% draft. Remaining items are AACon, RNA visualization/editing and Protein disorder analysis exercises.
-24th September 2020
+25th September 2020
\end{center}
\end{center}
\end{figure}
-This tutorial is based on the Jalview
-Desktop application. Much of the information will also be useful for users of
-the JalviewJS, which has the same core editing, analysis and visualization capabilities. The Jalview Desktop, however, is much more powerful, and
-includes additional support for interaction with external web services, and
-production of publication quality graphics.
-
-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 `Launch Jalview Desktop
-button' at the top right hand side 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
-
-%% this paragraph needs to be rewritten for the new signed certificate from Certum.
-
-When the application is launched with webstart, dialogs may appear before
-the application starts. If your browser is not set up to handle webstart, then
-clicking the launch link may download a file that needs to be opened
-manually, or prompt you to select the program to handle the webstart
-file. If that is the case, you will need to locate the {\bf javaws} program
-on your system\footnote{The file that is downloaded will have a type of {\bf
-application/x-java-jnlp-file} or {\bf .jnlp}. The {\bf javaws} program that can run
-this file is usually found in the {\bf bin} directory of your Java
-installation}. Once java webstart has been launched, you may also be prompted to
-accept a security certificate signed by the Barton Group.\footnote{On some
-systems, the certificate may be signed by 'UNKNOWN'. In this case, clicking
-through the dialogs to look at the detailed information about the certificate
-should reveal it to be a Barton group certificate.} You can always trust us, so
-click trust or accept as appropriate. The splash screen (Figure \ref{splash})
-gives information about the version and build date that you are running,
+This tutorial is based on the Jalview Desktop application. Much of the
+information will also be useful for users of the JalviewJS, which has the same
+core editing, analysis and visualization capabilities. The Jalview Desktop,
+however, is much more powerful, and includes additional support for interaction
+with external web services, powerful molecular graphics programs, and production
+of publication quality graphics.
+
+The Jalview Desktop application can be downloaded from the download link on the
+Jalview website, which takes you to
+\href{http://www.jalview.org/download}{(www.jalview.org/download)}. The page
+automatically displays the options available for your computer (e.g. if you have
+Mac or PC), and a button to show all available downloads. These include special
+'executable Jar' distributions useful if you want to run a specific version of
+Jalview.
+To ensure you are running the latest version of Jalview, we recommend
+downloading the Jalview Desktop Installer package for your platform, clicking on
+the downloaded file and following the instructions to install it.
+Once installed, the Jalview Application will automatically update itself when a
+new version is released.
+
+When the Jalview Desktop application is launched, you will first see a loading
+screen whilst it checks for updates, then the program will start with the
+Jalview splash screen (Figure \ref{splash}).
+This 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 at
+publications. This information is also available on the Jalview web site at
\url{http://www.jalview.org}.
%[fig 2]
\end{center}
\end{figure}
-
-\subsubsection{Jalview News RSS Feed}
-
-Announcements are made available to users of the
-Jalview Desktop {\sl via} the Jalview Newsreader. 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.
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[height=3in]{images/jvrssnews.pdf}
-\caption{{\bf The Jalview News Reader.} The newsreader opens automatically
-when new articles are available from the Jalview Desktop's news channel.}
-\label{jalviewrssnews}
-\end{center}
-\end{figure}
-
-
\exercise{Launching Jalview from the Jalview Website}{
\label{start}
\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 {Dialog boxes
-will open and ask if you want to open the jalview.jnlp file as the file is an application downloaded from the
-Internet, click {\sl Open}. (Note you may be 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
-its version may affect this process.}
+in your web browser. To instal Jalview, first click the 'Download' link in the top right hand corner of the Jalview homepage. This
+will open the download webpage, the options available will reflect if you have Mac or PC computer.}
+\exstep {Download the application by clicking the download link as appropriate for your computer operating system.}
+\exstep {Instal the Jalview application by going to the download folder and
+clicking on the downloaded file, and follow the instructions.}
+\exstep {If you are having any issues, it may help changing the browser.}
\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
`Visual' preferences tab.
