replaced all instances of 'dialogue' with 'dialog'.

shortened 'a video about this exercise' to 'See the video at' for all exercises.
fixed database fetcher exercise.
moved undoing edits to top of 'introducing gaps' section, reordered exercises.
tidied up for Kira's comments up to end chapter 3.
Tidied up chapter 3 summary.

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index d5c0951..a51cab1 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -74,7 +74,7 @@ Exercise \theecount  :  #1  }
 
 {\Huge
  
 
 {\Huge
  

-Jalview 2.10.00}
+Jalview 2.10.0}

 \vspace{0.5in}
 {\huge 
 
 \vspace{0.5in}
 {\huge 
 

@@ -344,7 +344,7 @@ when new articles are available from the Jalview Desktop's news channel.}
 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.}
 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
+\exstep {Dialog 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 {\sl Open}. (Note you may be asked to update Java, if you agree
 then it will automatically update the Java software). As Jalview opens, four demo
 will open and ask if you want to open the jalview.jnlp file as the file is an application downloaded from the
 Internet, click {\sl Open}. (Note you may be asked to update Java, if you agree
 then it will automatically update the Java software). As Jalview opens, four demo

@@ -355,7 +355,7 @@ its 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'

-dialogue box opens, untick the box adjacent to the `Open file' entry in the
+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
 `Visual' preferences tab.
 Click {\sl OK} to save the preferences.}
 \exstep{Launch another Jalview workbench from the web site by clicking on the

@@ -376,7 +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 the jnlp file will allow Jalview to be launched offline.
 
 may want to move this from the downloads folder to another folder.
 Opening from the jnlp file will allow Jalview to be launched offline.
 

-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:

 \url{http://www.jalview.org/Help/Getting-Started}.}
  }
 
 \url{http://www.jalview.org/Help/Getting-Started}.}
  }
 

@@ -471,7 +471,7 @@ usual `close' icon (indicated by arrows on Mac OS X). If you want to close all
 the alignments and analysis windows at once, then use the {\sl Window
 $\Rightarrow$ Close All} option from the Jalview desktop.
 
 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
+{\bf \em{Warning: Make sure you have saved your work because this cannot be

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

@@ -538,7 +538,8 @@ column 13 by typing {\bf 1 3 , 5} [RETURN].}
 Documentation window. Select topic from the navigation panel on the left hand side or use the
 Search tab to select specific key words.
 
 Documentation window. Select topic from the navigation panel on the left hand side or use the
 Search tab to select specific key words.
 

-{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
+{\sl\bf See the video at: 
+\url{http://www.jalview.org/Help/Getting-Started}.}

 }
 
 \section{Loading Sequences and Alignments}
 }
 
 \section{Loading Sequences and Alignments}

@@ -610,11 +611,11 @@ Documents such as those produced by Microsoft Word cannot be readily understood
 by Jalview. The way to read sequences from these documents is to select the
 data from the document and copy it to the clipboard. There are two ways to
 do this. One is to right-click on the desktop background, and select the
 by Jalview. The way to read sequences from these documents is to select the
 data from the document and copy it to the clipboard. There are two ways to
 do this. One is to right-click on the desktop background, and select the

-`Paste to new alignment' option in the menu that appears. The other is to select
+`Paste to new window' option in the menu that appears. The other is to select

 {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the
 {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the

-main menu, and paste the sequences into the textbox window that will appear
-(Figure \ref{loadtext}). In both cases, presuming that they are in the right
-format, Jalview will happily read them into a new alignment window.
+main menu, paste the sequences into the text window that will appear, and select
+{sl New Window} (Figure \ref{loadtext}). In both cases, presuming that they are
+in the right format, Jalview will happily read them into a new alignment window.

 %[fig 8]
 
 \begin{figure}[htbp]
 %[fig 8]
 
 \begin{figure}[htbp]

@@ -703,8 +704,8 @@ download directory and open it in a text editor.)}
 
 \exstep{{\bf The text editor:} (i) Open the alignment.fa file using text editor.
 Copy the sequence text from the file into the clipboard and paste it into the desktop
 
 \exstep{{\bf The text editor:} (i) Open the alignment.fa file using text editor.
 Copy the sequence text from the file into the clipboard and paste it into the desktop

-background by right-clicking and selecting {\sl Paste to New Window} to new
-alignment option.
+background by right-clicking and selecting the {\sl Paste to New Window} menu
+option.

 
 (ii) In the text editor, copy the sequence text from
 alignment.fa  into the clipboard (usually {\sl via} the browser's {\sl Edit
 
 (ii) In the text editor, copy the sequence text from
 alignment.fa  into the clipboard (usually {\sl via} the browser's {\sl Edit

@@ -717,38 +718,38 @@ Paste} text box menu option. Click {\sl New Window} and the alignment will be
 loaded.}
 
 \exstep{{\bf Loading sequences from Public Database:} (i) Select {\sl File
 loaded.}
 
