second commit (to test the process)

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 55bafc2..1a9eda5 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -1025,7 +1025,9 @@ together when they are re-ordered using the up and down arrow keys.} }
 \label{hidingregions}
 It is sometimes convenient to exclude some sequences or residues in the alignment without actually deleting them. Jalview allows sequences or alignment columns within a view to be hidden, and this facility has been used to create the several different views in the example alignment file that is loaded when Jalview is first started (See Figure \ref{startpage}).
 
-To hide a set of sequences, select them and right-click the mouse on the selected sequence IDs to bring up the context menu. Select {\sl Hide Sequences} and the sequences will be concealed, with a small blue triangle indicating their position (Figure \ref{hideseq}). To unhide (reveal) the sequences, right click on the triangle and select {\sl Reveal Sequences} from the context menu.
+To hide a set of sequences, select them and right-click the mouse on the
+selected sequence IDs to bring up the context pop-up menu. Select {\sl Hide
+Sequences} and the sequences will be concealed, with a small blue triangle indicating their position (Figure \ref{hideseq}). To unhide (reveal) the sequences, right click on the triangle and select {\sl Reveal Sequences} from the context menu.
 
 
  \begin{figure}[htbp]
@@ -1039,7 +1041,10 @@ triangle in the sequence ID panel.}
 \end{center}
 \end{figure}
 
-A similar mechanism applies to columns (Figure \ref{hidecol}). Selected columns (indicated by a red marker) can be hidden and revealed in the same way {\sl via} the context menu by right clicking on the ruler bar. The hidden column selection is indicated by a small blue triangle in the ruler bar.
+A similar mechanism applies to columns (Figure \ref{hidecol}). Selected columns
+(indicated by a red marker) can be hidden and revealed in the same way {\sl via}
+the context pop-up menu by right clicking on the ruler bar. The hidden column
+selection is indicated by a small blue triangle in the ruler bar.
 
  \begin{figure}[htbp]
 \begin{center}
@@ -1062,20 +1067,29 @@ to hide the unselected region.
 Instead of hiding a group completely, it is sometimes useful to work with just one representative sequence. The {\sl $<$Sequence ID$>$ $\Rightarrow$ Represent group with $<$Sequence ID$>$ } option from the sequence ID pop-up menu enables this variant of the hidden groups function. The remaining representative sequence can be visualized and manipulated like any other. However, any alignment edits that affect the sequence will also affect the whole sequence group. 
 
 \exercise{Hiding and revealing regions}{
-\exstep{Close all windows then open the PFAM accession PF03460. Select a contiguous set of sequences by clicking and dragging on the sequence ID panel. Right click on the selected sequence IDs and select {\sl Hide Sequences}.
+\exstep{Close all windows, open the PFAM accession PF03460. Select a
+contiguous set of sequences by clicking and dragging on the sequence ID panel.
+Right click on the selected sequence IDs to bring up the selection pop-up menu, select {\sl Hide Sequences}.
 }
 \exstep{
-Right click on the blue triangle indicating hidden sequences and select {\sl Reveal Sequences}. (If you have hidden all sequences then you will need to use the alignment window menu option {\sl View $\Rightarrow$ Show $\Rightarrow$ All Sequences.})
-}
+Right click on the blue triangle indicating hidden sequences and select {\sl
+Reveal Sequences} in the panel. (If you have hidden all sequences then you will
+need to use the alignment window menu option {\sl View $\Rightarrow$ Show $\Rightarrow$ All Sequences.}) }
 \exstep{
-Repeat but using a non-contiguous set of sequences. Note that when multiple regions are hidden there are two options, {\sl Reveal Sequences} and {\sl Reveal All}.
-}
-\exstep{Repeat the above but hiding and revealing columns instead of sequences.
-}
-\exstep{Select a region of the alignment, add in some additional columns to the
-selection, and experiment with the `Hide all but selected region' function. }
-\exstep{Select some sequences and pick one to represent the rest. Bring up the sequence ID pop-up menu for that sequence and select the {\sl Represent group with $<$Sequence ID$>$ } option. Use the pop-up menu again to reveal the hidden sequences that you just picked a representative for.}
-}
+Repeat the process but use a non-contiguous set of sequences. Note that when
+multiple regions are hidden there are two options, {\sl Reveal Sequences} and {\sl Reveal All}.
+}
+\exstep{Repeat the above using columns to hide and reveale columns
+instead of sequences.
+}
+\exstep{Select a region of the alignment, then add in some additional columns to
+the selection, and experiment with the `Hide all but selected region' function
+in {\sl View $\Rightarrow$ Hide $\Rightarrow$ All but selected region.}}
+\exstep{Select some sequences and pick one to represent the rest by hoovering
+the mouse over this sequence. Bring up the selection pop-up menu by right
+clicking and then seelct {\sl (Sequence ID) $\Rightarrow$ Represent group
+with (Sequence ID)}. To reveal these hidden sequences, right click on the
+Sequence ID and in the the pop-up menu select Reveal All.}}