Click {\sl 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{Quit Jalview and open it again to check that the
+%%The example alignment is not loaded wehn 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 (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_7.jar})
+box) to view the files, select exampleFile\_2\_7.jvp
+(shown as \url{https://www.jalview.org/examples/exampleFile_2_7.jvp})
then click {\sl OK}.}
\begin{list}{$\circ$}{\newline
\newline {\bf
to the {\sl Tools $\Rightarrow$
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}.}
}
+\subsubsection{Jalview News RSS Feed}
+
+Announcements are made available to users of the
+Jalview Desktop {\sl via} the Jalview Newsreader. 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.
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[height=3in]{images/jvrssnews.pdf}
+\caption{{\bf The Jalview News Reader.} The newsreader opens automatically
+when new articles are available from the Jalview Desktop's news channel.}
+\label{jalviewrssnews}
+\end{center}
+\end{figure}
+
\subsection{Getting Help}
\label{gettinghelp}
\subsubsection{Built in Documentation}
navigation panel on the left hand side. To search for a specific topic, click
the `search' tab and enter keywords in the box which appears.
+\subsubsection{Email Lists}
+
+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
+kept informed of new releases and developments.
+
+Archives and mailing list
+subscription details can be found in the Jalview web site's \href{http://www.jalview.org/community}{community section}.
\begin{figure}[htbp]
\begin{center}
\end{center}
\end{figure}
-\subsubsection{Email Lists}
-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
-kept informed of new releases and developments.
-
-Archives and mailing list
-subscription details can be found in the Jalview web site's \href{http://www.jalview.org/community}{community section}.
\section{Navigation}
\end{center}
\end{figure}
+ \exercise{Navigation}{
+\label{navigationEx}
+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, the key
+combination {\bf Fn and F2} keys are needed, as the {\bf F2} button is
+often assigned to screen brightness. Jalview always starts up in 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}
+on the dialog box is an easy way to access it.)}
+\exstep{Scroll around the alignment using the alignment (vertical) and ruler (horizontal) scroll bars.}
+\exstep{Find the Overview Window, {\sl View
+$\Rightarrow$ Overview Window} and open it. Move around the
+alignment by clicking and dragging the red box in the overview window.}
+\exstep{Return to the alignment window, 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] key, or [Fn]-[F2] on Mac, to enter Cursor mode. Use
+the direction 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
+{\sl Help} in desktop window menu, clicking on {\sl Documentation} will open a
+Documentation window. Select topics from the navigation panel on the left hand
+side or use the Search tab to locate specific key words.
+
+{\sl\bf See the video at:
+\url{http://www.jalview.org/Help/Getting-Started}.}
+}
+
\subsection{Navigation in Normal Mode}
Jalview always starts up in Normal mode, where the mouse is used to interact
\parbox[c]{3in}{\centerline{\includegraphics[width=2.5in]{images/start_closeall.pdf}
}}
+
\subsection{Navigation in Cursor Mode}
\label{cursormode}
\parbox[c]{5in}{Cursor mode navigation enables the user to quickly
expressions that can be used with it.
%TODO insert a figure for the Find dialog box
-\exercise{Navigation}{
-\label{navigationEx}
-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, the key
-combination {\bf Fn and F2} keys are needed, as the {\bf F2} button is
-often assigned to screen brightness. Jalview always starts up in 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}
-on the dialog box is an easy way to access it.)}
-\exstep{Scroll around the alignment using the alignment (vertical) and ruler (horizontal) scroll bars.}
-\exstep{Find the Overview Window, {\sl View
-$\Rightarrow$ Overview Window} and open it. Move around the
-alignment by clicking and dragging the red box in the overview window.}
-\exstep{Return to the alignment window, 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] key, or [Fn]-[F2] on Mac, to enter Cursor mode. Use
-the direction 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
-{\sl Help} in desktop window menu, clicking on {\sl Documentation} will open a
-Documentation window. Select topics from the navigation panel on the left hand
-side or use the Search tab to locate specific key words.
