update version/date

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 1c1f637..52e2343 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -100,11 +100,11 @@ Dundee, Scotland DD1 5EH, UK
 
 \vspace{2in}
 
 
 \vspace{2in}
 

-Manual Version 1.5 
+Manual Version 1.5.0 

 % post CLS lifesci course on 15th January
 % draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
 
 % post CLS lifesci course on 15th January
 % draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
 

-4th December 2014
+12th December 2014

 
 
 \end{center}
 
 
 \end{center}

@@ -362,7 +362,7 @@ The example alignment should not be loaded as Jalview starts up.}
 \exstep{To reload the original demo file select the
 {\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
 the URL history button on the right hand side of the dialog box to view the
 \exstep{To reload the original demo file select the
 {\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
 the URL history button on the right hand side of the dialog box to view the

-files, selected exampleFile-2-7.jar, then click OK.}
+files, select exampleFile\_2\_7.jar, then click OK.}

 {\bf Note:} Should you want to reload the example alignment or load your own
 sequence during the launch process, then go
 to the {\sl Tools $\Rightarrow$
 {\bf Note:} Should you want to reload the example alignment or load your own
 sequence during the launch process, then go
 to the {\sl Tools $\Rightarrow$

@@ -1094,6 +1094,27 @@ with (Sequence ID name )}. To reveal these hidden sequences, right click on the
 Sequence ID and in the pop-up menu select Reveal All.}}
 
 
 Sequence ID and in the pop-up menu select Reveal All.}}
 
 

+\begin{figure}[htb]
+\begin{center}
+\includegraphics[width=3in]{images/edit1.pdf}
+\includegraphics[width=3in]{images/edit2.pdf}
+\caption{{\bf Introducing gaps in a single sequence.} Gaps are introduced as the
+selected sequence is dragged to the right while pressing and holding [SHIFT].}
+\label{gapseq}
+\end{center}
+\end{figure}
+
+\begin{figure}[htb]
+\begin{center}
+\includegraphics[width=3in]{images/edit3.pdf}
+\includegraphics[width=3in]{images/edit4.pdf}
+\caption{{\bf Introducing gaps in a group.} Gaps are introduced as the selected
+group is dragged to the right with [CTRL] pressed.}
+\label{gapgroup}
+\end{center}
+\end{figure}
+
+

 
 
 \subsection{Introducing and Removing Gaps}
 
 
 \subsection{Introducing and Removing Gaps}

@@ -1221,27 +1242,6 @@ backwards and replay the edits you have made.}
 
 }
 
 
 }
 

-\begin{figure}[htb]
-\begin{center}
-\includegraphics[width=3in]{images/edit1.pdf}
-\includegraphics[width=3in]{images/edit2.pdf}
-\caption{{\bf Introducing gaps in a single sequence.} Gaps are introduced as the
-selected sequence is dragged to the right while pressing and holding [SHIFT].}
-\label{gapseq}
-\end{center}
-\end{figure}
-
-\begin{figure}[htb]
-\begin{center}
-\includegraphics[width=3in]{images/edit3.pdf}
-\includegraphics[width=3in]{images/edit4.pdf}
-\caption{{\bf Introducing gaps in a group.} Gaps are introduced as the selected
-group is dragged to the right with [CTRL] pressed.}
-\label{gapgroup}
-\end{center}
-\end{figure}
-
-

 \subsubsection{Editing in Cursor mode}
 
 Gaps can be easily inserted when in cursor mode (toggled with [F2]) by
 \subsubsection{Editing in Cursor mode}
 
 Gaps can be easily inserted when in cursor mode (toggled with [F2]) by

@@ -2557,7 +2557,7 @@ Services tab of the {\sl Preferences} dialog box.
 \exercise{Changing the Layout of the Web Services Menu}{
 \label{changewsmenulayoutex}
 \exstep{Make sure you have loaded an alignment into Jalview, and examine the
 \exercise{Changing the Layout of the Web Services Menu}{
 \label{changewsmenulayoutex}
 \exstep{Make sure you have loaded an alignment into Jalview, and examine the

-current layout of the alignment windowÔøΩs {\sl Web Service} menu.}
+current layout of the alignment window's {\sl Web Service} menu.}

 \exstep{Open the preferences dialog box and select the web services tab.}
 \exstep{Ensure the {\sl Enable JABAWS services} checkbox is selected, and unselect
 the {\sl Enable Enfin Services} checkboxes.}
 \exstep{Open the preferences dialog box and select the web services tab.}
 \exstep{Ensure the {\sl Enable JABAWS services} checkbox is selected, and unselect
 the {\sl Enable Enfin Services} checkboxes.}

@@ -2601,7 +2601,7 @@ services advertised by the server are functional. The colour codes are:
 
 Test results from JABAWS are reported on Jalview's console output (opened from
 the Tools menu). Tests are re-run every time Jalview starts, and when the
 
 Test results from JABAWS are reported on Jalview's console output (opened from
 the Tools menu). Tests are re-run every time Jalview starts, and when the

-[Refresh] button is pressed on the Jalview JABAWS configuration panel.
+[Refresh Services] button is pressed on the Jalview JABAWS configuration panel.

 
 \subsubsection{Resetting the JABA services setting to their defaults}
 Once you have configured a JABAWS server and selected the OK button of the
 
 \subsubsection{Resetting the JABA services setting to their defaults}
 Once you have configured a JABAWS server and selected the OK button of the

@@ -2822,7 +2822,7 @@ problem. For instance, the Muscle service provides the following presets:
 
 The presets are displayed in the JABA web services submenu, and can also be
 accessed from the parameter editing dialog box, which is opened by selecting
 
 The presets are displayed in the JABA web services submenu, and can also be
 accessed from the parameter editing dialog box, which is opened by selecting

-the `{\sl Edit settings and run ...}' option from the web serviceÔøΩs menu. If you have used
+the `{\sl Edit settings and run ...}' option from the web services menu. If you have used

 a preset, then it will be mentioned at the beginning of the job status file shown
 in the web service job progress window.
 
 a preset, then it will be mentioned at the beginning of the job status file shown
 in the web service job progress window.
 

@@ -3166,7 +3166,7 @@ annotation panel and selecting \textbf{Show hidden annotation}.
 \exstep{Open the alignment at
 \url{http://www.jalview.org/tutorial/interleukin7.fa}. }
 
 \exstep{Open the alignment at
 \url{http://www.jalview.org/tutorial/interleukin7.fa}. }
 

-\exstep{Run the DISEMBL disorder predictor {\slvia} the {\slWeb Services
+\exstep{Run the DisEMBL disorder predictor {\slvia} the {\slWeb Services

 $\Rightarrow$ Disorder Prediction } submenu.}
 
 \exstep{Use {\sl Sequence ID $\Rightarrow$ Structure $\Rightarrow$ Discover PDB
 $\Rightarrow$ Disorder Prediction } submenu.}
 
 \exstep{Use {\sl Sequence ID $\Rightarrow$ Structure $\Rightarrow$ Discover PDB