{\Huge
-Jalview 2.8
+Jalview 2.8.2
}
\vspace{0.5in}
{\huge
-A manual and introductory tutorial }
+A Manual with Introductory Tutorial }
\vspace{2.4in}
{\large
-David Martin, James Procter, Andrew Waterhouse, Saif Shehata and Geoff Barton
+David Martin, James Procter, Andrew Waterhouse, Saif Shehata, Nancy Giang,
+Suzanne Duce and Geoff Barton
-With additional material by Nancy Giang.
+
}
\vspace{1.2in}
\vspace{2in}
-Manual version 1.4.1
+Manual Version 1.5
% post CLS lifesci course on 15th January
% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-18th January 2013
+
+4th December 2014
\end{center}
\subsection{Jalview}
Jalview is a multiple sequence alignment viewer, editor and analysis tool.
Jalview is designed to be platform independent (running on Mac, MS Windows, Linux
-and any other platform that supports Java), capable of editing and analysing
-large alignments (thousands of sequences) with minimal degradation in
+and any other platforms that supports Java). Jalview is capable of editing and
+analysing large alignments (thousands of sequences) with minimal degradation in
performance, and able to show multiple integrated views of the alignment and
other data. Jalview can read and write many common sequence formats including
FASTA, Clustal, MSF(GCG) and PIR.
embedded in a web page,\footnote{A demonstration version of Jalview (Jalview Micro
Edition) also runs on a mobile phone but the functionality is limited to sequence
colouring.} and includes a javascript API to allow customisable display of alignments for web sites such as
-{\bf pfam}.\footnote{\url{http://pfam.sanger.ac.uk}}
+{\bf Pfam}.\footnote{\url{http://pfam.sanger.ac.uk}}
-Jalview 2.8 was released in November 2012. The Jalview Desktop in this version
+Jalview 2.8.2 was released in December 2014. The Jalview Desktop in this version
provides access to protein and nucleic acid sequence, alignment and structure
databases, and includes the Jmol\footnote{ Provided under the LGPL licence at
\url{http://www.jmol.org}} viewer for molecular structures, and the VARNA\footnote{Provided under GPL licence at \url{http://varna.lri.fr}} program for the visualization of RNA secondary structure. A
\subsection{Jalview's Capabilities}
% TODO add references to appropriate sections for each capability described here.
-Figure \ref{jvcapabilities} gives an overview of the main features of the Jalview desktop application. Its primary function is the editing and visualization of sequence alignments, and their interactive analysis. Tree building, principal components analysis, physico-chemical property conservation and sequence consensus analyses are built in to the program. Web services enable Jalview to access remote alignment and secondary structure prediction programs, as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation. Sequences, alignments, trees, structures, features and alignment annotation may also be exchanged with the local filesystem. Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout. Alignment views are dynamically linked with Jmol structure displays, a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment's structure. The application provides its own Jalview project file format in order to store the current state of an alignment and analysis windows. Jalview also provides WYSIWIG\footnote{WYSIWIG: What You See Is What You Get.} style figure generation capabilities for the preparation of alignments for publication.
+Figure \ref{jvcapabilities} gives an overview of the main features of the
+Jalview desktop application. Its primary function is the editing and
+visualization of sequence alignments, and their interactive analysis. Tree
+building, principal components analysis, physico-chemical property conservation
+and sequence consensus analyses are built into the program. Web services enable
+Jalview to access on line alignment and secondary structure prediction programs,
+as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation. Sequences, alignments, trees, structures, features and alignment annotation may also be exchanged with the local filesystem. Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout. Alignment views are dynamically linked with Jmol structure displays, a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment's structure. The application provides its own Jalview project file format in order to store the current state of an alignment and analysis windows. Jalview also provides WYSIWIG\footnote{WYSIWIG: What You See Is What You Get.} style figure generation capabilities for the preparation of alignments for publication.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5.8in]{images/jvcapabilities.pdf}
between Jalview, TOPALi and AstexViewer.} in 2004, enabling Andrew Waterhouse and
Jim Procter to re-engineer the original program to introduce contemporary developments
in bioinformatics and take advantage of the latest web and Java technology.
-Jalview's development is now supported for a further 5 years from October 2009
-by an award from the BBSRC's Tools and Resources fund. In 2010, 2011, and 2012, Jalview
-benefitted from the \href{http://code.google.com/soc/}{Google Summer of Code},
-when Lauren Lui and Jan Engelhardt introduced new features for handling RNA
-alignments and secondary structure annotation, in collaboration with Yann Ponty.\footnote{\url{http://www.lix.polytechnique.fr/~ponty/}}
+Jalview's development was supported from 2009
+by an award from the BBSRC's Tools and Resources fund. Jalview's development is
+currently being funded by a BBSRC `Extending The Jalview Resource for
+Biological Sequence Alignment and Analysis' grant and a Wellcome Trust
+`Extending The Jalview Resource for Biological Sequence Alignment and Analysis'
+grant. In 2010, 2011, and 2012, Jalview benefitted from the
+\href{http://code.google.com/soc/}{Google Summer of Code}, when Lauren Lui and Jan Engelhardt introduced new features for handling RNA alignments and secondary structure annotation, in collaboration with Yann Ponty.\footnote{\url{http://www.lix.polytechnique.fr/~ponty/}}
%TODO describe future plans in history ? not a good idea.
\subsubsection{Citing Jalview}
If you use Jalview in your work you should cite:\newline
-{\sl ``Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"}\newline
-Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009) \newline {\sl Bioinformatics} doi: 10.1093/bioinformatics/btp033
+{\sl "Jalview Version 2 - a multiple sequence alignment editor and analysis
+workbench"}\newline Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009) \newline {\sl Bioinformatics} doi: 10.1093/bioinformatics/btp033
-This paper supersedes the original Jalview publication:\newline {\sl ``The Jalview Java alignment
-editor"} \newline Michele Clamp, James Cuff, Stephen M. Searle and Geoffrey J. Barton (2004) \newline {\sl Bioinformatics} {\bf 20} 426-427.
