Revised intro about launching Jalview and removed commented out JNLP stuff

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 361dfba..c8560c8 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -259,49 +259,33 @@ Alignment' submenu of a window's `File' dropdown menu.
 \end{center}
 \end{figure}
 
-This tutorial is based on the Jalview
-Desktop application. Much of the information will also be useful for users of
-the JalviewJS, which has the same core editing, analysis and visualization capabilities. The Jalview Desktop, however, is much more powerful, and
-includes additional support for interaction with external web services, and
-production of publication quality graphics.
-
-The Jalview Desktop application can be downloaded from the Jalview website.
-Click the Download link in the top right hand corner of the Jalview homepage.
-This opens the download webpage, the options available will reflect if you have Mac or PC computer.
-The application is downloaded by clicking the link as appropriate for your computer operating system.
-Instal the Jalview application by clicking on the downloaded file and following the instructions.
-Jalview has the functionality to automatically update itself when a new version is released.
-%%launched from the
-%%web {\sl via} Java webstart, or as an application loaded onto your hard drive. 
-%%The webstart version is launched from the `Launch Jalview Desktop
-%%button' at the top right hand side of pages of the website 
-%%\href{http://www.jalview.org}{(www.jalview.org)}.
-%%To download the locally installable version, follow the links on the download
-%%page
-%%\href{http://www.jalview.org/download}{(www.jalview.org/download) }
-%% (Figure \ref{download}).
-%%These links will launch the latest stable release of Jalview.\par
-
-%% this paragraph needs to be rewritten for the new signed certificate from Certum.
-
-%%When the application is launched with webstart, dialogs may appear before
-%%the application starts. If your browser is not set up to handle webstart, then
-%%clicking the launch link may download a file that needs to be opened
-%%manually, or prompt you to select the program to handle the webstart
-%%file. If that is the case, you will need to locate the {\bf javaws} program
-%%on your system\footnote{The file that is downloaded will have a type of {\bf
-%%application/x-java-jnlp-file} or {\bf .jnlp}. The {\bf javaws} program that can run
-%%this file is usually found in the {\bf bin} directory of your Java
-%%installation}. Once java webstart has been launched, you may also be prompted to
-%%accept a security certificate signed by the Barton Group.\footnote{On some
-%%systems, the certificate may be signed by 'UNKNOWN'. In this case, clicking
-%%through the dialogs to look at the detailed information about the certificate
-%%should reveal it to be a Barton group certificate.} You can always trust us, so
-%%click trust or accept as appropriate. The splash screen (Figure \ref{splash})
-%%gives information about the version and build date that you are running,
-%%information about later versions (if available), and the paper to cite in your
-%%publications. This information is also available on the Jalview web site at 
-%%\url{http://www.jalview.org}.
+This tutorial is based on the Jalview Desktop application. Much of the
+information will also be useful for users of the JalviewJS, which has the same
+core editing, analysis and visualization capabilities. The Jalview Desktop,
+however, is much more powerful, and includes additional support for interaction
+with external web services, powerful molecular graphics programs, and production
+of publication quality graphics.
+
+The Jalview Desktop application can be downloaded from the download link on the
+Jalview website, which takes you to
+\href{http://www.jalview.org/download}{(www.jalview.org/download)}. The page
+automatically displays the options available for your computer (e.g. if you have
+Mac or PC), and a button to show all available downloads. These include special
+'executable Jar' distributions useful if you want to run a specific version of
+Jalview.
+To ensure you are running the latest version of Jalview, we recommend
+downloading the Jalview Desktop Installer package for your platform, clicking on
+the downloaded file and following the instructions to install it.
+Once installed, the Jalview Application will automatically update itself when a
+new version is released.
+
+When the Jalview Desktop application is launched, you will first see a loading
+screen whilst it checks for updates, then the program will start with the
+Jalview splash screen (Figure \ref{splash}).
+This gives information about the version and build date that you are running,
+information about later versions (if available), and the paper to cite in your
+publications. This information is also available on the Jalview web site at
+\url{http://www.jalview.org}.
 
 %[fig 2] 
 \begin{figure}[htbp]