minor tweaks after proofing prior to 17th November 2017 course

diff --git a/TheJalviewTutorial.tex b/TheJalviewTutorial.tex
index 02bde7a..5f2ba63 100644 (file)
--- a/TheJalviewTutorial.tex
+++ b/TheJalviewTutorial.tex
@@ -27,7 +27,7 @@
 \newtheorem{definition}{Definition}
 
 
 \newtheorem{definition}{Definition}
 
 

-\title{Jalview 2.5: A manual and introductory tutorial }
+\title{Jalview 2.10.3: A manual and introductory tutorial }

 \author{David Martin, James Procter, Andrew Waterhouse, Saif Shehata, Nancy Giang,Suzanne Duce and Geoff Barton}
 \date{Manual version 1.2.3 6th May 2011}
 
 \author{David Martin, James Procter, Andrew Waterhouse, Saif Shehata, Nancy Giang,Suzanne Duce and Geoff Barton}
 \date{Manual version 1.2.3 6th May 2011}
 

@@ -74,7 +74,7 @@ Exercise \theecount  :  #1  }
 
 {\Huge
  
 
 {\Huge
  

-Jalview 2.10.1}
+Jalview 2.10.3}

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

@@ -106,7 +106,7 @@ Manual Version 1.9.1
 % draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
 
 
 % draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
 
 

-17th November 2017
+21st November 2017

 
 
 \end{center}
 
 
 \end{center}

@@ -248,7 +248,7 @@ Keystroke combinations are denoted with a `-' symbol ({\em
 e.g.} [CTRL]-C means press [CTRL] and the `C' key simultaneously).
 
 Menu options are given as a path from the menu
 e.g.} [CTRL]-C means press [CTRL] and the `C' key simultaneously).
 
 Menu options are given as a path from the menu

-that contains them - for example {\sl File $\Rightarrow$ Input Alignment
+that contains them. For example {\sl File $\Rightarrow$ Input Alignment

 $\Rightarrow$ From URL} means to select the `From URL' option from the `Input
 Alignment' submenu of a window's `File' dropdown menu.
 
 $\Rightarrow$ From URL} means to select the `From URL' option from the `Input
 Alignment' submenu of a window's `File' dropdown menu.
 

@@ -358,7 +358,7 @@ Jalview windows automatically load.}
 \exstep {If
 you are having trouble, it may help changing the browser you are using, as the browsers and
 its version may affect this process.}
 \exstep {If
 you are having trouble, it may help changing the browser you are using, as the browsers and
 its version may affect this process.}

-\exstep{To deactivate the opening of the 4 demo sequences during the launch, go
+\exstep{To disable opening of the demonstration project during the launch, go

 to the {\sl Tools $\Rightarrow$
 Preferences...} menu on the desktop. A `Preference'
 dialog box opens, untick the box adjacent to the `Open file' entry in the
 to the {\sl Tools $\Rightarrow$
 Preferences...} menu on the desktop. A `Preference'
 dialog box opens, untick the box adjacent to the `Open file' entry in the

@@ -371,17 +371,19 @@ The example alignment should not be loaded as Jalview starts up.}
 {\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
 the URL history button (a downward arrow on the right hand side of the dialog
 box) to view the files, select exampleFile\_2\_7.jar
 {\em File$\Rightarrow$ From URL} entry in the Desktop menu. Click on
 the URL history button (a downward arrow on the right hand side of the dialog
 box) to view the files, select exampleFile\_2\_7.jar

-(\url{http://www.jalview.org/examples/exampleFile_2_3.jar}) 
+(\url{http://www.jalview.org/examples/exampleFile_2_7.jar}) 

 then click {\sl OK}.}
 then click {\sl OK}.}

-{\bf Note:} Should you want to load your own sequence during the launch process, then go
+\begin{list}{$\circ$}{\newline
+  \newline {\bf
+  Notes}}
+  
+\item {To make Jalview display a different alignment when it is launched, then go

 to the {\sl Tools $\Rightarrow$
 to the {\sl Tools $\Rightarrow$

-Preferences...} menu on the desktop. The tick the `Open file' entry of `Visual'
-preferences tab, type in the URL of the sequence you want to load.
-
-
-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.
+Preferences...} menu on the desktop. Then tick the `Open file' entry of `Visual'
+preferences tab, type in the URL of the sequence you want to load.}
+\item {You may want to move the jalview.jnlp file from your {\bf downloads} to another folder.}
+\item {Opening Jalview via the jnlp file will also allow Jalview to be launched offline.}
+\end{list}

 
 {\bf See the video at:
 \url{http://www.jalview.org/Help/Getting-Started}.}
 
 {\bf See the video at:
 \url{http://www.jalview.org/Help/Getting-Started}.}

@@ -408,7 +410,7 @@ the `search' tab and enter keywords in the box which appears.
 
