SLD has completed her text and exercise edits in Chapter 1.

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 1574b35..7f1954a 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -79,7 +79,7 @@ Jalview 2.8.2
 \vspace{0.5in}
 {\huge 
 
 \vspace{0.5in}
 {\huge 
 

-A Manual with Introductory Tutorial }
+Manual with Introductory Tutorial }

 
 \vspace{2.4in}
 
 
 \vspace{2.4in}
 

@@ -140,8 +140,8 @@ other data. Jalview can read and write many common sequence formats including
 FASTA, Clustal, MSF(GCG) and PIR.
 
 
 FASTA, Clustal, MSF(GCG) and PIR.
 
 

-There are two types of Jalview program. The {\bf Jalview Desktop} is a stand
-alone application that provides powerful editing, visualization, annotation and
+There are two types of Jalview program. The {\bf Jalview Desktop} is a standalone 
+application that provides powerful editing, visualization, annotation and

 analysis capabilities. The {\bf JalviewLite} applet has the same core
 visualization, editing and analysis capabilities as the desktop, without the
 desktop's webservice and figure generation capabilities. It is designed to be
 analysis capabilities. The {\bf JalviewLite} applet has the same core
 visualization, editing and analysis capabilities as the desktop, without the
 desktop's webservice and figure generation capabilities. It is designed to be

@@ -267,7 +267,7 @@ production of publication quality graphics.
 The Jalview Desktop can be run in two ways; as an application launched from the
 web {\sl via} Java webstart, or as an application loaded onto your hard drive. 
 The webstart version is launched from the pink `Launch Jalview Desktop
 The Jalview Desktop can be run in two ways; as an application launched from the
 web {\sl via} Java webstart, or as an application loaded onto your hard drive. 
 The webstart version is launched from the pink `Launch Jalview Desktop

-button' at the top right handside of pages of the website 
+button' at the top right hand side of pages of the website 

 \href{http://www.jalview.org}{(www.jalview.org)}.
 To download the locally installable version, follow the links on the download
 page
 \href{http://www.jalview.org}{(www.jalview.org)}.
 To download the locally installable version, follow the links on the download
 page

@@ -323,14 +323,14 @@ from Jalview version 2.7).
 \subsubsection{Jalview News RSS Feed}
 
 Announcements are made available to users of the
 \subsubsection{Jalview News RSS Feed}
 
 Announcements are made available to users of the

-Jalview Desktop {\sl via} the Jalview News reader. This window will open
+Jalview Desktop {\sl via} the Jalview Newsreader. This window will open

 automatically when new news is available, and can also be accessed {\sl via} the
 Desktop's {\sl Tools $\Rightarrow$ Show Jalview News} menu entry. 
 
 \begin{figure}[htbp]
 \begin{center}
 \includegraphics[height=3in]{images/jvrssnews.pdf}
 automatically when new news is available, and can also be accessed {\sl via} the
 Desktop's {\sl Tools $\Rightarrow$ Show Jalview News} menu entry. 
 
 \begin{figure}[htbp]
 \begin{center}
 \includegraphics[height=3in]{images/jvrssnews.pdf}

-\caption{{\bf The Jalview News Reader.} The news reader opens automatically
+\caption{{\bf The Jalview News Reader.} The newsreader opens automatically

 when new articles are available from the Jalview Desktop's news channel.}
 \label{jalviewrssnews}
 \end{center}
 when new articles are available from the Jalview Desktop's news channel.}
 \label{jalviewrssnews}
 \end{center}

@@ -343,13 +343,15 @@ when new articles are available from the Jalview Desktop's news channel.}
 site \href{http://www.jalview.org}{(www.jalview.org)}
 in your web browser. Launch Jalview by clicking on the
 pink `Launch Jalview' Desktop button in the top right hand corner. This
 site \href{http://www.jalview.org}{(www.jalview.org)}
 in your web browser. Launch Jalview by clicking on the
 pink `Launch Jalview' Desktop button in the top right hand corner. This