+This paper supersedes the original Jalview publication:\newline {\sl "The
+Jalview Java alignment editor"} \newline Michele Clamp, James Cuff, Stephen M. Searle and Geoffrey J. Barton (2004) \newline {\sl Bioinformatics} {\bf 20} 426-427.
-\subsection{About this tutorial }
+\subsection{About this Tutorial }
This tutorial is written in a manual format with short exercises where
appropriate, typically at the end of each section. This chapter concerns the
-basic operation of Jalview and should be sufficient for those who just want to
+basic operation of Jalview and should be sufficient for those who want to
load Jalview (Section \ref{startingjv}), open an alignment (Section \ref{loadingseqs}), perform basic editing and colouring (Section \ref{selectingandediting} and Section \ref{colours}), and produce publication
and presentation quality graphical output (Section \ref{layoutandoutput}).
Keystrokes using the special non-symbol keys are represented in the tutorial by
enclosing the pressed keys with square brackets ({\em e.g.} [RETURN] or [CTRL]).
+
Keystroke combinations are combined with a `-' symbol ({\em e.g.} [CTRL]-C means
-press [CTRL] and the `C' key). Menu options are given as a path from the menu
+press [CTRL] and the `C' key).
+
+Menu options are given as a path from the menu
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.
-\section{Obtaining and starting The Jalview Desktop Application}
+\section{Obtaining and Starting the Jalview Desktop Application}
\label{startingjv}
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4.5in]{images/download.pdf}
-\caption{{\bf Download page on the Jalview web site}}
+\caption{\bf Download page on the Jalview web site at www.jalview.org.}
\label{download}
\end{center}
\end{figure}
-This tutorial is based on the application version of Jalview, the Jalview
-Desktop. Much of the information will also be useful for users of the JalviewLite
-applet, which has the same core editing, analysis and visualization capabilities (see the
+This tutorial is based on the Jalview
+Desktop application. Much of the information will also be useful for users of
+the JalviewLite applet, which has the same core editing, analysis and visualization capabilities (see the
\href{http://www.jalview.org/examples/applets.html}{JalviewLite Applet Examples}
page for examples). The Jalview Desktop, however, is much more powerful, and
includes additional support for interaction with external web services, and
The Jalview Desktop can be run in two ways; as an application launched from the
web {\sl via} Java webstart, or as an application loaded onto your hard drive.
-The webstart version is launched from the {\bf Launch Jalview Desktop} link at
-the top-right of pages at \url{http://www.jalview.org}. To download the locally
-installable version, follow the links from the
-\href{http://www.jalview.org/download}{Download page} (Figure \ref{download}).
-These links will always launch the latest stable release of Jalview.\par
+The webstart version is launched from the pink `Launch Jalview Desktop
+button' at the top right handside of pages of the website
+\href{http://www.jalview.org}{(www.jalview.org)}.
+To download the locally installable version, follow the links on the download
+page
+\href{http://www.jalview.org/download}{(www.jalview.org/download) }
+ (Figure \ref{download}).
+These links will launch the latest stable release of Jalview.\par
When the application is launched with webstart, two dialogs may appear before
the application starts. If your browser is not set up to handle webstart, then
click trust or accept as appropriate. The splash screen (Figure \ref{splash})
gives information about the version and build date that you are running,
information about later versions (if available), and the paper to cite in your
-publications. This information is also available on the Jalview web site and
-from the Desktop's {\sl Help $\Rightarrow$ About} menu option.
+publications. This information is also available on the Jalview web site at
+\url{http://www.jalview.org}.
%[fig 2]
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4.5in]{images/splash.pdf}
-\caption{{\bf Jalview splash screen}}
+\caption{{\bf Jalview splash screen.}}
\label{splash}
\end{center}
\end{figure}
When Jalview starts it will automatically load an example alignment from the
-Jalview site. This behaviour can be changed in the Jalview Desktop preferences
-dialog opened from the Desktop's {\sl Tools $\Rightarrow$ Preferences..} menu.
-This alignment will look like the one in Figure \ref{startpage} (this is taken
+Jalview site. This behaviour can be switched off in the Jalview Desktop
+preferences dialog by unchecking the open file option.
+This alignment will look like the one in Figure \ref{startpage} (taken
from Jalview version 2.7).
%[figure 3 ]
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4in]{images/start.pdf}
-\caption{{\bf Default startup for Jalview}}
+\caption{{\bf Default startup for Jalview.}}
\label{startpage}
\end{center}
\end{figure}
\subsubsection{Jalview News RSS Feed}
-From time to time, important announcements are made available to users of the
+Announcements are made available to users of the
Jalview Desktop {\sl via} the Jalview News reader. This window will open
automatically when new news is available, and can also be accessed {\sl via} the
Desktop's {\sl Tools $\Rightarrow$ Show Jalview News} menu entry.
\end{figure}
-\exercise{Starting Jalview}{
+\exercise{Launching Jalview from the Jalview website}{
\label{start}
-\exstep{Point your web browser at the \href{http://www.jalview.org}{Jalview web site} and start Jalview by clicking on the `Launch Jalview Desktop' button.}
-\exstep{Open the Jalview Desktop's user preferences dialog (from the Tools
-menu), and untick the checkbox adjacent to the `Open file' entry in the
-`Visual' preferences tab.}
-\exstep{Click OK to save the preferences, then \em{launch {\bf another} Jalview
-instance from the web site}. The example alignment should not be
-loaded when the new Jalview instance starts up.}
-{\sl Note: Should you want to reload the example alignment, then select the
-{\em File$\Rightarrow$ From URL} entry from the Desktop menu, and click on the
-URL history button on the right hand side of the dialog box that opens.
