-
-\exercise{Loading Sequences}{
-\label{load}
-\exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
-close all windows.}
-%% TODO: omit or combine this exercise
-%% NB. Edge (MS default browser) doesn't actually allow you to 'save' the page, apparently
-\exstep{{\bf Loading sequences from URL:} Selecting {\sl File $\Rightarrow$
-Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \url{http://www.jalview.org/tutorial/alignment.fa} in the box.
-Click {\sl OK} to load the alignment.}
-
-%%TODO: omit or combine
-\exstep{{\bf Loading sequences from a file:} Close all windows using the
-{\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.
-Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
-your web browser and save the fasta file (.fa) file to your desktop using {\sl File
-$\Rightarrow$ Save Page as}.
-Open the file you have just saved in Jalview by selecting {\sl File
-$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu.
-Select the file and click {\sl OK} to load.}
-
-\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
-
-(i) Drag the alignment.fa file that you have just saved from its folder and
-drop it onto the Jalview desktop window, the alignment should open.
-
-(ii) Open
-\url{http://www.jalview.org/examples/estrogenReceptorProtein.fa} in a web
-browser. Test the differences
-between (a) dragging the URL directly from browser onto the Jalview
-desktop.
-(If the URL is downloaded, alternatively locate the file in your download
-directory and drag it onto the desktop.) (b) dragging the URL from
-browser onto the existing alignment.fa alignment window in the Jalview desktop.
-
-(iii) Open \url{http://www.jalview.org/examples/estrogenReceptorCdna.fa} in a web
-browser. Note that this is a cDNA file. Drag the URL from
-browser onto the estrogenReceptorProtein.fa protein alignment window in
-the Jalview desktop. A dialogue box opens asking `Would you like to open as split
-window, with cDNA and protein linked?' select `Split Window' option. A
-split window opens in the Jalview desktop.
-}
-
-\exstep{{\bf The text editor:}
-
-(i) Open the alignment.fa file using text editor.
-Copy the sequence text into the clipboard using [CTRL]-A and then [CTRL]-C.
-
-(ii) Move the mouse pointer onto the Jalview desktop window's background and right-click
-to open the context window. Select the {\sl Paste to New Window} menu option.
-
-(iii) In the Jalview desktop menu, select {\sl File
-$\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox}.
-Paste the clipboard into the large window using [CTRL]-V. Click {\sl New Window}
-and the alignment will be loaded.}
-
-\exstep{{\bf Loading sequences from Public Database:} (i) Select {\sl File
-$\Rightarrow$ Fetch Sequences...} from the Jalview desktop menu. The {\sl
-Select Database Retrieval Source} dialog will open listing all the database
-sources. Select the {\bf PFAM seed} database and click {\sl OK}.
-
-(ii) The {\sl New
-Sequence Fetcher} window will open. Enter the accession number {\bf PF03460}
-and click {\sl OK}.
-An alignment of about 174 sequences should load.}
-\exstep{These can be viewed using the Overview window accessible from {\sl View
-$\Rightarrow$ Overview Window.}}
-{\bf See the video at:
-\url{http://www.jalview.org/Help/Getting-Started}} }
-
-\subsection{Memory Limits}