-will download and open a jalview.jnlp webstart file.} \exstep {Dialogue boxes
-will open and ask if you want to open the the jalview.jnlp file as the file is an application downloaded from the
+will download and open a jalview.jnlp webstart file.}
+\exstep {Dialogue boxes
+will open and ask if you want to open the jalview.jnlp file as the file is an application downloaded from the

 Internet, click Open. (Note you maybe asked to update Java, if you agree then it
 will automatically update the Java software). As Jalview opens, four demo
 Internet, click Open. (Note you maybe asked to update Java, if you agree then it
 will automatically update the Java software). As Jalview opens, four demo

-Jalview windows automatically load.} \exstep {If
+Jalview windows automatically load.}
+\exstep {If

 you are having trouble, it may help changing the browser you are using, as the browsers and
 you are having trouble, it may help changing the browser you are using, as the browsers and

-it's version may effect this process.}
+it's version may affect this process.}

 \exstep{To deactivate the opening of the 4 demo sequences during the launch, go
 to the {\sl Tools $\Rightarrow$
 Preferences...} menu on the desktop. A `Preference'
 \exstep{To deactivate the opening of the 4 demo sequences during the launch, go
 to the {\sl Tools $\Rightarrow$
 Preferences...} menu on the desktop. A `Preference'

@@ -374,7 +376,7 @@ As the jalview.jnlp file launches Jalview on your desktop, you
 may want to move this from the downloads folder to another folder.
 Opening from this file will allow Jalview to be launched offline.
 
 may want to move this from the downloads folder to another folder.
 Opening from this file will allow Jalview to be launched offline.
 

-{\bf Help launching Jalview is avaliable in a video on
+{\bf Help launching Jalview is available in a video on

 \href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
 the website.}}
 
 \href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
 the website.}}
 

@@ -416,19 +418,19 @@ The major features of the Jalview Desktop are illustrated in Figure \ref{anatomy
  editing and navigation is performed using the mouse, and {\bf cursor mode}
  where editing and navigation are performed using the keyboard. The {\bf F2 key}
  is used to switch between these two modes. With a Mac as the F2 is
  editing and navigation is performed using the mouse, and {\bf cursor mode}
  where editing and navigation are performed using the keyboard. The {\bf F2 key}
  is used to switch between these two modes. With a Mac as the F2 is

- often assigned to screen brightness, one maay often need to  type {\bf function
+ often assigned to screen brightness, one may often need to  type {\bf function

  [Fn] key with F2}.
 
 \begin{figure}[htb]
 \begin{center}
 \includegraphics[width=6.5in]{images/jalview_anatomy.pdf}
  [Fn] key with F2}.
 
 \begin{figure}[htb]
 \begin{center}
 \includegraphics[width=6.5in]{images/jalview_anatomy.pdf}

-\caption{{\bf The anatomy of Jalview.} The major features of the Jalview Desktop Application are labelled.}
+\caption{{\bf The anatomy of Jalview.} The major features of the Jalview Desktop Application are labeled.}

 % TODO: modify text labels to be clearer - black on grey and black border for clarity
 \label{anatomy}
 \end{center}
 \end{figure}
 
 % TODO: modify text labels to be clearer - black on grey and black border for clarity
 \label{anatomy}
 \end{center}
 \end{figure}
 

-\subsection{Navigation in Normal mode}
+\subsection{Navigation in Normal Mode}

 
 Jalview always starts up in Normal mode, where the mouse is used to interact
 with the displayed alignment view. You can move about the alignment by clicking
 
 Jalview always starts up in Normal mode, where the mouse is used to interact
 with the displayed alignment view. You can move about the alignment by clicking

@@ -469,11 +471,11 @@ the alignments and analysis windows at once, then use the {\sl Window
 $\Rightarrow$ Close All} option from the Jalview desktop.
 
 {\bf \em{Warning: make sure you have saved your work because this cannot be
 $\Rightarrow$ Close All} option from the Jalview desktop.
 
