From c7851eabc849d376ea8927e771aab64960b32369 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 5 Dec 2011 10:28:44 +0000 Subject: [PATCH] fix left-right page numbering and incorrect menu item --- TheJalviewTutorial.tex | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index 339ed2e..ab8bb26 100644 --- 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} -- 1.7.10.2