-You can then select the example file's URL, followed by OK to open the file. } }
+\exstep{Open the Jalview web
+site \href{http://www.jalview.org}{(www.jalview.org)}
+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
+will open and ask if you want to open the the jalview.jnlp file as the file is an application downloaded from the
+Internet, click Open. (Note you maybe asked to update Java, if you agree then it
+will automatically update the Java software). As Jalview opens, four demo
+Jalview windows automatically load.} \exstep {If
+you are having trouble, it may help changing the browser you are using, as the browsers and
+it's version may effect 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'
+dialogue box opens, untick the box adjacent to the `Open file' entry in the
+`Visual' preferences tab.
+Click OK to save the preferences.}
+\exstep{Launch another Jalview workbench from the web site by clicking on the
+pink Launch button.
+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.}
+{\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 $\Rightarrow$
+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. This
+file will load during the start up process.\\
+
+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 this file will allow Jalview to be launched offline.
+
+{\bf Help launching Jalview is avaliable in a video on
+\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
+the website.}}
\subsection{Getting Help}
\label{gettinghelp}
\begin{center}
\parbox[c]{2in}{\centerline{\includegraphics[width=2.75in]{images/help1.pdf}}}
\parbox[c]{4in}{\includegraphics[width=4in]{images/help2.pdf}}
-\caption{{\bf Accessing the built in Jalview documentation}}
+\caption{{\bf Accessing the built in Jalview documentation.}}
\label{help}
\end{center}
\end{figure}
\label{jvnavigation}
The major features of the Jalview Desktop are illustrated in Figure \ref{anatomy}. The alignment window is the primary window for editing and visualization, and can contain several independent views of the alignment being worked with. The other windows (Trees, Structures, PCA plots, etc) are linked to a specific alignment view. Each area of the alignment window has a separate context menu accessed by clicking the right mouse button.
- Jalview has two navigation and editing modes: normal mode, where editing and navigation is performed using the mouse, and cursor mode where editing and navigation are performed using the keyboard. The F2 key is used to switch between these two modes.
+ Jalview has two navigation and editing modes: {\bf normal mode}, where
+ editing and navigation is performed using the mouse, and {\bf cursor mode}
+ where editing and navigation are performed using the keyboard. The {\bf F2 key}
+ is used to switch between these two modes. With a Mac as the F2 is
+ often assigned to screen brightness, one maay often need to type {\bf function
+ [Fn] key with F2}.
\begin{figure}[htb]
\begin{center}
\subsection{Navigation in Cursor mode}
\label{cursormode}
-\parbox[c]{5in}{Cursor mode navigation enables the experienced user to quickly
+\parbox[c]{5in}{Cursor mode navigation enables the user to quickly
and precisely navigate, select and edit parts of an alignment. On pressing F2 to
enter cursor mode the position of the cursor is indicated by a black background
and white text. The cursor can be placed using the mouse or moved by pressing
\exercise{Navigation}{
\label{navigate}
-\exstep{Reload the example file by accessing the Desktop's
-{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} dialog and
-clicking on the {\sl down arrow} to retrieve the example file URL stored in its history
- (\url{http://www.jalview.org/examples/exampleFile_2_7.jar})}
+Jalview has two navigation and editing modes: {\bf normal} mode (where editing
+and navigation are via the mouse) and the {\bf cursor} mode (where editing and
+navigation are via the keyboard).
+The {\bf F2 key} is used to switch between these two modes. With a Mac often
+need to type function {\bf Fn key and F2}, as button is often assigned to
+screen brightness. Jalview always starts up in {\bf normal mode}.
+
+\exstep{Load an example alignment from its URL
+(\url{http://www.jalview.org/examples/exampleFile_2_7.jar}) via the Desktop
+using {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} dialog
+box.
+(The URL should be stored in its history and clicking on the {\sl down arrow} is
+an easy way to access it.)}
\exstep{Scroll around the alignment using the alignment (vertical) and ruler (horizontal) scroll bars.}
-\exstep{Find and open the Overview Window. Move around the alignment by clicking and dragging the red box in the overview window.}
-\exstep{Look at the status bar as you move the mouse over the alignment. It
-should indicate information about the sequence and residue under the cursor.
-} \exstep{Press [F2] to enter Cursor mode. Use the arrow keys to move the cursor
-around the alignment.
-Move to sequence 7 by pressing {\sl 7 S}. Move to column 18 by pressing {\sl 1 8
-C}. Move to residue 18 by pressing {\sl 1 8 P}. Note that these can be two
-different positions if gaps are inserted into the sequence. Move to sequence 5,
-column 13 by typing {\sl 1 3 , 5 [RETURN]}.
-} }
+\exstep{Find the Overview Window, {\sl Views
+$\Rightarrow$ Overview Window} and open it. Move around the
+alignment by clicking and dragging the red box in the overview window.}
+\exstep{Look at the status bar (lower left hand corner of the alignment window) as
+you move the mouse over the alignment. It indicates information about the
+sequence and residue under the cursor.}
+\exstep{Press [F2] to enter {\bf Cursor mode}. Use the direction {\bfarrow
+keys} to move the cursor around the alignment.}
+\exstep{Move to sequence 7 by pressing {\bf 7 S}. Move to column 18 by pressing
+{\bf 1 8 C}. Move to residue 18 by pressing {\bf 1 8 P}. Note that these can be
+two different positions if gaps are inserted into the sequence. Move to sequence 5,
+column 13 by typing {\bf 1 3 , 5 [RETURN]}.}
+
+{\bf Note:} To view Jalview's comprehensive on-line help documentations select
+Help on desktop menu, clicking on 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
+
+{\bf Help navigating Jalview is avaliable in a video on
+\href{http://www.jalview.org/Help/Getting-Started}{the Getting Started page} of
+the website.}}
+
\subsection{The Find Dialog Box}
\label{searchfunction}
A further option for navigation is to use the {\sl Select $\Rightarrow$
expressions for searching sequences and sequence IDs, or sequence numbers.