 {\bf \em{Warning: make sure you have saved your work because this cannot be

-undone !}} }
+undone!}} }

 \parbox[c]{3in}{\centerline{\includegraphics[width=2.5in]{images/start_closeall.pdf}
 }}
 
 \parbox[c]{3in}{\centerline{\includegraphics[width=2.5in]{images/start_closeall.pdf}
 }}
 

-\subsection{Navigation in Cursor mode}
+\subsection{Navigation in Cursor Mode}

 \label{cursormode}
 \parbox[c]{5in}{Cursor mode navigation enables the user to quickly
 and precisely navigate, select and edit parts of an alignment. On pressing F2 to
 \label{cursormode}
 \parbox[c]{5in}{Cursor mode navigation enables the user to quickly
 and precisely navigate, select and edit parts of an alignment. On pressing F2 to

@@ -524,7 +526,7 @@ Help on desktop menu, clicking on Documentation will open a Documentation
 window. Select topic from the navigation panel on the left hand side or use the
 Search tab to select specific key words
 
 window. Select topic from the navigation panel on the left hand side or use the
 Search tab to select specific key words
 

-{\bf Help navigating Jalview is avaliable in a video on
+{\bf Help navigating Jalview is available in a video on

 \href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
 the website.}}
 
 \href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
 the website.}}
 

@@ -636,7 +638,7 @@ and the PDB, as well as any DAS sequence server registered at the configured DAS
 registry. Jalview's sequence fetching capabilities allow you to avoid having to
 manually locate and save sequences from a web page before loading them into
 Jalview. It also allows Jalview to gather additional metadata provided by the
 registry. Jalview's sequence fetching capabilities allow you to avoid having to
 manually locate and save sequences from a web page before loading them into
 Jalview. It also allows Jalview to gather additional metadata provided by the

-source, such as annotation and database cross references.
+source, such as annotation and database cross-references.

 Select {\sl File $\Rightarrow$ Fetch Sequence(s) \ldots} from the main menu and
 a window will appear (Figure \ref{loadseq}). Pressing the database selection
 button in the dialog box opens a new window showing all the database sources
 Select {\sl File $\Rightarrow$ Fetch Sequence(s) \ldots} from the main menu and
 a window will appear (Figure \ref{loadseq}). Pressing the database selection
 button in the dialog box opens a new window showing all the database sources

@@ -714,7 +716,7 @@ Select the {\bf PFAM seed} database and click ok, then enter the accession
 number {\bf PF03460} and click OK. An alignment of about 107 sequences should load.
 
 Several database IDs
 number {\bf PF03460} and click OK. An alignment of about 107 sequences should load.
 
 Several database IDs

-or accession numbers can be loaded by using semicolons to separated them.}}
+or accession numbers can be loaded by using semicolons to separate them.}}

 
 \subsection{Memory Limits}
 \label{memorylimits}
 
 \subsection{Memory Limits}
 \label{memorylimits}

@@ -788,7 +790,7 @@ alignment from PFAM (seed) data base using the PFAM seed accession number
 PF03460 (see Exercise \ref{load}). } \exstep{
 
 Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a
 PF03460 (see Exercise \ref{load}). } \exstep{
 
 Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a

-location into which to save the alignment and select your prefered format. All
+location into which to save the alignment and select your preferred format. All

 formats except {\sl  Jalview } jvp can be viewed in a normal text editor (e.g.
 Notepad) or in a web browser.
 Enter a file name and click {\sl Save}.
 formats except {\sl  Jalview } jvp can be viewed in a normal text editor (e.g.
 Notepad) or in a web browser.
 Enter a file name and click {\sl Save}.

@@ -973,9 +975,10 @@ Navigate to column 59, row 1 by pressing {\bf 5 9 , 1 [RETURN]}.
 Press {\bf Q} to mark this position.
 Navigate to column 65, row 8 by pressing {\bf 6 5 , 8 [RETURN]}. Press {\bf M}
 to complete the selection. Note to clear the selection press the {\bf[ESC]}
 Press {\bf Q} to mark this position.
 Navigate to column 65, row 8 by pressing {\bf 6 5 , 8 [RETURN]}. Press {\bf M}
 to complete the selection. Note to clear the selection press the {\bf[ESC]}

-key.} \exstep{To create a {\bf group} from the selected the region, click the
-right mouse button when mouse is on the selection, this opens the selection
-popup menu in the alignment window.
+key.}
+\exstep{To create a {\bf group} from the selected the region, click the
+right mouse button when mouse is on the selection, this opens a
+pop-up menu in the alignment window.

 
 Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
 } menu and select `Percentage Identity'.
 
 Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
 } menu and select `Percentage Identity'.

@@ -985,7 +988,7 @@ 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{ Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
 
 \exstep{The current selection can be {\bf exported} and saved by right clicking
 to include newly selected sequences, and the `Percentage Identity' colouring changes. } \exstep{ Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
 
 \exstep{The current selection can be {\bf exported} and saved by right clicking

-on the text area to open the selection popup-menu. Follow the menus and pick an
+on the text area to open the Sequence ID pop-up menu. Follow the menus and pick an

 output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
 \ldots} submenu.
 }
 output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
 \ldots} submenu.
 }

@@ -1069,7 +1072,8 @@ Instead of hiding a group completely, it is sometimes useful to work with just o
 \exercise{Hiding and revealing regions}{
 \exstep{Close all windows, open the PFAM accession PF03460. Select a
 contiguous set of sequences by clicking and dragging on the sequence ID panel.
 \exercise{Hiding and revealing regions}{
 \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}.
+Right click on the selected sequence IDs to bring up the sequence ID pop-up
+menu, select {\sl Hide Sequences}.

 }
 \exstep{
 Right click on the blue triangle indicating hidden sequences and select {\sl
 }
 \exstep{
 Right click on the blue triangle indicating hidden sequences and select {\sl

@@ -1079,17 +1083,17 @@ need to use the alignment window menu option {\sl View $\Rightarrow$ Show $\Righ
 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}.
 }
 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
+\exstep{Repeat the above using columns to hide and reveal 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.}}
 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
+\exstep{Select some sequences and pick one to represent the rest by hovering

 the mouse over this sequence. Bring up the Sequence ID pop-up menu by right
 the mouse over this sequence. Bring up the Sequence ID pop-up menu by right

-clicking and then seelct {\sl (Sequence ID name) $\Rightarrow$ Represent group
+clicking and then select {\sl (Sequence ID name) $\Rightarrow$ Represent group

 with (Sequence ID name )}. To reveal these hidden sequences, right click on the
 with (Sequence ID name )}. To reveal these hidden sequences, right click on the

-Sequence ID and in the the pop-up menu select Reveal All.}}
+Sequence ID and in the pop-up menu select Reveal All.}}

 
 
 
 
 
 

@@ -1101,13 +1105,19 @@ The alignment view provides an interactive editing interface, allowing gaps to b
 \subsubsection{Locked Editing}
 \label{lockededits}
 The Jalview alignment editing model is different to that used in other alignment
 \subsubsection{Locked Editing}
 \label{lockededits}
 The Jalview alignment editing model is different to that used in other alignment

-editors. Because edits are restricted to the insertion and deletion of gaps to the left of a particular sequence position, editing has the effect of shifting the rest of the sequence(s) being edited down or up-stream with respect to the rest of alignment. The {\sl Edit $\Rightarrow$ Pad Gaps} option can be enabled to eliminate `ragged edges' at the end of the alignment, but does not avoid the `knock-on' effect which is sometimes undesirable. However, its effect can be limited by performing the edit within a selected region. In this case, gaps will only be removed or inserted within the selected region. Edits are similarly constrained when they occur adjacent to a hidden column.
+editors. Because edits are restricted to the insertion and deletion of gaps to the left of a particular sequence position, 
+editing has the effect of shifting the rest of the sequence(s) being edited down or up-stream with respect to the rest of 
+alignment. The {\sl Edit $\Rightarrow$ Pad Gaps} option can be enabled to eliminate `ragged edges' at the end of the alignment, 
+but does not avoid the `knock-on' effect which is sometimes undesirable. 
+However, its effect can be limited by performing the edit within a selected region. 
+In this case, gaps will only be removed or inserted within the selected region. 
+Edits are similarly constrained when they occur adjacent to a hidden column.