 \exstep{{\bf Loading sequences from Public Database:} (i) Select {\sl File

-$\Rightarrow$ Fetch Sequence(s)...} from the Desktop to open up new window
-called Select Database Retrieval Source showing all the database
-sources. Select the {\bf PFAM seed} database and click {\sl OK}.
-
-(ii)This opens another window called New Sequence Fetcher, enter the
-accession number {\bf PF03460} and click {\sl OK}. An alignment of about 174 sequences should
-load.}
+$\Rightarrow$ Fetch Sequence(s)...} from the Desktop. The {\sl Select Database
+Retrieval Source} dialog will open showing all the database sources. Select the
+{\bf PFAM seed} database and click {\sl OK}.
+
+(ii)Once a source has been selected, 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.}
 Several database IDs can be loaded by using semicolons to separate them.}
 \exstep{These can be viewed using the Overview window accessible from {\sl View
 $\Rightarrow$ Overview Window.}
 Several database IDs can be loaded by using semicolons to separate them.}

-{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
-}
+{\bf See the video at:
+\url{http://www.jalview.org/Help/Getting-Started}} }

 
 \section{Saving Sequences and Alignments}
 \label{savingalignments} 
 
 \section{Saving Sequences and Alignments}
 \label{savingalignments} 

-\subsection{Saving Alignments} Jalview allows the
-current sequence alignments to be saved to file so they can be restored at a
-later date, passed to colleagues or analysed in other programs. From the
-alignment window menu select {\sl File $\Rightarrow$ Save As} and a dialog box
+\subsection{Saving Alignments} Jalview allows alignments to be saved to file
+in a variety of formats so they can be restored at a later date, passed to
+colleagues or analysed in other programs. From the alignment window menu select {\sl File $\Rightarrow$ Save As} and a dialog box

 will appear (Figure \ref{savealign}). You can navigate to an appropriate
 directory in which to save the alignment. Jalview will remember the last filename
 and format used to save (or load) the alignment, enabling you to quickly save
 will appear (Figure \ref{savealign}). You can navigate to an appropriate
 directory in which to save the alignment. Jalview will remember the last filename
 and format used to save (or load) the alignment, enabling you to quickly save

-the file during or after editing by using the {\sl File $\Rightarrow$ Save} entry.
+the file during or after editing by using the {\sl File $\Rightarrow$ Save}
+entry. The {\sl File $\Rightarrow$ Output To Textbox} menu option allows the alignment to be copied and pasted into
+other documents or web servers.

 
 

-Jalview offers several different formats in which an alignment can be saved. The
-jalview format (.jar) is the only format which will preserve the colours,
-groupings and other additional information in the alignment. The other formats
+Jalview offers several different formats in which an alignment can be saved.
+Of these, only the jalview project format (.jar or .jvp) will preserve the colours, groupings and other additional information in the alignment. The other formats

 produce text files containing just the sequences with no visualization information, although some
 allow limited annotation and sequence features to be stored (e.g. AMSA).
 produce text files containing just the sequences with no visualization information, although some
 allow limited annotation and sequence features to be stored (e.g. AMSA).

-Unfortunately only Jalview can read Jalview files. The {\sl File
-$\Rightarrow$ Output To Textbox} menu option allows the alignment to be copied and pasted into
-other documents or web servers.
+Unfortunately, as far as we are aware only Jalview can read Jalview
+project files.

 
 %[fig 10]
 \begin{figure}[htbp]
 
 %[fig 10]
 \begin{figure}[htbp]

@@ -769,8 +770,8 @@ other documents or web servers.
 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
 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

-Jalview when working with large alignments in Jalview projects. See Section \protect
-\ref{memorylimits} above for how to do this.}
+Jalview when working with large alignments in Jalview projects. See Section 
+\ref{memorylimits} for how to do 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,
 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,

@@ -808,7 +809,7 @@ suitable folder.}
 \exstep{Close all windows and then load the project {\sl via} the {\sl File
 $\Rightarrow$ Load Project} menu option. Observe how all the windows and
 positions are exactly as they were when they were saved. } 
 \exstep{Close all windows and then load the project {\sl via} the {\sl File
 $\Rightarrow$ Load Project} menu option. Observe how all the windows and
 positions are exactly as they were when they were saved. } 

-{\bf A video about this exercise is available on the Jalview website at \url{http://www.jalview.org/Help/Getting-Started}.}
+{\bf See the video at: \url{http://www.jalview.org/Help/Getting-Started}.}

 }
 
 
 }
 
 

@@ -927,19 +928,21 @@ button on the selection to bring up a context menu. Select {\sl Selection
 $\Rightarrow$ Group $\Rightarrow$ Edit name and description of
 current group}\footnote{In earlier versions of Jalview, this entry was variously
 `Group', `Edit Group Name', or `JGroupXXXXX' (Where XXXXX was some serial
 $\Rightarrow$ Group $\Rightarrow$ Edit name and description of
 current group}\footnote{In earlier versions of Jalview, this entry was variously
 `Group', `Edit Group Name', or `JGroupXXXXX' (Where XXXXX was some serial

-number).} then enter a name for the group in the dialogue box which appears.
+number).} then enter a name for the group in the dialog box which appears.

 
 By default the new group will have a box drawn around it. The appearance of the group can be changed (see Section \ref{colours} below). This group will stay defined even when the selection is removed.
 
 \exercise{Making Selections and Groups}{
 \label{exselect}
 \exstep{Close windows.
 
 By default the new group will have a box drawn around it. The appearance of the group can be changed (see Section \ref{colours} below). This group will stay defined even when the selection is removed.
 
 \exercise{Making Selections and Groups}{
 \label{exselect}
 \exstep{Close windows.