Hitting the [Find next] button will highlight the first (or next) occurrence of
that pattern in the sequence ID panel or the alignment, and will adjust the view
-in order to display the highlighted region. The Jalview help provides
+in order to display the highlighted region. The Jalview Help provides
comprehensive documentation for this function, and a quick guide to the regular
expressions that can be used with it.
%TODO insert a figure for the Find dialog box
-\section{Loading your own sequences}
+\section{Loading your Own Sequences}
\label{loadingseqs}
Jalview provides many ways to load your own sequences. %For this section of the tutorial you will need to download the file http://www.jalview.org/tutorial/alignment.fa to a suitable location on your hard drive.
\subsection{Drag and Drop}
In most operating systems you can just drag a file icon from a file browser
- window and drop it on an open Jalview application window. The file will then be opened as a new alignment window. %You can try this with the tutorial file you have downloaded. When you have opened the file, close it again by selecting the close control on the window. If you drop an alignment file onto an open alignment window it will be appended
-to that alignment. Drag and drop also works when loading data from a URL -
+ window and drop it on an open Jalview application window. The file will then be opened as a new alignment window. %You can try this with the tutorial file you have downloaded. When you have opened the file, close it again by selecting the close control on the window. If you drop an alignment file onto an open alignment window it will be appended.
+ Drag and drop also works when loading data from a URL -
simply drag the link or url from the address panel of your browser on to an
alignment or the Jalview desktop background and Jalview will load data from the
URL directly.
\begin{center}
\includegraphics[width=2in]{images/menuloadurl.pdf}
\includegraphics[width=3in]{images/loadurlbox.pdf}
-\caption{{\bf Opening an alignment from a URL }}
+\caption{{\bf Opening an alignment from a URL. }}
\label{loadurl}
\end{center}
\end{figure}
\begin{center}
\includegraphics[width=2in]{images/menuloadtext.pdf}
\includegraphics[width=3in]{images/loadtextbox.pdf}
-\caption{{\bf Opening an alignment from pasted text }}
+\caption{{\bf Opening an alignment from pasted text. }}
\label{loadtext}
\end{center}
\end{figure}
-\subsection{From a public database}
+\subsection{From a Public Database}
\label{fetchseq}
Jalview can retrieve sequences and sequence alignments from the public databases
housed at the European Bioinformatics Institute, including Uniprot, Pfam, Rfam
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=5in]{images/fetchseq.pdf}
-\caption{{\bf Retrieving sequences from a public database}}
+\caption{{\bf Retrieving sequences from a public database.}}
\label{loadseq}
\end{center}
\end{figure}
\exercise{Loading sequences}{
\label{load}
-\exstep{Start Jalview then close all windows (if necessary) by selecting {\sl Window $\Rightarrow$ Close All} from the Desktop window.}
-\exstep{Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \textsf{http://www.jalview.org/tutorial/alignment.fa} in the box. Click OK
-and the alignment should load.
-}
-\exstep{Close all windows using the {\sl Window $\Rightarrow$ Close All} menu option from the Desktop.
-
-Point your web browser at the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) and save the file to your desktop.
-
-Open this file in Jalview by selecting {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the main menu and selecting the file from your desktop. Click OK and load the alignment.}
-\exstep{Select {\sl Desktop $\Rightarrow$ Window $\Rightarrow$ Close All} and drag the alignment.fa file from the desktop onto the Jalview window. The alignment should open. Try dragging onto an empty Jalview and onto an existing
-alignment and observe the results. You can also try dragging the
-URL directly onto Jalview.
-}
-\exstep{ Select {\sl File $\Rightarrow$ Fetch Sequence(s)..} from the Desktop. Select the PFAM seed database and enter the accession number PF03460. Click OK. An alignment of about 107 sequences should load. }
-\exstep{Open \url{http://www.jalview.org/tutorial/alignment.fa} in a
-web browser.
-
-{\bf Note:} If the URL is downloaded instead of opened in the browser, then locate the file in your download directory and open it in a text editor.
-}
-\exstep{Select and copy the entire text to the clipboard (usually {\sl via} the
-browser's {\sl Edit $\Rightarrow$ Copy} menu option). Ensure Jalview is running
-and select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox}.
+\exstep{Use {\sl Window $\Rightarrow$ Close All} from the Desktop window menu to
+close all windows.}
+\exstep{{\bf Loading sequences from URL:} Selecting File {\sl $\Rightarrow$
+Input Alignment $\Rightarrow$ From URL} from the Desktop and enter \textsf{http://www.jalview.org/tutorial/alignment.fa} in the box.
+
+Click OK to load the alignment.}
+\exstep{{\bf Loading sequences from a file:} Close all windows using the
+{\sl Window $\Rightarrow$ Close All} menu option from the Desktop.
+Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
+your web browser and {\bf save} the file to your desktop.
+
+Open the file you have just saved in Jalview by selecting {\sl File
+$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu and
+selecting this file.
+Click OK to load the alignment.}
+\exstep{{\bf Loading sequences by `Drag and Drop' / `Cut and Paste':}
+
+(i) Select {\sl Desktop $\Rightarrow$ Window
+$\Rightarrow$ Close All}. Then drag the alignment.fa file from the desktop and
+drop it onto the Jalview window, the alignment should open.
+
+Test the differences
+between (a) dragging the sequence onto the empty Jalview desktop and (b)
+dragging the sequence onto an existing alignment window.
+
+(ii) Open \url{http://www.jalview.org/tutorial/alignment.fa} in a
+web browser. Drag the URL directly from browser window onto Jalview.
+
+(If the URL is downloaded instead of opened in the browser, then
+locate the file in your download directory and open it in a text editor.)