-
-{\sl\bf See the video at:
-\url{http://www.jalview.org/Help/Getting-Started}.}
-}
-
\section{Loading Sequences and Alignments}
\label{loadingseqs}
%Jalview provides many ways to load your own sequences. %For this section of the
\end{center}
\end{figure}
-\subsection{From a URL}
-Jalview can read sequence alignments directly from a URL. Please note that the
-files must be in a sequence alignment format - an HTML alignment or graphics
-file cannot be read by Jalview.
-Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the
-main menu and a window will appear asking you to enter the URL (Figure
-\ref{loadurl}). Jalview will attempt to automatically discover the file format.
-
-%[fig 7]
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2in]{images/menuloadurl.pdf}
-\includegraphics[width=3in]{images/loadurlbox.pdf}
-\caption{{\bf Opening an alignment from a URL. }}
-\label{loadurl}
-\end{center}
-\end{figure}
-
-\subsection{Cut and Paste}
-\label{cutpaste}
-Documents such as those produced by Microsoft Word cannot be readily understood
-by Jalview. The way to read sequences from these documents is to select the
-data from the document and copy it to the clipboard. There are two ways to
-do this. One is to right-click on the desktop background, and select the
-`Paste to new window' option in the menu that appears. The other is to select
-{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the
-main menu, paste the sequences into the text window that will appear, and select
-{\sl New Window} (Figure \ref{loadtext}). In both cases, presuming that they are
-in the right format, Jalview will happily read them into a new alignment window.
-%[fig 8]
-
-\begin{figure}[htbp]
-\begin{center}
-\includegraphics[width=2in]{images/menuloadtext.pdf}
-\includegraphics[width=3in]{images/loadtextbox.pdf}
-\caption{{\bf Opening an alignment from pasted text. }}
-\label{loadtext}
-\end{center}
-\end{figure}
-
-
-\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
-and the PDB. Jalview's sequence fetching capabilities allow you to avoid having to
-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.
-
-To begin retrieving data, select {\sl File $\Rightarrow$ Fetch Sequences \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}
-\includegraphics[width=5in]{images/fetchseq.pdf}
-\caption{{\bf Retrieving sequences from a public database.}}
-\label{loadseq}
-\end{center}
-\end{figure}
-
\exercise{Loading Sequences}{
\label{load}
\exstep{{\bf Loading sequences from a file:} Close all windows using the
{\sl Window $\Rightarrow$ Close All} menu option from the Jalview desktop.
Then type the same URL (\url{http://www.jalview.org/tutorial/alignment.fa}) into
-your web browser. Then from the brwoser, save the fasta file (.fa) file to your desktop using {\sl File
+your web browser. Then from the browser, save the fasta file (.fa) file to your desktop using {\sl File
$\Rightarrow$ Save Page as}.
Open the file you have just saved on your computer in Jalview by selecting {\sl File
$\Rightarrow$ Input Alignment $\Rightarrow$ From File} from the desktop menu.
{\bf See the video at:
\url{http://www.jalview.org/Help/Getting-Started}} }
-\subsection{Memory Limits}
+
+\subsection{From a URL}
+Jalview can read sequence alignments directly from a URL. Please note that the
+files must be in a sequence alignment format - an HTML alignment or graphics
+file cannot be read by Jalview.
+Select {\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From URL} from the
+main menu and a window will appear asking you to enter the URL (Figure
+\ref{loadurl}). Jalview will attempt to automatically discover the file format.
+
+%[fig 7]
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=2in]{images/menuloadurl.pdf}
+\includegraphics[width=3in]{images/loadurlbox.pdf}
+\caption{{\bf Opening an alignment from a URL. }}
+\label{loadurl}
+\end{center}
+\end{figure}
+
+\subsection{Cut and Paste}
+\label{cutpaste}
+Documents such as those produced by Microsoft Word cannot be readily understood
+by Jalview. The way to read sequences from these documents is to select the
+data from the document and copy it to the clipboard. There are two ways to
+do this. One is to right-click on the desktop background, and select the
+`Paste to new window' option in the menu that appears. The other is to select
+{\sl File $\Rightarrow$ Input Alignment $\Rightarrow$ From Textbox} from the
+main menu, paste the sequences into the text window that will appear, and select
+{\sl New Window} (Figure \ref{loadtext}). In both cases, presuming that they are
+in the right format, Jalview will happily read them into a new alignment window.