+

 Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM seed} database).
 Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM seed} database).

-Choose a residue and  place the mouse
+}
+\exstep{Selecting an arbitrary region. Choose a residue and place the mouse

 cursor on it (residue information will show in alignment window status
 bar).
 cursor on it (residue information will show in alignment window status
 bar).

-Click and drag the mouse to create a selection. As you drag, a red box
-will `rubber band' out to 
+Click and drag the mouse to the bottom-right to create a selection. As you drag,
+a red box will `rubber band' out to 

 show the extent of the selection.
 Release the mouse
 button and a red box borders the selected region.
 show the extent of the selection.
 Release the mouse
 button and a red box borders the selected region.

@@ -949,13 +952,13 @@ the sequence ID panel. Note that the sequence ID takes on a highlighted
 background and a red box appears around the selected sequence. 
 Hold down [SHIFT] and click another sequence ID a few positions above or below. 
 Note how the selection expands to include all the sequences between the two positions on which you clicked.
 background and a red box appears around the selected sequence. 
 Hold down [SHIFT] and click another sequence ID a few positions above or below. 
 Note how the selection expands to include all the sequences between the two positions on which you clicked.

-Hold down [CTRL] and then click on several sequences ID's both selected and
+Hold down [CTRL] and then click on several sequences' IDs - both selected and

 unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are 
 individually deselected.}
 unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are 
 individually deselected.}

-\exstep{ Select column by clicking on the Alignment Ruler. Note whole
-column is highlighted with a red box.
-Hold down [SHIFT] and click column beyond. Note the selection expands to include
-all the sequences between the two positions on which you clicked.}
+\exstep{ Select columns by clicking on the Alignment Ruler. Note
+that the selected column is marked with a red box.
+Hold down [SHIFT] and click a column beyond. Note the selection expands to
+include all the sequences between the two positions on which you clicked.}

 
 \exstep{Enter Cursor mode using [F2], or [Fn]-F2 for Macs.
 Navigate to column 59, row 1 by pressing {\bf 5 9 , 1 [RETURN]}.
 
 \exstep{Enter Cursor mode using [F2], or [Fn]-F2 for Macs.
 Navigate to column 59, row 1 by pressing {\bf 5 9 , 1 [RETURN]}.

@@ -981,10 +984,10 @@ 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.
 }
 menus 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, manually edit the
-alignment before clicking the {\sl New Window} button, this opens the
-edited alignment in a new alignment window.} {\bf A video about this exercise is
-available on the Jalview website at \url{http://www.jalview.org/training/Training-Videos}.}
+\exstep{In the Alignment output window that opens, try manually editing the
+alignment before clicking the {\sl New Window} button. This opens the
+edited alignment in a new alignment window.} {\bf See the video at:
+\url{http://www.jalview.org/training/Training-Videos}.}

 % more? change colouring style. set border colour.
 }
 
 % more? change colouring style. set border colour.
 }
 

@@ -1019,8 +1022,7 @@ this will not work in cursor mode)}
 sequences, use hold [SHIFT], and select two sequences separated by
 one or more un-selected sequences, repeat using the [CTRL] key. Note how
 multiple sequences are grouped together when they are re-ordered using the up and down arrow keys.}
 sequences, use hold [SHIFT], and select two sequences separated by
 one or more un-selected sequences, repeat using the [CTRL] key. Note how
 multiple sequences are grouped together when they are re-ordered using the up and down arrow keys.}

-{\bf A video about this exercise is available on the Jalview website
-at \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}

 }
 
 
 }
 
 

@@ -1083,8 +1085,9 @@ need to use the alignment window menu option {\sl View $\Rightarrow$ Show $\Righ
 All Sequences.}) }
 \exstep{
 Repeat the process but use a non-contiguous set of sequences. Note that when
 All Sequences.}) }
 \exstep{
 Repeat the process but use a non-contiguous set of sequences. Note that when

-multiple regions are hidden you may prefer to select {\sl
-Reveal Sequences} rather than {\sl Reveal All} option.
+multiple regions are hidden you can select either {\sl
+Reveal Sequences} to reveal the hidden sequences that were clicked, or {\sl
+Reveal All}.

 }
 \exstep{Repeat the above using columns to hide and reveal columns
 instead of sequences.}
 }
 \exstep{Repeat the above using columns to hide and reveal columns
 instead of sequences.}

@@ -1095,8 +1098,7 @@ 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
 Sequence ID and in the context menu select {\sl Reveal All}.}
 clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
 with (Sequence ID name )}. To reveal these hidden sequences, right click on the
 Sequence ID and in the context menu select {\sl Reveal All}.}

-{\bf A video about this exercise is available on the Jalview website
-at \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at:  \url{http://www.jalview.org/training/Training-Videos}.}

 }
 
 
 }
 
 

@@ -1123,6 +1125,16 @@ group is dragged to the right with [CTRL] pressed.}
 \section{Introducing and Removing Gaps}
 The alignment view provides an interactive editing interface, allowing gaps to be inserted or deleted to the left of any position in a sequence or sequence group. Alignment editing can only be performed whilst in keyboard editing mode (entered by pressing [F2]) or by clicking and dragging residues with the mouse when [SHIFT] or [CTRL] is held down (which differs from earlier versions of Jalview).
 