 
 

-\subsubsection{Introducing Gaps in a Single equence}
+\subsubsection{Introducing Gaps in a Single Sequence}

 
 To introduce a gap, place the cursor on the residue to the immediate right of
 where the gap should appear. Hold down the SHIFT key and the left mouse button,
 
 To introduce a gap, place the cursor on the residue to the immediate right of
 where the gap should appear. Hold down the SHIFT key and the left mouse button,

-then drag the sequence to the right untill the required number of gaps has been inserted.
+then drag the sequence to the right until the required number of gaps has been inserted.

 
 One common error is to forget to hold down [SHIFT]. This results in a selection which is one sequence high and one residue long. Gaps cannot be inserted in such a selection. The selection can be cleared and editing enabled by pressing the [ESC] key.
 
 
 One common error is to forget to hold down [SHIFT]. This results in a selection which is one sequence high and one residue long. Gaps cannot be inserted in such a selection. The selection can be cleared and editing enabled by pressing the [ESC] key.
 

@@ -1156,7 +1166,7 @@ ferredoxin alignment from PF03460.
 }
 
 \exstep{ Select the first 7 sequences, and press H to hide them (or right click
 }
 
 \exstep{ Select the first 7 sequences, and press H to hide them (or right click

-on the sequence IDs to open the sequence ID popup menu, and select {\sl Hide
+on the sequence IDs to open the sequence ID pop-up menu, and select {\sl Hide

 Sequences}). }
 
 \exstep{ Select FER3\_RAPSA and FER\_BRANA. Slide the sequences to
 Sequences}). }
 
 \exstep{ Select FER3\_RAPSA and FER\_BRANA. Slide the sequences to

@@ -1236,7 +1246,7 @@ group is dragged to the right with [CTRL] pressed.}
 
 \subsubsection{Editing in Cursor mode}
 
 
 \subsubsection{Editing in Cursor mode}
 

-Gaps can be be easily inserted when in cursor mode (toggled with [F2]) by
+Gaps can be easily inserted when in cursor mode (toggled with [F2]) by

 pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue
 under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then
 press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE]
 pressing [SPACE]. Gaps will be inserted at the cursor, shifting the residue
 under the cursor to the right. To insert {\sl n} gaps type {\sl n} and then
 press [SPACE]. To insert gaps into all sequences of a group, use [CTRL]-[SPACE]

@@ -1316,7 +1326,7 @@ Selections or groups can be coloured in two ways. The first is {\sl via} the Ali
  or the alignment view's ``background colourscheme'' when no selection exists.
 
 The second method is to select sequences and right click mouse to open pop-up
  or the alignment view's ``background colourscheme'' when no selection exists.
 
 The second method is to select sequences and right click mouse to open pop-up

-menu and seelct {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group
+menu and select {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group

 Colour} from context menu options
 (Figure \ref{colgrp}). This only changes the colour of the current selection or group.
 
 Colour} from context menu options
 (Figure \ref{colgrp}). This only changes the colour of the current selection or group.
 

@@ -1370,10 +1380,10 @@ Desktop's preferences.
 }\parbox[c]{3in}{
 \centerline{\includegraphics[width=2.8in]{images/col_byannot.pdf}}}
 
 }\parbox[c]{3in}{
 \centerline{\includegraphics[width=2.8in]{images/col_byannot.pdf}}}
 

-The {\bf per Sequency only} option in the {\bf Colour By Annotation} dialog
+The {\bf per Sequenc only} option in the {\bf Colour By Annotation} dialog

 allows each sequence to be shaded according to sequence associated annotation
 allows each sequence to be shaded according to sequence associated annotation

-rows, such as protein disorder scores. This functionality is described futher in
-Section \ref{protdisorderpred}.
+rows, such as protein disorder scores. This functionality is described further
+in Section \ref{protdisorderpred}.

