Dundee, Scotland DD1 5EH, UK
\vspace{2in}
-Manual Version 1.9. 3
+Manual Version 1.9.3
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
\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]
dialog box opens, untick the box adjacent to the `Open file' entry in the
`Visual' preferences tab.
Click {\sl OK} to save the preferences.}
-%%\exstep{Launch another Jalview workbench from the web site by clicking on the
-%%The example alignment should not be loaded as Jalview starts up.}
+%%\exstep{Quit Jalview and open it again to check that the
+%%The example alignment is not loaded wehn Jalview starts up.}
\exstep{To reload the original demo file select the
{\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
the URL history button (a downward arrow on the right hand side of the dialog
-box) to view the files, select exampleFile\_2\_7.jar
-(\url{http://www.jalview.org/examples/exampleFile_2_7.jar})
+box) to view the files, select exampleFile\_2\_7.jvp
+(shown as \url{https://www.jalview.org/examples/exampleFile_2_7.jvp})
then click {\sl OK}.}
\begin{list}{$\circ$}{\newline
\newline {\bf
to the {\sl Tools $\Rightarrow$
Preferences...} menu on the desktop. Then tick the `Open file' entry of `Visual'
preferences tab, type in the URL of the sequence you want to load.}
-%%\item {You may want to move the jalview.jnlp file from your {\bf downloads} to another folder.}
-%%\item {Opening Jalview via the jnlp file will also allow Jalview to be launched offline.}
\end{list}
{\bf See the video at:
git://source.jalview.org / jalview-manual.git / blobdiff