 \section{Introducing and Removing Gaps}
 The alignment view provides an interactive editing interface, allowing gaps to be inserted or deleted to the left of any position in a sequence or sequence group. Alignment editing can only be performed whilst in keyboard editing mode (entered by pressing [F2]) or by clicking and dragging residues with the mouse when [SHIFT] or [CTRL] is held down (which differs from earlier versions of Jalview).
 

+
+\subsection{Undoing Edits}
+Alignment edits can be undone {\sl via} the {\sl Edit $\Rightarrow$ Undo Edit}
+alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied
+with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the
+{\sl Undo} function only works for edits to the alignment or sequence ordering.
+Colouring of the alignment, showing and hiding of sequences or modification of
+annotation that only affect the alignment's display cannot
+be undone.
+

 \subsection{Locked Editing}
 \label{lockededits}
 The Jalview alignment editing model is different to that used in other alignment
 \subsection{Locked Editing}
 \label{lockededits}
 The Jalview alignment editing model is different to that used in other alignment

@@ -1158,6 +1170,22 @@ within a larger alignment.
 % % better idea to introduce hiding sequences, and use the invert selection, hide
 % others, to simplify manual alignment construction
 
 % % better idea to introduce hiding sequences, and use the invert selection, hide
 % others, to simplify manual alignment construction
 

+\subsection{Editing in Cursor mode}
+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]
+or [SHIFT]-[SPACE] (both keys held down together).
+
+Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you
+have everything unselected by pressing ESC. The gap under the cursor will be
+removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps
+will be deleted up to the number specified. To delete gaps from all sequences of
+a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down
+together). Note that the deletion will only occur if the gaps are in the same
+columns in all sequences in the selected group, and those columns are to the
+right of the selected residue.
+

 \exercise{Editing Alignments}
   %\label{mousealedit}
 % TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
 \exercise{Editing Alignments}
   %\label{mousealedit}
 % TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF

@@ -1166,8 +1194,8 @@ alignment available at
  \href{http://www.jalview.org/examples/exampleFile.jar}
  {http://www.jalview.org/examples/exampleFile.jar}.
 
  \href{http://www.jalview.org/examples/exampleFile.jar}
  {http://www.jalview.org/examples/exampleFile.jar}.
 

-{\sl Note: If you are using OSX, and a key combination - such as [CTRL]-A - does
- not work, then try the [CMD] key instead of [CTRL].}
+{\sl {\bf Mac Users: Please use the Apple or [CMD] key in place of [CTRL]
+for key combinations such as [CTRL]-A.} }

 
 Remember to use [CTRL]-Z to undo an edit, or the {\sl File $\Rightarrow$
  Reload } function to revert the alignment back to the original version if you
 
 Remember to use [CTRL]-Z to undo an edit, or the {\sl File $\Rightarrow$
  Reload } function to revert the alignment back to the original version if you

@@ -1234,21 +1262,6 @@ option, or their keyboard shortcuts ([CTRL]-Z and [CTRL]-Y) to step
 backwards and replay the edits you have made.}
 }
 
 backwards and replay the edits you have made.}
 }
 

-\subsection{Editing in Cursor mode}
-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]
-or [SHIFT]-[SPACE] (both keys held down together).
-
-Gaps can be removed in cursor mode by pressing [BACKSPACE]. First make sure you
-have everything unselected by pressing ESC. The gap under the cursor will be
-removed. To remove {\sl n} gaps, type {\sl n} and then press [BACKSPACE]. Gaps
-will be deleted up to the number specified. To delete gaps from all sequences of
-a group, press [CTRL]-[BACKSPACE] or [SHIFT]-[BACKSPACE] (both keys held down
-together). Note that the deletion will only occur if the gaps are in the same
-columns in all sequences in the selected group, and those columns are to the
-right of the selected residue.

 
 \exercise{Keyboard Edits}
 {This continues on from the previous exercise, and recreates the final part of the example ferredoxin
 
 \exercise{Keyboard Edits}
 {This continues on from the previous exercise, and recreates the final part of the example ferredoxin

@@ -1287,14 +1300,6 @@ Press {\sl 34C [BACKSPACE]  38C 2 [SPACE]}. Delete three gaps at column 44 and
 insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}.  The top five sequences are 
 now aligned.}}
 
 insert one at column 47 by pressing {\sl 44C 3 [BACKSPACE] 47C [SPACE]}.  The top five sequences are 
 now aligned.}}
 

-\section{Undoing Edits}
-Jalview supports the undoing of edits {\sl via} the {\sl Edit $\Rightarrow$ Undo Edit}
-alignment window menu option, or CTRL-Z. An edit, if undone, may be re-applied
-with {\sl Edit $\Rightarrow$ Redo Edit}, or CTRL-Y. Note, however, that the
-{\sl Undo} function only works for edits to the alignment or sequence ordering.
-Colouring of the alignment, showing and hiding of sequences or modification of
-annotation cannot be undone.
-

 \chapter{Colouring Sequences and Figure Generation}
 \label{colouringfigures}
 \section{Colouring Sequences}
 \chapter{Colouring Sequences and Figure Generation}
 \label{colouringfigures}
 \section{Colouring Sequences}

@@ -1510,9 +1515,10 @@ secondary structure row is present on the alignment.
 
 \exercise{Colouring Alignments}{
 \label{color}
 
 \exercise{Colouring Alignments}{
 \label{color}

-Note: Ensuring that the {\sl Apply Colour To All Groups} flag is not
-selected in {\sl Colour} menu in the alignment window.
-This must be turned {\sl off} specifically as it is on by default.
+Note: Before you begin this exercise, ensure that the {\sl Apply Colour
+To All Groups} flag is not selected 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.

 
 \exstep{Open a sequence alignment, for example the PFAM domain PF03460 in PFAM
 seed database. Select the alignment menu option {\sl Colour $\Rightarrow$
 
 \exstep{Open a sequence alignment, for example the PFAM domain PF03460 in PFAM
 seed database. Select the alignment menu option {\sl Colour $\Rightarrow$

@@ -1529,17 +1535,16 @@ not the whole alignment (this also explains the colouring changes observed in ex
 \exstep{Keeping the same selection as before, colour the complete alignment except
 the group using {\sl Colour  $\Rightarrow$ Taylor}.
 Select the menu option  {\sl Colour  $\Rightarrow$ By Conservation}. 
 \exstep{Keeping the same selection as before, colour the complete alignment except
 the group using {\sl Colour  $\Rightarrow$ Taylor}.
 Select the menu option  {\sl Colour  $\Rightarrow$ By Conservation}. 

-Slide the selector in the Conservation Colour Increment dialogue box from side
+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. The features colours can be
 toggled off by going to {\sl View  $\Rightarrow$ Show Sequence Features}.
 
 to side and observe the changes in the alignment colouring in the selection and in the complete alignment.}
 Note: Feature colours overlay residue colouring. The features colours can be
 toggled off by going to {\sl View  $\Rightarrow$ Show Sequence Features}.
 

-{\bf A video about this exercise is
-available on the Jalview website at \url{http://www.jalview.org/training/Training-Videos}.}
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}

 }
 
 \subsubsection{User Defined}
 }
 
 \subsubsection{User Defined}

-This dialogue allows the user to create any number of named colour schemes at will. Any residue may be assigned any colour. The colour scheme can then be named. If you save the colour scheme, this name will appear on the Colour menu (Figure \ref{usercol}).
+This dialog allows the user to create any number of named colour schemes at will. Any residue may be assigned any colour. The colour scheme can then be named. If you save the colour scheme, this name will appear on the Colour menu (Figure \ref{usercol}).

 
 
 \begin{figure}[htbp]
 
 
 \begin{figure}[htbp]

@@ -1554,12 +1559,12 @@ This dialogue allows the user to create any number of named colour schemes at wi
 
 
 \exercise{User Defined Colour Schemes}{
 
 
 \exercise{User Defined Colour Schemes}{

-\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialogue window will open.}
+\exstep{Load a sequence alignment. Select the alignment menu option {\sl Colour $\Rightarrow$ User Defined}. A dialog window will open.}

 \exstep{Click on an amino acid button, then select a colour for that amino acid. Repeat till all amino acids are coloured to your liking.}
 \exstep{Click on an amino acid button, then select a colour for that amino acid. Repeat till all amino acids are coloured to your liking.}

-\exstep{ Insert a name for the colourscheme in the appropriate field and click {\sl Save Scheme}. You will be prompted for a file name in which to save the colour scheme. The dialogue window can now be closed.}
+\exstep{ Insert a name for the colourscheme in the appropriate field and click {\sl Save Scheme}. You will be prompted for a file name in which to save the colour scheme. The dialog window can now be closed.}

 \exstep{The new colour scheme appears in the list of colour schemes in the {\sl Colour} menu and can be selected in future Jalview sessions.
 
 \exstep{The new colour scheme appears in the list of colour schemes in the {\sl Colour} menu and can be selected in future Jalview sessions.
 

-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:

 \url{http://www.jalview.org/training/Training-Videos}.}} }
 
 \section{Formatting and Graphics Output}
 \url{http://www.jalview.org/training/Training-Videos}.}} }
 
 \section{Formatting and Graphics Output}

@@ -1704,30 +1709,37 @@ Preview (Mac OS X). Zoom in and note that the image has near-infinite
 resolution.} 
 }
 
