fix left-right page numbering and incorrect menu item

[jalview-manual.git] / TheJalviewTutorial.tex

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 339ed2e..ab8bb26 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -97,14 +97,16 @@ Dundee, Scotland DD1 5EH, UK
 
 \vspace{2in}
 
-Manual version 1.3
+Manual version 1.3.01
 
-30th November 2011
+6th December 2011
 
 
 \end{center}
 
-\clearemptydoublepage
+\newpage
+
+% \clearemptydoublepage
 
 % ($Revision$) 11th October 2010.}
 % TODO revise for 2.6
@@ -2523,10 +2525,10 @@ Feature retrieval can take some time if a large number of sources is selected an
 
 \exercise{Retrieving features with DAS}{
 \label{dasfeatretrexcercise}
-\exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}.  Select {\sl View $\Rightarrow$ Sequence Features\ldots} from the alignment window menu. Select the {\sl DAS Settings} tab. A long list of available DAS sources is listed. Select a small number, eg Uniprot, DSSP, signalP and netoglyc. Click {\sl OK}. A window may prompt whether you wish Jalview to map the sequence IDs onto Uniprot IDs. Click {\sl Yes}. Jalview will start retrieving features. As features become available they will be mapped onto the alignment.
-}
-\exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button. Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip. Close the Feature Settings window.
-}
+\exstep{Load the alignment at
+\textsf{http://www.jalview.org/tutorial/alignment.fa}.  Select {\sl View
+$\Rightarrow$ Feature Settings \ldots} from the alignment window menu. Select
+the {\sl DAS Settings} tab. A long list of available DAS sources is listed. Select a small number, eg Uniprot, DSSP, signalP and netoglyc. Click {\sl OK}. A window may prompt whether you wish Jalview to map the sequence IDs onto Uniprot IDs. Click {\sl Yes}. Jalview will start retrieving features. As features become available they will be mapped onto the alignment. } \exstep{If Jalview is taking too long to retrieve features, the process can be cancelled with the {\sl Cancel Fetch} button. Rolling the mouse cursor over the sequences reveals a large number of features annotated in the tool tip. Close the Feature Settings window. }
 \exstep{Move the mouse over the sequence ID panel. Non-positional features such as literature references and protein localisation predictions are given in the tooltip, below any database cross references associated with the sequence.}
 \exstep{Search through the alignment to find a feature with a link symbol next to it. Right click to bring up the alignment view popup menu, and find a corresponding entry in the {\sl Link } sub menu. }
 % TODO this doesn't work ! \includegraphics[width=.3in]{images/link.pdf}