 
 \subsection{Colour Schemes} 
 
 
 \subsection{Colour Schemes} 
 

@@ -1534,7 +1544,10 @@ The new colour scheme appears in the list of colour schemes in the {\sl Colour}
 
 \section{Alignment Formatting and Graphics Output}
 \label{layoutandoutput}
 
 \section{Alignment Formatting and Graphics Output}
 \label{layoutandoutput}

-Jalview is a WYSIWIG alignment editor. This means that for most kinds of graphics output, the layout that is seen on screen will be the same as what is output in an exported graphics file. It is therefore important to pick the right kind of display layout prior to generating figures. 
+Jalview is a WYSIWIG alignment editor. This means that for most kinds of graphics output, 
+the layout that is seen on screen will be the same as what is outputted in an
+exported graphics file.
+It is therefore important to pick the right kind of display layout prior to generating figures. 

 
 \subsection{Multiple Alignment Views}
 
 
 \subsection{Multiple Alignment Views}
 

@@ -1551,7 +1564,7 @@ Jalview is able to create multiple independent visualizations of the same underl
 \subsection{Alignment Layout}
 Jalview provides two screen layout modes, unwrapped (the default) where the alignment is in one long line across the window, and wrapped, where the alignment is on multiple lines, each the width of the window. Most layout options are controlled by the Format menu option in the alignment window, and control the overall look of the alignment in the view (rather than just a selected region).
 
 \subsection{Alignment Layout}
 Jalview provides two screen layout modes, unwrapped (the default) where the alignment is in one long line across the window, and wrapped, where the alignment is on multiple lines, each the width of the window. Most layout options are controlled by the Format menu option in the alignment window, and control the overall look of the alignment in the view (rather than just a selected region).
 

-\subsubsection{Wrapped alignments}
+\subsubsection{Wrapped Alignments}

 Wrapped alignments can be toggled on and off using the {\sl Format $\Rightarrow$ Wrap} menu option (Figure \ref{wrap}). Note that the annotation lines are also wrapped. Wrapped alignments are great for publications and presentations but are of limited use when working with large numbers of sequences. 
 
 If annotations are not all visible in wrapped mode, expand the alignment window to view them. Note that alignment annotation (see Section \ref{featannot}) cannot be interactively created or edited in wrapped mode, and selection of large regions is difficult. 
 Wrapped alignments can be toggled on and off using the {\sl Format $\Rightarrow$ Wrap} menu option (Figure \ref{wrap}). Note that the annotation lines are also wrapped. Wrapped alignments are great for publications and presentations but are of limited use when working with large numbers of sequences. 
 
 If annotations are not all visible in wrapped mode, expand the alignment window to view them. Note that alignment annotation (see Section \ref{featannot}) cannot be interactively created or edited in wrapped mode, and selection of large regions is difficult. 

@@ -1570,13 +1583,13 @@ If annotations are not all visible in wrapped mode, expand the alignment window
 \parbox[c]{4in}{The text appearance in a view can be modified {\sl via} the {\sl Format $\Rightarrow$ Font\ldots} alignment window menu. This setting applies for all alignment and annotation text except for that displayed in tool-tips. Additionally, font size and spacing can be adjusted rapidly by clicking the middle mouse button and dragging across the alignment window.}
 \parbox[c]{2in}{\centerline{\includegraphics[width=1.75in]{images/font.pdf}}}
 
 \parbox[c]{4in}{The text appearance in a view can be modified {\sl via} the {\sl Format $\Rightarrow$ Font\ldots} alignment window menu. This setting applies for all alignment and annotation text except for that displayed in tool-tips. Additionally, font size and spacing can be adjusted rapidly by clicking the middle mouse button and dragging across the alignment window.}
 \parbox[c]{2in}{\centerline{\includegraphics[width=1.75in]{images/font.pdf}}}
 

-\subsubsection{Numbering and label justification}
+\subsubsection{Numbering and Label Justification}

 Options in the {\sl Format} menu are provided to control the alignment view, and provide a range of options to control the display of sequence and alignment numbering, the justification of sequence IDs and annotation row column labels on the annotation rows shown below the alignment.
 