 resolution.} 
 }
 

-The next chapters introduce Jalview's analysis features. Chapter \ref{featannot}
-describes the mechanisms provided by Jalview for interactive creation of sequence and alignment annotation, and how they can be displayed, 
-imported and exported and used to reorder the alignment. Chapter
-\ref{featuresfromdb} discusses the retrieval of database references and
-establishment of sequence coordinate systems for the retrieval and display of
-features from databases.
-Chapter \ref{msaservices} describes how to use the range of multiple alignment
-programs provided by JABAWS, and Chapter \ref{aacons} introduces JABAWS AACon
-service for protein multiple alignment conservation analysis.
- In Chapter \ref{alignanalysis}, you will find
-descriptions and exercises on building and displaying trees, PCA analysis,
-alignment redundancy removal, pairwise alignments and alignment conservation
-analysis. 
-Chapter \ref{wkwithstructure} introduces the structure visualization
-capabilities of Jalview.
-Chapter \ref{protsspredservices} explains how to perform protein secondary
-structure predictions with JPred, and JABAWS protein disorder prediction
-services are introduced in Chapter \ref{protdisorderpred}.
-Chapter \ref{workingwithnuc} describes functions and visualization techniques relevant
-to working with nucleotide sequences, coding region annotation and nucleotide
-sequence alignments.
-Chapter \ref{jvwebservices} introduces the various web based services
-available to Jalview users, and Chapter \ref{jabaservices} explains how to
-configure the Jalview Desktop for access to new JABAWS servers.
+\newpage
+
+\section{Summary - the rest of the manual}
+
+The first few chapters have covered the basics of Jalview operation: from
+starting the program, importing, exporting, selecting, editing and colouring
+aligments, to the generation of figures for publication, presentation and web
+pages.
+
+The remaining chapters in the manual cover:
+
+\begin{list}{$\circ$}{}
+\item{Chapter \ref{featannot} covers the creation, manipulation and visualisation
+of sequence and alignment annotation, and retrieval of sequence and feature data
+from databases.}
+\item {Chapter \ref{msaservices} explores the range of multiple alignment
+programs offered via Jalview's web services, and introduces the use of
+AACon for protein multiple alignment conservation analysis.}
+\item {Chapter \ref{alignanalysis} introduces Jalview's built in tools for
+multiple sequence alignment analysis, including trees, PCA, and alignment
+conservation analysis. }
+\item {Chapter \ref{3Dstructure} demonstrates the structure visualization
+capabilities of Jalview.}
+\item {Chapter \ref{proteinprediction} introduces protein sequence based
+secondary structure and disorder prediction tools, including JPred.}
+\item {Chapter \ref{dnarna} covers the special functions and
+visualization techniques for working with RNA alignments and protein coding
+sequences.}
+\item {Chapter \ref{jvwebservices} provides instructions on the
+installation of your own Jalview web services.}
+\end{list}

 
 \chapter{Annotation and Features}
 \label{featannot}
 
 \chapter{Annotation and Features}
 \label{featannot}

@@ -1804,11 +1816,11 @@ alignment window.
 \subsection{Creating User Defined Annotation}
 
 To create a new annotation row, right click on the annotation label panel and select the {\sl Add New Row} menu option (Figure \ref{newannotrow}).
 \subsection{Creating User Defined Annotation}
 
 To create a new annotation row, right click on the annotation label panel and select the {\sl Add New Row} menu option (Figure \ref{newannotrow}).

-A dialogue box appears. Enter the label to use for this row and a new row will appear.
+A dialog box appears. Enter the label to use for this row and a new row will appear.

 
 To create a new annotation, first select all the positions to be annotated on the appropriate row. 
 Right-clicking on this selection brings up the context menu which allows the insertion of graphics for secondary structure ({\sl Helix} or {\sl Sheet}), 
 
 To create a new annotation, first select all the positions to be annotated on the appropriate row. 
 Right-clicking on this selection brings up the context menu which allows the insertion of graphics for secondary structure ({\sl Helix} or {\sl Sheet}), 

-text {\sl Label} and the colour in which to present the annotation (Figure \ref{newannot}). On selecting {\sl Label} a dialogue box will appear, 
+text {\sl Label} and the colour in which to present the annotation (Figure \ref{newannot}). On selecting {\sl Label} a dialog box will appear, 

 requesting the text to place at that position. After the text is entered, the selection can be removed and the annotation becomes clearly 
 visible\footnote{When annotating a block of positions, the text can be partly obscured by the selection highlight. Pressing the  [ESC] key clears 
 the selection and the label is then visible.}. Annotations can be coloured or deleted as desired.
 requesting the text to place at that position. After the text is entered, the selection can be removed and the annotation becomes clearly 
 visible\footnote{When annotating a block of positions, the text can be partly obscured by the selection highlight. Pressing the  [ESC] key clears 
 the selection and the label is then visible.}. Annotations can be coloured or deleted as desired.

@@ -1855,7 +1867,7 @@ calculations can be found in the on-line documentation.
 \exercise{Annotating Alignments}{
 \exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. 
 Right-click on the {\sl Conservation} annotation row to
 \exercise{Annotating Alignments}{
 \exstep{Load the alignment at \textsf{http://www.jalview.org/tutorial/alignment.fa}. 
 Right-click on the {\sl Conservation} annotation row to

-bring up the context menu and select {\sl Add New Row}. A dialogue box will
+bring up the context menu and select {\sl Add New Row}. A dialog box will

 appear asking for {\sl Annotation Name} and {\sl Annotation Description}.
 Enter ``Iron binding site" and click {\sl OK}. A new, empty, row appears.
 }
 appear asking for {\sl Annotation Name} and {\sl Annotation Description}.
 Enter ``Iron binding site" and click {\sl OK}. A new, empty, row appears.
 }

@@ -1865,7 +1877,7 @@ Navigate to column 97. Move down and on the new annotation row called
 Right click at this selection and select {\sl Label} from the context menu.
 Enter ``Fe" in the box and click {\sl OK}. Right-click on the selection again
 and select {\sl Colour}.
 Right click at this selection and select {\sl Label} from the context menu.
 Enter ``Fe" in the box and click {\sl OK}. Right-click on the selection again
 and select {\sl Colour}.

