / downstream descriptions & $--$ & $++$\\
- Comprehensible error messages & $-$ & $++$\\
- Using a protein reference & $\pm$ & $--$\\
- Batch checkers & $\pm$ & $++$\\
- GenBank uploader & $+$ & $++$\\
- Position conversion & $--$ & $++$\\
- Programmatic access & $--$ & $++$\\
- Other organisms / organelles & $\pm$ & $++$\\
- \end{tabular}
-
- \vfill
-\end{slide}
-
-\begin{slide}
- \slideheading{Comparison to the old version (1.0.4): runtime}
- \begin{center}
- \colorbox{white} {
- \includegraphics[scale = 0.65]{genes}
- }
- \end{center}
- A $229\times$ speedup was measured (from almost $12min$ to about $3s$).
- \vfill
-\end{slide}
-
-\begin{slide}
- \slideheading{Comparison to the old version (1.0.4): code}
-
- \begin{tabular}{l|r|r}
- & Mutalyzer 1.0.4 & Mutalyzer 2.0\\
- \hline
- Total (lines) & $7,\!752$ & $11,\!396$\\
- Total (bytes) & $365,\!736$ & $390,\!316$\\
- Minimised (lines) & $5,\!102$ & $4,\!320$\\
- Minimised (bytes) & $232,\!611$ & $156,\!803$\\
- Percentage of code (lines) & $66\%$ & $38\%$\\
- Percentage of code (bytes) & $64\%$ & $42\%$
- \end{tabular}
- \bigskip
- \bigskip
-
- The total amount of \emph{source code} in Mutalyzer~2.0 is $107\%$ of that in
- Mutalyzer~1.0.4, but the amount of \emph{program code} is only $67\%$.
- \vfill
-\end{slide}
-
-\begin{slide}
- \slideheading{Scalability: runtime with increasing complexity}
- \begin{center}
- \colorbox{white} {
- \includegraphics[scale = 0.65]{allele}
- }
- \end{center}
- The overhead ($\pm 2.5s$) is due to loading the reference sequence.
- \vfill
-\end{slide}
-
diff --git a/src/Mutalyzer.py b/src/Mutalyzer.py
index 3a3edeaa22db37995152afd7c1797fb1fef888f0..f3c4b45c401438384ceee839047401ce8731ee9b 100644
--- a/src/Mutalyzer.py
+++ b/src/Mutalyzer.py
@@ -1431,6 +1431,11 @@ def __ppp(MUU, parts, GenRecordInstance, O) :
cdsm = Bio.Seq.reverse_complement(cdsm)
#if
+ if not __checkDNA(cds) :
+ O.addMessage(__file__, 4, "ENODNA", "Invalid letters in "
+ "reference sequence.")
+ return
+ #if
if '*' in cds.translate(table = W.txTable)[:-1] :
O.addMessage(__file__, 3, "ESTOP", "In frame stop codon found.")
return