 \subsubsection{Email Lists}
 
 
 \subsubsection{Email Lists}
 

-The Jalview Discussion list {\tt jalview-discuss@jalview.org} provides a forum
+The Jalview Discussion list ({\tt jalview-discuss@jalview.org}) provides a forum

 for Jalview users and developers to raise problems and exchange ideas - any
 problems, bugs, and requests for help should be raised here. The {\tt
 jalview-announce@jalview.org} list can also be subscribed to if you wish to be
 for Jalview users and developers to raise problems and exchange ideas - any
 problems, bugs, and requests for help should be raised here. The {\tt
 jalview-announce@jalview.org} list can also be subscribed to if you wish to be

@@ -453,9 +455,9 @@ scroll bars will not be visible.
  Each alignment view shown in the alignment window presents a window onto the
  visible regions of the alignment. This means that with anything more than a few
  residues or sequences, alignments can become difficult to visualize on the
  Each alignment view shown in the alignment window presents a window onto the
  visible regions of the alignment. This means that with anything more than a few
  residues or sequences, alignments can become difficult to visualize on the

- screen because only a small area can be shown at a time. It can help,
- especially when examining a large alignment, to have an overview of the whole
- alignment. Select {\sl View $\Rightarrow$ Overview Window} from the Alignment
+ screen because only a small area can be shown at a time. Here, it helps, to
+ have an overview of the whole alignment, especially when it is large.
+ Select {\sl View $\Rightarrow$ Overview Window} from the Alignment

  window menu bar (Figure \ref{overview}\footnote{the menu shown in this figure
  is from Jalview 2.2, later versions have more options.}).
 % (Figure4)
  window menu bar (Figure \ref{overview}\footnote{the menu shown in this figure
  is from Jalview 2.2, later versions have more options.}).
 % (Figure4)

@@ -546,8 +548,8 @@ column 13 by typing {\bf 1 3 , 5} [RETURN].}
 
 {\bf Note:} To view Jalview's comprehensive on-line help documentations select
 {\sl Help} in desktop menu, clicking on {\sl Documentation} will open a
 
 {\bf Note:} To view Jalview's comprehensive on-line help documentations select
 {\sl Help} in desktop menu, clicking on {\sl 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.
+Documentation window. Select topics from the navigation panel on the left hand
+side and use the Search tab to locate specific key words.

 
 {\sl\bf See the video at: 
 \url{http://www.jalview.org/Help/Getting-Started}.}
 
 {\sl\bf See the video at: 
 \url{http://www.jalview.org/Help/Getting-Started}.}

@@ -647,16 +649,17 @@ and the PDB. Jalview's sequence fetching capabilities allow you to avoid having
 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.
 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.

-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
-Jalview can access (grouped by the type of database). Once you've selected the
-appropriate database, hit OK close the database selection window, and then enter
-one or several database IDs or accession numbers separated by a semicolon and
-press OK. Jalview will then attempt to retrieve them from the chosen database.
-Example queries are provided for some databases to test that a source is
-operational, and can also be used as a guide for the type of accession numbers
-understood by the source.
+
+To begin retrieving data, select {\sl File $\Rightarrow$ Fetch Sequence(s) \ldots} 
+from the main menu. A window will then appear (Figure \ref{loadseq}) showing all 
+the database sources Jalview can access (grouped by the type of database). Once 
+you've selected the appropriate database by double clicking it or hitting OK, the 
+database selection window will close and the sequence fetcher for that database 
+will appear. You can then enter one or several database IDs or accession numbers 
+separated by a semicolon and press OK. Jalview will then attempt to retrieve them 
+from the chosen database. Example queries are provided for some databases to test
+that a source is operational, and can also be used as a guide for the type of 
+accession numbers understood by the source.

 % [fig 9]
 \begin{figure}[htbp]
 \begin{center}
 % [fig 9]
 \begin{figure}[htbp]
 \begin{center}

@@ -700,6 +703,7 @@ $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu.
 Select the file and click {\sl OK} to load.}
 
 \exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
 Select the file and click {\sl OK} to load.}
 
 \exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}

+

 (i) Drag the alignment.fa file that you have just saved from its folder and
 drop it onto the Jalview desktop window, the alignment should open.
 
 (i) Drag the alignment.fa file that you have just saved from its folder and
 drop it onto the Jalview desktop window, the alignment should open.
 