-Choose a colour from the colour chooser dialogue 
+Choose a colour from the colour chooser dialog 

 and click {\sl OK}. Press [ESC] to remove the selection.
 }
 \exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the
 and click {\sl OK}. Press [ESC] to remove the selection.
 }
 \exstep{ Select columns 70-77 on the annotation row. Right-click and choose {\sl Sheet} from the

@@ -2078,7 +2090,7 @@ create the new alignment ordering.
 % }
 
 \subsection{Creating Sequence Features}
 % }
 
 \subsection{Creating Sequence Features}

-Sequence features can be created simply by selecting the area in a sequence (or sequences) to form the feature and selecting {\sl Selection $\Rightarrow$ Create Sequence Feature } from the right-click context menu (Figure \ref{features}). A dialogue box allows the user to customise the feature with respect to name, group, and colour. The feature is then associated with the sequence. Moving the mouse over a residue associated with a feature brings up a tool tip listing all features associated with the residue.
+Sequence features can be created simply by selecting the area in a sequence (or sequences) to form the feature and selecting {\sl Selection $\Rightarrow$ Create Sequence Feature } from the right-click context menu (Figure \ref{features}). A dialog box allows the user to customise the feature with respect to name, group, and colour. The feature is then associated with the sequence. Moving the mouse over a residue associated with a feature brings up a tool tip listing all features associated with the residue.

 
 \begin{figure}[htbp]
 \begin{center}
 
 \begin{figure}[htbp]
 \begin{center}

@@ -2100,7 +2112,7 @@ $\Rightarrow$ Show Sequence Features} menu option. When multiple features are
 present it is usually necessary to customise the display. Jalview allows the
 display, colour, rendering order and transparency of features to be modified
 {\sl via} the {\sl View $\Rightarrow$ Feature Settings\ldots} menu option. This
 present it is usually necessary to customise the display. Jalview allows the
 display, colour, rendering order and transparency of features to be modified
 {\sl via} the {\sl View $\Rightarrow$ Feature Settings\ldots} menu option. This

-brings up a dialogue window (Figure \ref{custfeat}) which allows the
+brings up a dialog window (Figure \ref{custfeat}) which allows the

 visibility of individual feature types to be selected, colours changed (by
 clicking on the colour of each sequence feature type) and the rendering order
 modified by dragging feature types to a new position in the list. Dragging the
 visibility of individual feature types to be selected, colours changed (by
 clicking on the colour of each sequence feature type) and the rendering order
 modified by dragging feature types to a new position in the list. Dragging the

@@ -2141,7 +2153,7 @@ We know that the Cysteine residues at columns 97, 102, 105 and 135 are involved
 iron binding so we will create them as features. Navigate to column 97, sequence 1. 
 Select the entire column by clicking in the ruler bar. Then right-click on the selection 
 to bring up the context menu and select {\sl Selection $\Rightarrow$ Create Sequence Feature}. 
 iron binding so we will create them as features. Navigate to column 97, sequence 1. 
 Select the entire column by clicking in the ruler bar. Then right-click on the selection 
 to bring up the context menu and select {\sl Selection $\Rightarrow$ Create Sequence Feature}. 

-A dialogue box will appear.
+A dialog box will appear.

 }
 \exstep{
 Enter a suitable Sequence Feature Name  (e.g. ``Iron binding site") in the
 }
 \exstep{
 Enter a suitable Sequence Feature Name  (e.g. ``Iron binding site") in the

@@ -2154,7 +2166,7 @@ To demonstrate that there is one feature per sequence, clear all selections by p
 Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
 }
 \exstep{
 Roll the mouse over the features and you will see that the feature has moved with the sequence. Delete the gap you created.
 }
 \exstep{

-Add a similar feature to column 102. When the feature dialogue box appears, clicking the Sequence Feature 
+Add a similar feature to column 102. When the feature dialog box appears, clicking the Sequence Feature 

 Name box brings up a list of previously described features. Using the same Sequence Feature Name allows the features to be grouped.}
 \exstep{Select {\sl View $\Rightarrow$ Feature Settings\ldots} from the
 alignment window menu. The Sequence Feature Settings window will appear. Move
 Name box brings up a list of previously described features. Using the same Sequence Feature Name allows the features to be grouped.}
 \exstep{Select {\sl View $\Rightarrow$ Feature Settings\ldots} from the
 alignment window menu. The Sequence Feature Settings window will appear. Move

@@ -2293,7 +2305,7 @@ region in the result with the corresponding region of the original alignment.}
 select and hide a few more columns in the N-terminal region, and submit the alignment to the 
 service again and explore the effect of local alignment on the non-homologous parts of the 
 N-terminal region.}
 select and hide a few more columns in the N-terminal region, and submit the alignment to the 
 service again and explore the effect of local alignment on the non-homologous parts of the 
 N-terminal region.}

-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:

 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 
 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 

@@ -2509,7 +2521,7 @@ Place the mouse cursor on the tree window so that the
 tree partition location will divide the alignment into a number of groups, each of a different colour.
 Note how the colour of the sequence ID label matches both the colour of
 the partitioned tree and the points in the PCA plot.} 
 tree partition location will divide the alignment into a number of groups, each of a different colour.
 Note how the colour of the sequence ID label matches both the colour of
 the partitioned tree and the points in the PCA plot.} 

-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:

 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 
 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 

@@ -2650,7 +2662,7 @@ column 60 to sequence 12 column 123. Select  {\sl Calculate $\Rightarrow$ Calcul
 Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the 
 alignment for the calculation of trees.
 
