From bee8eba8a24de3c4dd2cd4ae90475d268cc910b8 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 12 Dec 2014 13:28:22 +0000 Subject: [PATCH] update version/date --- TheJalviewTutorial.tex | 56 ++++++++++++++++++++++++------------------------ 1 file changed, 28 insertions(+), 28 deletions(-) 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 -- 1.7.10.2