@@ -720,10 +724,12 @@ window, with cDNA and protein linked?' select `Split Window' option. A
 split window opens in the Jalview desktop.
 }
 
 split window opens in the Jalview desktop.
 }
 

-\exstep{{\bf The text editor:} (i) Open the alignment.fa file using text editor.
+\exstep{{\bf The text editor:} 
+
+(i) Open the alignment.fa file using text editor.

 Copy the sequence text into the clipboard  using [CTRL]-A and then [CTRL]-C.
 
 Copy the sequence text into the clipboard  using [CTRL]-A and then [CTRL]-C.
 

-(ii) Place the mouse on the Jalview desktop and right-click the mouse
+(ii) Move the mouse pointer onto the Jalview desktop window's background and right-click 

 to open the context window. Select the {\sl Paste to New Window} menu option.
 
 (iii) In the Jalview desktop menu, select {\sl File
 to open the context window. Select the {\sl Paste to New Window} menu option.
 
 (iii) In the Jalview desktop menu, select {\sl File

@@ -816,14 +822,14 @@ The alignment can then be pasted into any application of choice, e.g. a word pro
 }
 \exstep{Ensure at least one alignment window is active in Jalview. Open the
 overview window {\sl View $\Rightarrow$ Overview Window}
 }
 \exstep{Ensure at least one alignment window is active in Jalview. Open the
 overview window {\sl View $\Rightarrow$ Overview Window}

- and scroll red box to any part of the alignment.
+ and click and drag to move the red box to any part of the alignment.

 Select {\sl File
 $\Rightarrow$ Save Project} from the main menu and save the project in a
 suitable folder.}
 
 \exstep{Close all windows and then load the project {\sl via} the {\sl File
 $\Rightarrow$ Load Project} menu option. Observe how many of the windows
 Select {\sl File
 $\Rightarrow$ Save Project} from the main menu and save the project in a
 suitable folder.}
 
 \exstep{Close all windows and then load the project {\sl via} the {\sl File
 $\Rightarrow$ Load Project} menu option. Observe how many of the windows

-reopen. Are they the same as were saved. } {\bf See the video at:
+reopen. Are they the same as when they were saved ? } {\bf See the video at:

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

@@ -891,9 +897,8 @@ selection. }
 \end{figure}
 
 To select multiple complete sequences, click and drag the mouse down the
 \end{figure}
 
 To select multiple complete sequences, click and drag the mouse down the

-sequence ID panel. The same techniques as used for columns (above) can be used
-with [SHIFT]-Click for continuous and [CTRL]-Click (or
-[CMD]-Click for Mac) to select discontinuous
+sequence ID panel. The same techniques can be used as for columns above ([SHIFT]-Click for continuous and [CTRL]-Click {\sl (Or
+[CMD]-Click for Mac)}) to select discontinuous

 ranges of sequences (Figure \ref{selectrows}).
 %[fig 14]
 
 ranges of sequences (Figure \ref{selectrows}).
 %[fig 14]
 

@@ -1634,7 +1639,7 @@ simultaneously in their own separate windows. To delete a group, press [CTRL]-W.
 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}
 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}

-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. 
+Wrapped alignments can be toggled on and off using the {\sl Format $\Rightarrow$ Wrap} menu option (Figure \ref{wrap}). Note that the annotation tracks 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. 
 \begin{figure}[htbp]
 
 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. 
 \begin{figure}[htbp]

@@ -2340,7 +2345,7 @@ number allowed by the server.
 
 \exercise{Multiple Sequence Alignment}{
 \label{msaex}
 
 \exercise{Multiple Sequence Alignment}{
 \label{msaex}

-\exstep{ Close all windows and open the alignment at {\sf
+\exstep{ Close all windows. Open the alignment at {\sf

 http://www.jalview.org/tutorial/unaligned.fa}.  Select {\sl
 Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}. 
 A window will open giving the job status. After a short time, a second window will open
 http://www.jalview.org/tutorial/unaligned.fa}.  Select {\sl
 Web Service $\Rightarrow$ Alignment $\Rightarrow$ Muscle with Defaults}. 
 A window will open giving the job status. After a short time, a second window will open

@@ -2647,13 +2652,14 @@ option. Leaf names on imported trees will be matched to the associated alignment
 
