X-Git-Url: http://source.jalview.org/gitweb/?p=jalview-manual.git;a=blobdiff_plain;f=TheJalviewTutorial.tex;h=790781992c4a8a3248f7072a4ab2953c8dda5b76;hp=361dfbabf9ce61e0d106426b78ed201cbda28468;hb=f6365177a901fc77db3702038086805457143b92;hpb=5c017201542714176129a89b96e7b1961f2bb27b diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex index 361dfba..7907819 100644 --- 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] @@ -344,13 +328,13 @@ Preferences...} menu on the desktop. A `Preference' 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 @@ -360,8 +344,6 @@ then click {\sl OK}.} 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: