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:
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,
Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
} menu and select {\sl Percentage Identity}.
This will turn the selected region into a group and colour it accordingly.}
-\exstep{Hold down [CTRL] ([CMD] on Mac) or [SHIFT] and use the mouse to select and deselect sequences in
+\exstep{Hold down [CTRL] ([CMD] on Mac) and use the mouse to select and deselect sequences in
the alignment by clicking on their Sequence ID label. Note how the group expands
to include newly selected sequences, and the Percentage Identity colouring changes. }
-\exstep{ Another way to resize the group is by using the mouse to click and drag
+\exstep{ Another way to resize the group is simply to use the mouse to click and drag
the right-hand edge of the selected group.}
\exstep{The current selection can be exported and saved, place mouse on the text
}
\exstep{Repeat the above using columns to hide and reveal columns
instead of sequences.}
-\exstep{Select a region of the alignment, and experiment with the {\sl Hide all
-but selected region} option. In the alignment window menu, {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
-but selected region.}} \exstep{Select some sequences, pick one to represent the rest by hovering
+\exstep{Select a region of the alignment, and experiment with {\sl View $\Rightarrow$ Hide $\Rightarrow$ Hide all
+but selected region} and {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
+but selected region} options in the alignment window menu.} \exstep{Select some sequences, pick one to represent the rest by hovering
the mouse over this sequence. Bring up the Sequence ID context menu by right
clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
with (Sequence ID name )}. To reveal these hidden sequences, right click on the
columns in all sequences in the selected group, and those columns are to the
right of the selected residue.
+{\bf That's it for this chapter. Don't forget the exercises on the next page!}
+\newpage
-\exercise{Editing Alignments Homework Exercise}
+\exercise{Editing Alignments}
%\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
{
alignment available at
\href{http://www.jalview.org/examples/exampleFile.jvp}
{http://www.jalview.org/examples/exampleFile.jvp}.
+
+ {\sl {\bf Note: this is a homework exercise for jalview course participants!}}
{\sl {\bf Mac Users:} Please use the Apple or [CMD] key in place of [CTRL]
for key combinations such as [CTRL]-A. }
}
-\exercise{Keyboard Edits Homework Exercise}
+\exercise{Keyboard Edits}
{
\label{keyboardsex}
This continues on from the previous exercise, and recreates the final part of the example ferredoxin
alignment from the unaligned sequences using Jalview's keyboard editing mode.
+{\bf Note: This is a homework exercise for jalview course participants}
+
{\bf Window users:} Please {\em only use} [SHIFT]-[SPACE] in this
exercise.
displayed, and you may have to disable it using the {\sl View $\Rightarrow$
Show Sequence Features} option before you can see your colourscheme.
-There are two main types of colouring styles: {\bf simple static residue}
+There are two main types of colouring styles: simple {\bf static residue}
colourschemes and {\bf dynamic schemes} which use conservation and consensus
analysis to control colouring. {\bf Hybrid colouring} is also possible, where
static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme}.
\exercise{Colouring Alignments}{
\label{color}
Note: Ensure that the {\sl Apply Colour
-To All Groups} flag is not selected (ie unticked) in {\sl Colour} menu in the alignment window.
+To All Groups} flag is not selected (i.e. not ticked) in {\sl Colour} menu in the alignment window.
% patch needed for 2.10 This must be turned {\sl off} specifically as it is on
% by default.
Clustalx} and note the colour change. Now try all the other colour schemes in the {\sl Colour} menu.
Note that some colour schemes do not colour all residues.}
\exstep{Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62 score}. Select a group
-of around 4 similar sequences. Use the context menu (right click on the residues in the group)
+of around 4 similar sequences. Use the context menu (opened by right clicking on the residues in the group)
option {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
$\Rightarrow$ Blosum62 score} to colour the selection. Notice how some residues which
were not coloured are now coloured. The calculations performed for dynamic
Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
Slide the selector in the Conservation Colour Increment dialog box from side
to side and observe the changes in the alignment colouring in the selection and in the complete alignment.}
-Note: Feature colours overlay residue colouring, and this may mask residue colouring. If this is an issue, he features colours can be
-toggled off by going to {\sl View $\Rightarrow$ Show Sequence Features}.
+
+Note: If you don't see any changes in appearance, it might be because sequence
+features are currently displayed (these are introduced later, in Section
+\ref{featannot}). To see if features are obscuring your colour scheme settings, look to see if the {\sl View
+$\Rightarrow$ Show Sequence Features} option in the alignment window menu is
+ticked. If it is, select it to disable feature colouring.
{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
}
git://source.jalview.org / jalview-manual.git / blobdiff