From: Suzanne Duce <sduce@issues.jalview.org>
Date: Fri, 24 Nov 2017 13:27:05 +0000 (+0000)
Subject: Two issues were reported  during the Jalview workshop day so  I fixed them.
X-Git-Tag: Version_1.9.2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5f700828653846bd135d5a5e59a4e48ac845f26b;p=jalview-manual.git

Two issues were reported  during the Jalview workshop day so  I fixed them.
---

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 5f2ba63..f581b76 100644
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -1001,10 +1001,10 @@ to include newly selected sequences, and the Percentage Identity colouring chang
 \exstep{ Another way to resize the group is by using the mouse to click and drag
 the right-hand edge of the selected group.}
 
-\exstep{The current selection can be exported and saved by right clicking the
-mouse when on the text area to open the Sequence ID context menu. Follow the
-menus and pick an output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
-\ldots} submenu.
+\exstep{The current selection can be exported and saved, place mouse on the text
+area and right clicking the mouse to open the Sequence ID context menu.
+Select appropriate menu option and pick an output format (eg BLC) from the
+{\sl Selection $\Rightarrow$ Output to Textbox \ldots} submenu.
 }
 \exstep{In the Alignment output window that opens, try manually editing the
 alignment before clicking the {\sl New Window} button. This opens the
@@ -2823,7 +2823,12 @@ it is used in the next set of exercises. }
 
 \subsection{Redundancy Removal}
 
-The redundancy removal dialog box is opened using the {\sl Edit $\Rightarrow$ Remove Redundancy\ldots} option in the alignment menu. As its menu option placement suggests, this is actually an alignment editing function, but it is convenient to describe it here. The redundancy removal dialog box presents a percentage identity slider which sets the redundancy threshold. Aligned sequences which exhibit a percentage identity greater than the current threshold are highlighted in black. The [Remove] button can then be used to delete these sequences from the alignment as an edit operation\footnote{Which can usually be undone. A future version of Jalview may allow redundant sequences to be hidden, or represented by a chosen sequence, rather than deleted.}.
+The redundancy removal dialog box is opened using the {\sl Edit $\Rightarrow$ Remove Redundancy\ldots} option 
+in the alignment menu. As its menu option placement suggests, this is actually an alignment editing function, 
+but it is convenient to describe it here. The redundancy removal dialog box presents a percentage identity 
+slider which sets the redundancy threshold. Aligned sequences which exhibit a percentage identity greater 
+than the current threshold are highlighted in black. The [Remove] button can then be used to delete these 
+sequences from the alignment as an edit operation.
 \begin{figure}
 \begin{center}
 \includegraphics[width=5.5in]{images/redundancy.pdf}