From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 12 Dec 2014 13:28:22 +0000 (+0000)
Subject: update version/date
X-Git-Tag: Version_1.9.2~42
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview-manual.git;a=commitdiff_plain;h=bee8eba8a24de3c4dd2cd4ae90475d268cc910b8

update version/date
---

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 1c1f637..52e2343 100644
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -100,11 +100,11 @@ Dundee, Scotland DD1 5EH, UK
 
 \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.
 
-4th December 2014
+12th December 2014
 
 
 \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
-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 $\Rightarrow$
@@ -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.}}
 
 
+\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}
@@ -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
@@ -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
-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.}
@@ -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
-[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
@@ -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 `{\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.
 
@@ -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{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