+
+(iii) 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 Paste to new alignment option.
+
+(iv) In the text editor, copy the sequence text from
+alignment.fa into the clipboard (usually {\sl via} the browser's {\sl Edit
+$\Rightarrow$ Copy} menu option). In the Desktop menu, select {\sl File
+$\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox}.
Paste the clipboard into the large window using the {\sl Edit $\Rightarrow$
Paste} text box menu option. Click {\sl New Window} and the alignment will be
-loaded. } }
+loaded.}
+\exstep{{\bf Loading sequences from Public Database:} Select {\sl File
+$\Rightarrow$ Fetch Sequence(s)...} from the Desktop to open up new window
+called New Sequence Fetcher.
+Press database selection button at the top of the dialog box, this opens
+another window called Select Database Retrieval Source showing all the database
+sources.
+
+Select the {\bf PFAM seed} database and click ok, then enter the accession
+number {\bf PF03460} and click OK. An alignment of about 107 sequences should load.
+
+Several database IDs
+or accession numbers can be loaded by using semicolons to separated them.}}
\subsection{Memory Limits}
\label{memorylimits}
parameters page (\url{http://www.jalview.org/jvmmemoryparams.html}).
-\section{Writing sequence alignments}
-\label{savingalignments} \subsection{Saving the alignment} Jalview allows the
+\section{Writing Sequence Alignments}
+\label{savingalignments} \subsection{Saving the Alignment} 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
the file during or after editing by using the {\sl File $\Rightarrow$ Save} entry.
Jalview offers several different formats in which an alignment can be saved. The
-jalview format (.jar) is the only one which will preserve the colours, groupings
-and similar information in the alignment. The other formats produce text files
-containing just the sequences with no visualization information, although some
+jalview format (.jar) is the only format which 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).
-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
+Unfortunately only Jalview program 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.
%[fig 10]
\parbox[c]{4in}{
\includegraphics[width=4in]{images/saveas2.pdf}
}
-\caption{{\bf Saving alignments in Jalview to disk}}
+\caption{{\bf Saving alignments in Jalview to disk.}}
\label{savealign}
\end{center}
\end{figure}
\subsection{Jalview Projects}
-\parbox[c]{4in}{If you wish to save the complete Jalview session rather than
-just one alignment (e.g. because you have calculated trees or multiple different
-alignments) then your work should be saved as a Jalview Project
-file.\footnote{Tip: Ensure that you have allocated plenty of memory to Jalview
-when working with large alignments in Jalview projects. See Section \protect
+\parbox[c]{4in}{If you wish to save a complete Jalview session rather than
+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.}
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
\exercise{Saving Alignments}{
\label{save}
-\exstep{Start Jalview, close all windows and load the ferredoxin alignment from
-PFAM (PFAM seed accession number PF03460 (see Exercise \ref{load}). }
-\exstep{
-Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a location into which to save the alignment and select a format. All formats except {\sl Jalview } can be viewed in a normal text editor (e.g. Notepad) or in a web browser. Enter a file name and click {\sl Save}. Check this file by closing all windows and opening it with Jalview or by
-browsing to it with your web browser.
-}
-\exstep{ Repeat the previous step trying different file formats.}
-\exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}. You can select and copy this alignment to the clipboard using the textbox menu options {\sl Edit $\Rightarrow$ Select All} followed by {\sl Edit $\Rightarrow$ Copy}. The alignment can then be pasted into any application of choice, e.g. a word processor or web form.
-}
-\exstep{Ensure at least one alignment window is shown in Jalview. Open the
-overview window and scroll to any part of the alignment. Select {\sl File
-$\Rightarrow$ Save Project} from the main menu and save in a suitable place.
-Close all windows and then load the project {\sl via} the {\sl File $\Rightarrow$ Load Project} menu option. Note how all the windows and positions are exactly as they were when they were saved. } }
-
-
-\section{Selecting and editing sequences}
+\exstep{Launch Jalview, or use close all windows.
+Load the ferredoxin
+alignment from PFAM (seed) data base using the PFAM seed accession number
+PF03460 (see Exercise \ref{load}). } \exstep{
+
+Select {\sl File $\Rightarrow$ Save As} from the alignment window menu. Choose a
+location into which to save the alignment and select your prefered format. All
+formats except {\sl Jalview } jvp can be viewed in a normal text editor (e.g.
+Notepad) or in a web browser.
+Enter a file name and click {\sl Save}.
+
+Check this file by closing all windows and opening it with Jalview, or by
+browsing to it with your web browser.}
+\exstep{ Repeat the previous step saving the files in different file formats.}
+\exstep{Select {\sl File $\Rightarrow$ Output to Textbox $\Rightarrow$ FASTA}.
+Select and copy this alignment to the clipboard using the textbox menu options
+{\sl Edit $\Rightarrow$ Select All} followed by {\sl Edit $\Rightarrow$ Copy}.
+The alignment can then be pasted into any application of choice, e.g. a word processor or web form.
+}
+\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.
+Select {\sl File
+$\Rightarrow$ Save Project} from the main menu and save the project in a
+suitable folder.
+
+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. } }
+
+
+\section{Selecting and Editing Sequences}
\label{selectingandediting}
Jalview makes extensive use of selections - most of the commands available from
its menus operate on the {\sl currently selected region} of the alignment, either to
change their appearance or perform some kind of analysis. This section
illustrates how to make and use selections and groups.
-\subsection{Selecting parts of an alignment}
+\subsection{Selecting Parts of an Alignment}
Selections can be of arbitrary regions in an alignment, one or more complete columns, or one or more complete sequences.
A selected region can be copied and pasted as a new alignment using the {\sl Edit $\Rightarrow$ Copy} and {\sl Edit $\Rightarrow$ Paste $\Rightarrow$ To New Alignment} in the alignment window menu options.