 Options in the {\sl Format} menu are provided to control the alignment view, and provide a range of options to control the display of sequence and alignment numbering, the justification of sequence IDs and annotation row column labels on the annotation rows shown below the alignment.
 

-\subsubsection{Alignment and Group colouring and appearance}
+\subsubsection{Alignment and Group Colouring and Appearance}

 The display of hidden row/column markers and gap characters can be turned off with {\sl Format $\Rightarrow$ Hidden Markers} and {\sl Format $\Rightarrow$ Show Gaps}, respectively. The {\sl Text} and {\sl Colour Text} option controls the display of sequence text and the application of alignment and group colouring to it. {\sl Boxes } controls the display of the background area behind each residue that is coloured by the applied coloursheme.  
 
 The display of hidden row/column markers and gap characters can be turned off with {\sl Format $\Rightarrow$ Hidden Markers} and {\sl Format $\Rightarrow$ Show Gaps}, respectively. The {\sl Text} and {\sl Colour Text} option controls the display of sequence text and the application of alignment and group colouring to it. {\sl Boxes } controls the display of the background area behind each residue that is coloured by the applied coloursheme.  
 

-\subsubsection{Highlighting nonconserved symbols}
+\subsubsection{Highlighting Nonconserved Symbols}

 The alignment layout and group sub-menu both contain an option to hide
 conserved symbols from the alignment display ({\sl Format $\Rightarrow$ Show
 nonconserved } in the alignment window or {\sl Selection $\Rightarrow$ Group
 The alignment layout and group sub-menu both contain an option to hide
 conserved symbols from the alignment display ({\sl Format $\Rightarrow$ Show
 nonconserved } in the alignment window or {\sl Selection $\Rightarrow$ Group

@@ -1591,9 +1604,9 @@ column, and render all others with a `.'.
 The annotation lines which appear below the sequence alignment are described in
 detail in Section \ref{featannot}. They can be hidden by toggling the {\sl View
 $\Rightarrow$ Show Annotations} menu option. Additionally, each annotation line
 The annotation lines which appear below the sequence alignment are described in
 detail in Section \ref{featannot}. They can be hidden by toggling the {\sl View
 $\Rightarrow$ Show Annotations} menu option. Additionally, each annotation line

-can be hidden and revealed in the same way as sequences {\sl via} the context menu on
-the annotation name panel (Figure \ref{annot}). Annotations can be reordered by
-dragging the annotation line label on the annotation label panel. Placing the
+can be hidden and revealed in the same way as sequences {\sl via} the
+pop-up context menu on the annotation name panel (Figure \ref{annot}).
+Annotations can be reordered by dragging the annotation line label on the annotation label panel. Placing the

 mouse over the top annotation label brings up a resize icon on the left. When this is
 displayed, Click-dragging up and down provides more space in the alignment window for viewing the annotations, and less space for the sequence alignment.
 
 mouse over the top annotation label brings up a resize icon on the left. When this is
 displayed, Click-dragging up and down provides more space in the alignment window for viewing the annotations, and less space for the sequence alignment.
 

@@ -1609,11 +1622,19 @@ View} menu (left) or individually from the context menu (right).}
 
 \exercise{Alignment Layout}{
 \label{exscreen}
 
 \exercise{Alignment Layout}{
 \label{exscreen}

-\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jar}. Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu. Experiment with the various options from the {\sl Format} menu. to adjust the ruler placement, sequence ID format and so on. }
+\exstep{Start Jalview and open the URL \textsf{http://www.jalview.org/examples/exampleFile.jar}. 
+Select {\sl Format $\Rightarrow$ Wrap} from the alignment window menu. 
+Experiment with the various options from the {\sl Format} menu, for example adjust the ruler placement, 
+sequence ID format and so on. }