 Comparing the location of individual sequences between the three trees illustrates the importance of selecting appropriate regions of the 
 alignment for the calculation of trees.
 

-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:

 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 
 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 

@@ -2670,7 +2682,7 @@ gaps ensures all the sequences are the same length after editing.}
 can be set in Preferences using
 {\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}.
 
 can be set in Preferences using
 {\sl Tool $\Rightarrow$ Preference $\Rightarrow$ Editing}.
 

-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:

 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 
 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 

@@ -2696,7 +2708,7 @@ BLOSUM62 (whilst ensuring that {\sl Apply Colour to All Groups} is selected).}
 {\sl Note: You may want to save the alignment and tree as a project file, since
 it is used in the next set of exercises. }
 
 {\sl Note: You may want to save the alignment and tree as a project file, since
 it is used in the next set of exercises. }
 

-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:

 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 
 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 

@@ -2815,7 +2827,7 @@ non-adjacent columns.
 both of the columns that you wish to use to subdivide the alignment.}}
 \exstep{Switch back to the original view, and experiment with subdividing
 the tree groups made in the previous exercise.}
 both of the columns that you wish to use to subdivide the alignment.}}
 \exstep{Switch back to the original view, and experiment with subdividing
 the tree groups made in the previous exercise.}

-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:

 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 
 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 

@@ -2966,13 +2978,13 @@ file with any sequences with matching IDs. }
 The structure viewer is launched from the sequence ID context
 menu. To view a particular structure associated with a sequence in the
 alignment, select the sequence and right click the mouse to open context
 The structure viewer is launched from the sequence ID context
 menu. To view a particular structure associated with a sequence in the
 alignment, select the sequence and right click the mouse to open context

-menu {\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$} opens a Structure Chooser dialogue box.
+menu {\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$} opens a Structure Chooser dialog box.

 The second way is most useful if you want to view all structural data available for
 a set of sequences in an alignment. Select all the sequence ids in the sequence
 ID panel and right click the mouse to open context
 menu {\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$}. If any of
 the {\bf currently selected} sequences have structures associated they will
 The second way is most useful if you want to view all structural data available for
 a set of sequences in an alignment. Select all the sequence ids in the sequence
 ID panel and right click the mouse to open context
 menu {\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$}. If any of
 the {\bf currently selected} sequences have structures associated they will

-appear in the Structure Chooser dialogue box. The structures can be ranked by
+appear in the Structure Chooser dialog box. The structures can be ranked by

 different parameters, 'Best Quality' is defaul option. Select the
 structures required and click {\sl View} to open a structure viewer containing
 the associated structures superposed according to the alignment.
 different parameters, 'Best Quality' is defaul option. Select the
 structures required and click {\sl View} to open a structure viewer containing
 the associated structures superposed according to the alignment.

@@ -3104,7 +3116,7 @@ using the {\sl Jmol $\Rightarrow$ Select (n) $\Rightarrow$ All} command (where {
 \exstep{In the alignment window, use the {\sl File $\Rightarrow$ Save As.. }
 function to save the alignment as a Jalview Project. Now close the alignment and the structure view, and load the project file you just saved.
 Verify that the Jmol display is as it was when you just saved the file.}
 \exstep{In the alignment window, use the {\sl File $\Rightarrow$ Save As.. }
 function to save the alignment as a Jalview Project. Now close the alignment and the structure view, and load the project file you just saved.
 Verify that the Jmol display is as it was when you just saved the file.}

-{\bf A video about this exercise is available on the Jalview website at
+{\bf See the video at:

 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 
 \url{http://www.jalview.org/training/Training-Videos}.}
 }
 

@@ -3126,8 +3138,7 @@ Jalview, Chimera should open as the default viewer.}
 the Chimera structure viewer sits outside the Jalview desktop and a Chimera
 view window sits inside the Jalview desktop.}
 
 the Chimera structure viewer sits outside the Jalview desktop and a Chimera
 view window sits inside the Jalview desktop.}
 

-{\bf A video about this exercise is available on the Jalview website at
-\url{http://www.jalview.org/training/Training-Videos}.} }
+{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.} }

 
 \subsection{Superimposing Structures}
 \label{superposestructs}
 
 \subsection{Superimposing Structures}
 \label{superposestructs}

@@ -3146,7 +3157,7 @@ for more information.} to recreate 3D structure superpositions based on the
 correspondences defined by one or more sequence alignments involving structures shown in the Jmol display. Superposition based on the currently displayed alignment view
  happens automatically if a
 structure is added to an existing Jmol display using 
 correspondences defined by one or more sequence alignments involving structures shown in the Jmol display. Superposition based on the currently displayed alignment view
  happens automatically if a
 structure is added to an existing Jmol display using 

-{\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$} to open the Structure Chooser dialogue box.
+{\sl Structure $\Rightarrow$ 3D Structure data $\Rightarrow$} to open the Structure Chooser dialog box.

 Select structures required and select {\sl View}. A new Jmol view
 opens containing superposed structures if the current selection contains two or more sequences with associated
 structures.
 Select structures required and select {\sl View}. A new Jmol view
 opens containing superposed structures if the current selection contains two or more sequences with associated
 structures.