-To clear (unselect) the selection press the [ESC] (escape) key.
+{\bf To clear (unselect) the selection press the [ESC] (escape) key.}
-\subsubsection{Selecting arbitrary regions}
+\subsubsection{Selecting Arbitrary Regions}
To select part of an alignment, place the mouse at the top left corner of the region you wish to select. Press and hold the mouse button and drag the mouse to the bottom right corner of the chosen region then release the mouse button. A dashed red box appears around the selected region (Figure \ref{select}).
%[fig 12]
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=4in]{images/select1.pdf}
-\caption{{\bf Selecting a region in an alignment}}
+\caption{{\bf Selecting a region in an alignment.}}
\label{select}
\end{center}
\end{figure}
-\subsubsection{Selecting columns}
-To select the same residues in all sequences, click and drag along the alignment ruler. This selects the entire height of the alignment. Ranges of positions can also be selected by clicking on the first position then holding down the [SHIFT] key whilst clicking the other end of the selection. Discontinuous regions can be selected by holding down [CTRL] and clicking on positions to add to the column selection. Note that each [CTRL]-Click changes the current selected sequence region to that column, but adds to the column selection. Selected columns are indicated by red highlighting in the ruler bar (Figure \ref{selectcols}).
+\subsubsection{Selecting Columns}
+To select the same residues in all sequences, click and drag along the alignment ruler.
+This selects the entire column of the alignment. Ranges of positions from the
+alignment ruler can also be selected by clicking on the first position and then
+holding down the [SHIFT] key whilst clicking the other end of the selection.
+Discontinuous regions can be selected by holding down [CTRL] and clicking on positions to add to the column selection. Note that each [CTRL]-Click changes the current selected sequence region to that column, but adds to the column selection. Selected columns are indicated by red highlighting in the ruler bar (Figure \ref{selectcols}).
%[fig 13]
\begin{figure}[htbp]
\end{center}
\end{figure}
-\subsubsection{Selecting sequences}
+\subsubsection{Selecting Sequences}
\begin{figure}[htb]
\begin{center}
\end{figure}
To select multiple complete sequences, click and drag the mouse down the
-sequence ID panel. The same technique as used for columns above can be used with [SHIFT]-Click for continuous and [CTRL]-Click to select discontinuous ranges of sequences (Figure \ref{selectrows}).
+sequence ID panel. The same techniques as used for columns (above) can be used
+with [SHIFT]-Click for continuous and [CTRL]-Click to select discontinuous
+ranges of sequences (Figure \ref{selectrows}).
%[fig 14]
-\subsubsection{Making selections in Cursor mode}
+\subsubsection{Making Selections in Cursor Mode}
To define a selection in cursor mode (which is enabled by pressing [F2] when the alignment window is selected),
navigate to the top left corner of the proposed selection (using the mouse, the arrow keys, or the keystroke
\includegraphics[width=1.5in]{images/csel2.pdf}
\includegraphics[width=1.5in]{images/csel3.pdf}
\includegraphics[width=1.5in]{images/csel4.pdf}
-\caption{{\bf Making a selection in cursor mode.} Navigate to the top left corner (left), press [Q] (left center), navigate to the bottom right corner (right center) and press [M] (right)}
+\caption{{\bf Making a selection in cursor mode.} Navigate to the top left
+corner (left), press [Q] (left center), navigate to the bottom right corner (right center) and press [M] (right).}
\label{cselect}
\end{center}
\end{figure}
-\subsubsection{Inverting the current selection}
+\subsubsection{Inverting the Current Selection}
The current sequence or column selection can be inverted, using {\sl Select
$\Rightarrow$ Invert Sequence/Column Selection} in the alignment window.
visible, invert the selection, then select {\sl View $\Rightarrow$ Hide
$\Rightarrow$ Selected Region }.
-\subsection{Creating groups}
+\subsection{Creating Groups}
Selections are lost as soon as a different region is selected. Groups can be
created which are labeled regions of the alignment. To create a group, first
select the region which is to comprise the group. Then click the right mouse
\begin{center}
\includegraphics[width=3in]{images/group1.pdf}
\includegraphics[width=1.5in]{images/newgroup.pdf}
-\caption{{\bf Creating a new group from a selection}}
+\caption{{\bf Creating a new group from a selection.}}
\label{makegroup}
\end{center}
\end{figure}
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.
-\subsection{Exporting the current selection}
+\subsection{Exporting the Current Selection}
The current selection can be copied to the clipboard (in PFAM format). It can
also be output to a textbox using the output functions in the pop-up menu
Save As } pulldown menu option from the text box.
-\exercise{Making selections and groups}{
+\exercise{Making Selections and Groups}{
\label{exselect}
-\exstep{Close all windows in Jalview and load the ferredoxin alignment (PFAM
-ID PF03460). Choose a residue and place the mouse cursor on it. Click and drag the mouse cursor 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 should border the selected region. Now press [ESC] to clear the selection.} \exstep{
-Select one sequence by clicking on the ID panel. Note that the sequence ID takes on a highlighted background and a red box appears around the selected sequence. Now 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.
-Now hold down [CTRL] and click on several sequences ID's both selected and unselected. Note how unselected IDs are individually added to the selection and previously selected IDs are individually deselected.
-}
-\exstep{ Repeat the step above but selecting columns by clicking on the ruler bar instead of selecting rows by clicking on the sequence ID.
