X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=TheJalviewTutorial.tex;h=ab7feb705736100f59d99a61157a18a81c10ebf7;hb=5671102611f89821666a40265856cd1953a35333;hp=c8560c813aa419485b3399d126ad01463fdf8023;hpb=ec7f056b715ae663ae710a53fe1655cd2fb5a981;p=jalview-manual.git

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index c8560c8..ab7feb7 100644
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -328,13 +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
@@ -344,8 +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:
@@ -807,13 +805,14 @@ $\Rightarrow$ Load Project} menu option. Observe how many of the windows
 reopen. Are they the same as when they were saved ? } {\bf See the video at:
 \url{http://www.jalview.org/Help/Getting-Started}.} }
 
+%% Suzanne: Jim's comment: this now appears at the end of the section, over the page from the exercise. I doubt anyone will read it there.
 \subsection{Jalview Projects}
 \parbox[c]{4in}{If you wish to save a complete Jalview session rather than
 just a single alignment (e.g. because you have calculated trees or multiple
 different alignments) then save your work as a Jalview Project
-file (.jvp).\footnote{Tip: Ensure that you have allocated plenty of memory to
+file (.jvp).\footnote{Tip: Ensure that that plenty of memory is available to
 Jalview when working with large alignments in Jalview projects. See Section 
-\ref{memorylimits} for how to do this.}
+\ref{memorylimits} for how to check this.}
 From the main menu select {\sl File $\Rightarrow$ Save Project} and a file save
 dialog box will appear. Loading a project will restore Jalview to exactly the
 view at which the file was saved, complete with all alignments, trees,