 \exstep{Hide all the annotation rows by selecting {\sl View $\Rightarrow$ Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.} 
 \exstep{Hide all the annotation rows by selecting {\sl View $\Rightarrow$ Show Annotations} from the alignment window menu. Reveal the annotations by selecting the same menu option.} 

-\exstep{{\bf Deselect} {\sl Format $\Rightarrow$ Wrap}, and right click on the annotation row labels to bring up the context menu.  Select {\sl Hide This Row}. Bring up the context menu again and select {\sl Show All Hidden Rows} to reveal them}
+\exstep{Deselect {\sl Format $\Rightarrow$ Wrap}. Right click on the
+annotation row labels to bring up the pop-up context menu, then select {\sl
+Hide This Row}. Bring up the pop-up context menu again and select {\sl
+Show All Hidden Rows} to reveal them.}

 \exstep{Annotations can be reordered by clicking and dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}. The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot} below.}
 \exstep{Annotations can be reordered by clicking and dragging the row to the desired position. Click on the {\sl Consensus} row and drag it upwards to just above {\sl Quality}. The rows should now be reordered. Features and annotations are covered in more detail in Section \ref{featannot} below.}

-\exstep{Move the mouse to the top left hand corner of the Secondary Structure annotation row label - a grey up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed by Clicking and dragging the mouse up or down.}
+\exstep{Move the mouse to the top left hand corner of the Secondary Structure annotation row label - 
+a grey up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed 
+by clicking and dragging the mouse up or down.}

 }
 
 \subsection{Graphical Output}
 }
 
 \subsection{Graphical Output}

@@ -1643,9 +1664,17 @@ For submission of alignment figures to journals, please use EPS\footnote{If the
 }
 \parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_png.pdf}} \par \centerline{Zoom Detail of PNG image.}}
  \exercise{Graphical Output}{
 }
 \parbox[c]{3.5in}{\centerline{\includegraphics[width=3in]{images/image_png.pdf}} \par \centerline{Zoom Detail of PNG image.}}
  \exercise{Graphical Output}{

-\exstep{Load the example Jalview Jar file in Exercise \ref{exscreen}. Customise it how you wish but leave it unwrapped. Select {\sl File $\Rightarrow$ Export Image $\Rightarrow$ HTML} from the alignment menu. Save the file and open it in your favourite web browser.  }
-\exstep{Now wrap the alignment and export the image to HTML again. Compare the two images. Note that the exported image matches the format displayed in the alignment window but {\bf annotations are not exported}.}
-\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ PNG} menu option. Open the file in an image viewer that allows zooming such as Paint or Photoshop (Windows), or Preview (Mac OS X) and zoom in. Notice that the image is a bitmap and it becomes pixelated very quickly. Note also that the {\bf annotation lines are included} in the image.}
+\exstep{Load the example Jalview Jar file in Exercise \ref{exscreen}. 
+Customise it how you wish but leave it unwrapped. 
+Select {\sl File $\Rightarrow$ Export Image $\Rightarrow$ HTML} from the alignment menu. 
+Save the file and open it in your favoured web browser.  }
+\exstep{Wrap the alignment and export the image to HTML again. Compare the two
+images. (Note that the exported image matches the format displayed in the
+alignment window but {\bf annotations are not exported}).}
+\exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ PNG} menu option. 
+Open the file in an image viewer that allows zooming such as Paint or Photoshop (Windows), or Preview (Mac OS X) and zoom in. 
+Notice that the image is a bitmap and it becomes pixelated very quickly. 
+(Note that the {\bf annotation lines are included} in the image.)}

 \exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image
 $\Rightarrow$ EPS} menu option. Open the file in a suitable program such as
 Photoshop, Illustrator, Inkscape, Ghostview, Powerpoint (Windows), or
 \exstep{Export the alignment using the {\sl File $\Rightarrow$ Export Image
 $\Rightarrow$ EPS} menu option. Open the file in a suitable program such as
 Photoshop, Illustrator, Inkscape, Ghostview, Powerpoint (Windows), or