-}
-\exstep{Press [F2] to enter Cursor mode. Navigate to column 59, row 1 by pressing {\sl 5 9 , 1 [RETURN]}. Press {\sl Q} to mark this position. Now navigate to column 65, row 8 by pressing {\sl 6 5 , 8 [RETURN]}. Press {\sl M} to complete the selection.}
-\exstep{\label{exselectgrpcolour}Open the popup menu by right-clicking the
-selected region with the mouse. Open the {\sl Selection $\Rightarrow$ Group $\Rightarrow$ Group Colour } menu and select `Percentage Identity'. This will turn the selected region into a group and colour it accordingly.}
-\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences by clicking on their Sequence ID label. Note how the group expands to include newly selected sequences, and the `Percentage Identity' colouring changes. }
-\exstep{
-Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
-
-\exstep{
-Right click on the text area to open the selection popup-menu. Follow the menus and pick an output format from the {\sl Selection $\Rightarrow$ Output to Textbox \ldots} submenu.
-}
-\exstep{Try manually editing the alignment and then press the [New Window] button to import the file into a new alignment window.}
+\exstep{Close all windows in Jalview.
+Load the ferredoxin alignment (PFAM
+ID PF03460 from PFAM seed database).
+Choose a residue and place the mouse
+cursor on it. Note residue information will show in alignment window status bar.
+Click and drag the mouse cursor 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 should border the selected region.
+Press [ESC] to clear the selection.}
+\exstep{ Select one sequence by clicking on
+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.
+
+Hold down [CTRL] and then click on several sequences ID's both selected and
+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{ To selecting arbitrary regions in alignment, place the mouse at the top
+left corner of the region you wish to select. Press and hold the mouse button.
+Drag the mouse to the bottom right corner of the chosen region and release the
+mouse button and a dashed red box appears around the selected region}
+\exstep{Enter Cursor mode using [F2] (or [Fn]-F2 for Macs).
+Navigate to column 59, row 1 by pressing {\bf 5 9 , 1 [RETURN]}.
+Press {\bf Q} to mark this position.
+Navigate to column 65, row 8 by pressing {\bf 6 5 , 8 [RETURN]}. Press {\bf M}
+to complete the selection. Note to clear the selection press the {\bf[ESC]}
+key.} \exstep{To create a {\bf group} from the selected the region, click the
+right mouse button when mouse is on the selection, this opens the selection
+popup menu in the alignment window.
+
+Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
+} menu and select `Percentage Identity'.
+This will turn the selected region into a group and colour it accordingly.}
+\exstep{Hold down [CTRL] and use the mouse to select and deselect sequences in
+the alignment by clicking on their Sequence ID label. Note how the group expands
+to include newly selected sequences, and the `Percentage Identity' colouring changes. } \exstep{ Use the mouse to click and drag the right-hand edge of the selected group. Note again how the group resizes.}
+
+\exstep{The current selection can be {\bf exported} and saved by right clicking
+on the text area to open the selection popup-menu. Follow the menus and pick an
+output format (eg BLC) from the {\sl Selection $\Rightarrow$ Output to Textbox
+\ldots} submenu.
+}
+\exstep{In the alignment output window, try manually editing the alignment,
+importing group into a new alignment window by clicking the [New Window] button to import the
+file into a new alignment window.}
% more? change colouring style. set border colour.
}
-\subsection{Reordering the alignment}
+\subsection{Reordering the Alignment}
Sequence reordering is simple. Highlight the sequences to be moved then press the up or down arrow keys as appropriate (Figure \ref{reorder}). If you wish to move a sequence up past several other sequences it is often quicker to select the group past which you want to move it and then move the group rather than the individual sequence.
\begin{figure}[htbp]
\begin{center}
\includegraphics[width=3in]{images/move1.pdf}
\includegraphics[width=3in]{images/move2.pdf}
-\caption{{\bf Reordering the alignment.} The selected sequence moves up one position on pressing the $\uparrow$ key}
+\caption{{\bf Reordering the alignment.} The selected sequence moves up one
+position on pressing the $\uparrow$ key.}
\label{reorder}
\end{center}
\end{figure}
-\exercise{Reordering the alignment}{
-\exstep{Open an alignment (e.g.the PFAM domain PF03460). Select one sequence. Using the up and down arrow keys, alter its position in the alignment. Note that this will not work in cursor mode.
-}
-\exstep{Hold [CTRL] and select two sequences separated by one or more un-selected sequences. Note how multiple sequences are grouped together when they are re-ordered using the up and down arrow keys.
-}
-}
+\exercise{Reordering the Alignment}{
+\exstep{Close all windows in Jalview from desktop. Load the ferredoxin alignment (e.g.the
+PFAM domain PF03460 from PFAM seed).
+Select one of the sequence in the sequence ID panel, use the up and down
+arrow keys to alter the sequence's position in the alignment. (Note that
+this will not work in cursor mode)}
+\exstep{To select and move multiple
+sequences, use hold [SHIFT] and [CTRL], and select two sequences separated by
+one or more un-selected sequences. Note how multiple sequences are grouped
+together when they are re-ordered using the up and down arrow keys.} }
-\subsection{Hiding regions}
+\subsection{Hiding Regions}
\label{hidingregions}
It is sometimes convenient to exclude some sequences or residues in the alignment without actually deleting them. Jalview allows sequences or alignment columns within a view to be hidden, and this facility has been used to create the several different views in the example alignment file that is loaded when Jalview is first started (See Figure \ref{startpage}).
\includegraphics[width=1.5in]{images/hide1.pdf}
\includegraphics[width=2.5in]{images/hide2.pdf}
\includegraphics[width=1.75in]{images/hide3.pdf}
-\caption{{\bf Hiding Sequences} Hidden sequences are represented by a small blue triangle in the sequence ID panel}
+\caption{{\bf Hiding Sequences} Hidden sequences are represented by a small blue
+triangle in the sequence ID panel.}
\label{hideseq}
\end{center}
\end{figure}
\includegraphics[width=2in]{images/hide4.pdf}
\includegraphics[width=3in]{images/hide5.pdf}
\includegraphics[width=1in]{images/hide6.pdf}
-\caption{{\bf Hiding Columns} Hidden columns are represented by a small blue triangle in the ruler bar}
+\caption{{\bf Hiding Columns} Hidden columns are represented by a small blue
+triangle in the ruler bar.}
\label{hidecol}
\end{center}
\end{figure}
$\Rightarrow$ All but Selected Region } menu entry, or press [Shift]+[Ctrl]+H
to hide the unselected region.