+%[fig 8]
+
+\begin{figure}[htbp]
+\begin{center}
+\includegraphics[width=2in]{images/menuloadtext.pdf}
+\includegraphics[width=3in]{images/loadtextbox.pdf}
+\caption{{\bf Opening an alignment from pasted text. }}
+\label{loadtext}
+\end{center}
+\end{figure}
+
+
+\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
+and the PDB. Jalview's sequence fetching capabilities allow you to avoid having to
+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.
+
+To begin retrieving data, select {\sl File $\Rightarrow$ Fetch Sequences \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}
+\includegraphics[width=5in]{images/fetchseq.pdf}
+\caption{{\bf Retrieving sequences from a public database.}}
+\label{loadseq}
+\end{center}
+\end{figure}
+
+ \subsection{Memory Limits}
\label{memorylimits}
Jalview 2.11 and later will automatically maximise the amount of memory available,
but if you are using an earlier version or launching Jalview in a specialised way
selecting {\sl Help $\Rightarrow$ Documentation}) and on the JVM memory
parameters page (\url{http://www.jalview.org/jvmmemoryparams.html}).
+
\section{Saving Sequences and Alignments}
\label{savingalignments}
\subsection{Saving Alignments} Jalview allows alignments to be saved to file
\end{center}
\end{figure}
-\subsection{Jalview Projects}
-\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
-\ref{memorylimits} 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
-view at which the file was saved, complete with all alignments, trees,
-annotation and displayed structures rendered appropriately.
-} \parbox[c]{2.3in}{ \centerline {
-\includegraphics[width=2.2in]{images/saveproj.pdf} }}
-
\exercise{Saving Alignments}{
\label{save}
\exstep{Launch Jalview afresh, or use {\sl Desktop $\Rightarrow$ Window
reopen. Are they the same as when they were saved ? } {\bf See the video at:
\url{http://www.jalview.org/Help/Getting-Started}.} }
+%% Suzanne: Jim's comment: this now appears at the end of the section, over the page from the exercise. I doubt anyone will read it there.
+\subsection{Jalview Projects}
+\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 that plenty of memory is available to
+Jalview when working with large alignments in Jalview projects. See Section
+\ref{memorylimits} for how to check 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
+view at which the file was saved, complete with all alignments, trees,
+annotation and displayed structures rendered appropriately.
+} \parbox[c]{2.3in}{ \centerline {
+\includegraphics[width=2.2in]{images/saveproj.pdf} }}
+
\chapter{Selecting and Editing Sequences }
\label{jalviewediting}
Open the {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
} menu and select {\sl Percentage Identity}.
This will turn the selected region into a group and colour it accordingly.}
-\exstep{Hold down [CTRL] ([CMD] on Mac) or [SHIFT] and use the mouse to select and deselect sequences in
+\exstep{Hold down [CTRL] ([CMD] on Mac) 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{ Another way to resize the group is by using the mouse to click and drag
+\exstep{ Another way to resize the group is simply to use the mouse to click and drag
the right-hand edge of the selected group.}
\exstep{The current selection can be exported and saved, place mouse on the text
Load the ferredoxin alignment ({\bf PF03460} from {\bf PFAM (seed)}).
}
-\exstep{Select one of the sequence in the sequence ID panel, use the up and down
+\exstep{Select one of the sequences 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
}
\exstep{Repeat the above using columns to hide and reveal columns
instead of sequences.}
-\exstep{Select a region of the alignment, and experiment with the {\sl Hide all
-but selected region} option. In the alignment window menu, {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
-but selected region.}} \exstep{Select some sequences, pick one to represent the rest by hovering
+\exstep{Select a region of the alignment, and experiment with {\sl View $\Rightarrow$ Hide $\Rightarrow$ Hide all
+but selected region} and {\sl View $\Rightarrow$ Hide $\Rightarrow$ All
+but selected region} options in the alignment window menu.} \exstep{Select some sequences, pick one to represent the rest by hovering
the mouse over this sequence. Bring up the Sequence ID context menu by right
clicking and select {\sl (Sequence ID name) $\Rightarrow$ Represent group
with (Sequence ID name )}. To reveal these hidden sequences, right click on the
columns in all sequences in the selected group, and those columns are to the
right of the selected residue.