 \exercise{Trees}
 {\label{treeex}
 
 \exercise{Trees}
 {\label{treeex}

-{\sl Ensure that you have at least 1G memory available in Jalview.
-(Start with link:
-\href{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}{http://www.jalview.org/services/launchApp?jvm-max-heap=1G},
-or in the table in the Development section of the Jalview web site
-(\href{http://www.jalview.org/development/development-builds}{http://www.jalview.org/development/development-builds}), go 
-to ``latest official build'' row and in the ``Webstart'' column, click
-on ``2G''.)}
+\begin{list}{$\circ$}{Ensure that you have at least 1G memory available in Jalview.}
+\item{Start with link:
+\url{http://www.jalview.org/services/launchApp?jvm-max-heap=1G}
+}
+\item{From 
+{\href{http://www.jalview.org/development/development-builds}{the Development Builds}} in the Jalview web site, use 
+the ``2G'' link in the``latest official build'' row and ``Webstart'' column.}
+\end{list}

 
 \exstep{Open the alignment at
 \textsf{http://www.jalview.org/tutorial/alignment.fa}.}
 
 \exstep{Open the alignment at
 \textsf{http://www.jalview.org/tutorial/alignment.fa}.}

@@ -2664,8 +2670,9 @@ Joining, in the drop-down list select BLOSUM62 and click the Calculate
 button. A tree window will open.}
 
 \exstep{Click on the
 button. A tree window will open.}
 
 \exstep{Click on the

-tree window, a cursor will appear. Note that placing this cursor divides the tree into a number of groups by colour.
-Place the cursor to give about 4 groups.}
+tree window, a cursor will appear as a vertical line. Note that clicking will
+place this cursor, and divides the tree into a number of groups, each highlighted
+with a different colour. Place the cursor to give about 4 groups.}

 
 
 \exstep{In the tree window, select {\sl View $\Rightarrow$ Sort Alignment
 
 
 \exstep{In the tree window, select {\sl View $\Rightarrow$ Sort Alignment

@@ -3472,8 +3479,8 @@ ensure each sequence fragment is associated with the {\bf same} Jmol view. }
 colourscheme for each alignment, and use the {\sl Colour by ..} submenu to
 ensure they are all used to colour the complex shown in the Jmol window.
 
 colourscheme for each alignment, and use the {\sl Colour by ..} submenu to
 ensure they are all used to colour the complex shown in the Jmol window.
 

-{\sl The different shading schemes will allow regions of strong physicochemical conservation are
-highlighted on the domains in the structure.}
+{\sl The different shading schemes will highlight regions of strong 
+physicochemical conservation on corresponding domains in the structure.}

 }
 
 \exstep{The final step needed to reproduce the shading in Figure
 }
 
 \exstep{The final step needed to reproduce the shading in Figure

@@ -3770,7 +3777,7 @@ annotation panel and selecting \textbf{Show hidden annotation}.
 {\sl Before starting this exercise, make sure you enable the \protect{`Add
 Temperature Factor'} option in your {\bf Structures} preferences. }
 
 {\sl Before starting this exercise, make sure you enable the \protect{`Add
 Temperature Factor'} option in your {\bf Structures} preferences. }
 

-\exstep{Open the alignment using
+\exstep{Open the alignment from

 \url{http://www.jalview.org/tutorial/interleukin7.fa}. } 
 
 \exstep{Run the DisEMBL disorder predictor {\sl via} the {\sl Web Service
 \url{http://www.jalview.org/tutorial/interleukin7.fa}. } 
 
 \exstep{Run the DisEMBL disorder predictor {\sl via} the {\sl Web Service

@@ -4085,6 +4092,9 @@ window. Click on different residues and located them in the sequence alignment w
  }
 
 \chapter{Webservices}
  }
 
 \chapter{Webservices}

+
+\section{What are Web Services ?}
+

 \label{jvwebservices}
 The term ``Webservices'' refers to a variety of data exchange
 mechanisms based on HTTP.\footnote{HTTP: Hyper-Text Transfer Protocol.} 
 \label{jvwebservices}
 The term ``Webservices'' refers to a variety of data exchange
 mechanisms based on HTTP.\footnote{HTTP: Hyper-Text Transfer Protocol.} 

@@ -4155,7 +4165,7 @@ successfully use web services from Jalview, since it periodically checks the
 progress of running jobs.
 
 
 progress of running jobs.
 
 

-\subsection{JABA Web Services for Sequence Alignment and Analysis}
+\section{JABA Web Services for Sequence Alignment and Analysis}

 \label{jabaservices}
 JABA stands for ``JAva Bioinformatics Analysis'', which is a system developed
 by Peter Troshin and Geoff Barton at the University of Dundee for running
 \label{jabaservices}
 JABA stands for ``JAva Bioinformatics Analysis'', which is a system developed
 by Peter Troshin and Geoff Barton at the University of Dundee for running