-\subsubsection{Representing a group with a single sequence}
+\subsubsection{Representing a Group with a Single Sequence}
Instead of hiding a group completely, it is sometimes useful to work with just one representative sequence. The {\sl $<$Sequence ID$>$ $\Rightarrow$ Represent group with $<$Sequence ID$>$ } option from the sequence ID pop-up menu enables this variant of the hidden groups function. The remaining representative sequence can be visualized and manipulated like any other. However, any alignment edits that affect the sequence will also affect the whole sequence group.
-\subsection{Introducing and removing gaps}
+\subsection{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).
\exstep{ Similarly delete the gap now at column 34, then insert two gaps at column 38. 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.}
}
-\section{Colouring sequences}
+\section{Colouring Sequences}
\label{colours}
Colouring sequences is a key aspect of alignment presentation. Jalview allows
There are two main types of colouring styles: simple static residue colourschemes and dynamic schemes which use conservation and consensus analysis to control colouring. A hybrid colouring is also possible, where static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme} below.
-\subsection{Colouring the whole alignment}
+\subsection{Colouring the Whole Alignment}
\parbox[c]{3.75in}{The alignment can be coloured {\sl via} the {\sl Colour} menu option in the alignment window. Selecting the colour scheme causes all residues to be coloured. The menu is divided into three sections. The first section gives options for the behaviour of the menu options, the second lists static and dynamic colourschemes available for selection. The last gives options for making hybrid colourschemes using conservation shading or colourscheme thresholding.
}
}
-\subsection{Colouring a group or selection}
+\subsection{Colouring a Group or Selection}
Selections or groups can be coloured in two ways. The first is {\sl via} the Alignment Window's {\sl Colour} menu as stated above, after first ensuring that the {\sl Apply Colour To All Groups} flag is not selected. This must be turned {\sl off} specifically as it is {\sl on} by default. When unticked, selections from the Colours menu will only change the colour for residues in the current selection, or the alignment view's ''background colourscheme'' when no selection exists.
\end{center}
\end{figure}
-\subsection{Shading by conservation}
+\subsection{Shading by Conservation}
For many colour schemes, the intensity of the colour in a column can be scaled
by the degree of amino acid property conservation. Selecting {\sl Colour
$\Rightarrow$ By Conservation} enables this mode, and {\sl Modify
\end{center}
\end{figure}
-\subsection{Thresholding by percentage identity}
+\subsection{Thresholding by Percentage Identity}
`Thresholding' is another hybrid colour model where a residue is only coloured
if it is not excluded by an applied threshold. Selecting {\sl Colour $\Rightarrow$ Above Identity Threshold} brings up a selection box with a slider controlling the minimum percentage identity threshold to be applied. Selecting a higher threshold (by sliding to the right) limits the colouring to columns with a higher percentage identity (as shown by the Consensus histogram in the annotation panel).
rows, such as protein disorder scores. This functionality is described futher in
Section \ref{protdisorderpred}.
-\subsection{Colour schemes}
+\subsection{Colour Schemes}
\label{colscheme}
Full details on each colour scheme can be found in the Jalview on-line help. A brief description of each one is provided below:
}
}
-\section{Alignment formatting and graphics output}
+\section{Alignment Formatting and Graphics Output}
\label{layoutandoutput}
Jalview is a WYSIWIG alignment editor. This means that for most kinds of graphics output, the layout that is seen on screen will be the same as what is output in an exported graphics file. It is therefore important to pick the right kind of display layout prior to generating figures.
% JBPNote make an excercise on views ?
-\subsection{Alignment layout}
+\subsection{Alignment Layout}
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}
\begin{center}
\parbox[c]{2in}{\includegraphics[width=2in]{images/wrap1.pdf}}
\parbox[c]{4in}{\includegraphics[width=4in]{images/wrap2.pdf}}
-\caption{{\bf Wrapping the alignment}}
+\caption{{\bf Wrapping the alignment.}}
\label{wrap}
\end{center}
\end{figure}
display gaps or sequence symbols that differ from the consensus for each
column, and render all others with a `.'.
%TODO add a graphic to illustrate this.
-\subsection{Annotation ordering and display}
+\subsection{Annotation Ordering and Display}
% TODO: describe consensus, conservation, quality user preferences, and group
% annotation preferences.
The annotation lines which appear below the sequence alignment are described in
\begin{center}
\includegraphics[width=2.5in]{images/annot1.pdf}
\includegraphics[width=2.5in]{images/annot2.pdf}
-\caption{{\bf Hiding Annotations} Annotations can either be hidden from the {\sl View} menu (left) or individually from the context menu (right)}
+\caption{{\bf Hiding Annotations} Annotations can either be hidden from the {\sl
+View} menu (left) or individually from the context menu (right).}
\label{annot}
\end{center}
\end{figure}
\exstep{Move the mouse to the top left hand corner of the Secondary Structure annotation row label - a grey up/down arrow symbol should appear - when this is shown, the height of the {\sl Annotation Area} can be changed by Clicking and dragging the mouse up or down.}
}
-\subsection{Graphical output}
+\subsection{Graphical Output}
\label{figuregen}
\parbox[c]{4in}{Jalview allows alignments figures to be exported in three different formats, each of which is suited to a particular purpose. Image export is {\sl via} the {\sl File $\Rightarrow$ Export Image $\Rightarrow$ \ldots } alignment window menu option. }
\parbox[c]{2in}{\centerline{\includegraphics[width=1.25in]{images/image.pdf}}}
git://source.jalview.org / jalview-manual.git / commitdiff