+{\bf That's it for this chapter. Don't forget the exercises on the next page!}
+\newpage
-\exercise{Editing Alignments Homework Exercise}
+\exercise{Editing Alignments}
%\label{mousealedit}
% TODO: VERIFY FOR 2.6.1 and 2.7 - NUMBERING/INSTRUCTIONS APPEAR OFF
{
alignment available at
\href{http://www.jalview.org/examples/exampleFile.jvp}
{http://www.jalview.org/examples/exampleFile.jvp}.
+
+ {\sl {\bf Note: this is a homework exercise for jalview course participants!}}
{\sl {\bf Mac Users:} Please use the Apple or [CMD] key in place of [CTRL]
for key combinations such as [CTRL]-A. }
}
-\exercise{Keyboard Edits Homework Exercise}
+\exercise{Keyboard Edits}
{
\label{keyboardsex}
This continues on from the previous exercise, and recreates the final part of the example ferredoxin
alignment from the unaligned sequences using Jalview's keyboard editing mode.
+{\bf Note: This is a homework exercise for jalview course participants}
+
{\bf Window users:} Please {\em only use} [SHIFT]-[SPACE] in this
exercise.
displayed, and you may have to disable it using the {\sl View $\Rightarrow$
Show Sequence Features} option before you can see your colourscheme.
-There are two main types of colouring styles: {\bf simple static residue}
+There are two main types of colouring styles: simple {\bf static residue}
colourschemes and {\bf dynamic schemes} which use conservation and consensus
analysis to control colouring. {\bf Hybrid colouring} is also possible, where
static residue schemes are modified using a dynamic scheme. The individual schemes are described in Section \ref{colscheme}.
\exercise{Colouring Alignments}{
\label{color}
Note: Ensure that the {\sl Apply Colour
-To All Groups} flag is not selected (ie unticked) in {\sl Colour} menu in the alignment window.
+To All Groups} flag is not selected (i.e. not ticked) in {\sl Colour} menu in the alignment window.
% patch needed for 2.10 This must be turned {\sl off} specifically as it is on
% by default.
Clustalx} and note the colour change. Now try all the other colour schemes in the {\sl Colour} menu.
Note that some colour schemes do not colour all residues.}
\exstep{Colour the alignment using {\sl Colour $\Rightarrow$ Blosum62 score}. Select a group
-of around 4 similar sequences. Use the context menu (right click on the residues in the group)
+of around 4 similar sequences. Use the context menu (opened by right clicking on the residues in the group)
option {\sl Selection $\Rightarrow$ Edit New Group $\Rightarrow$ Group Colour
$\Rightarrow$ Blosum62 score} to colour the selection. Notice how some residues which
were not coloured are now coloured. The calculations performed for dynamic
Select the menu option {\sl Colour $\Rightarrow$ By Conservation}.
Slide the selector in the Conservation Colour Increment dialog box from side
to side and observe the changes in the alignment colouring in the selection and in the complete alignment.}
-Note: Feature colours overlay residue colouring and this may mask residue colouring. If this is an issue, he features colours can be
-toggled off by going to {\sl View $\Rightarrow$ Show Sequence Features}.
+
+Note: If you don't see any changes in appearance, it might be because sequence
+features are currently displayed (these are introduced later, in Section
+\ref{featannot}). To see if features are obscuring your colour scheme settings, look to see if the {\sl View
+$\Rightarrow$ Show Sequence Features} option in the alignment window menu is
+ticked. If it is, select it to disable feature colouring.
{\bf See the video at: \url{http://www.jalview.org/training/Training-Videos}.}
}
\subsubsection{Alignment and Group Colouring and Appearance}
The display of hidden row/column markers and gap characters can be turned off with {\sl Format $\Rightarrow$ Show Hidden Markers} and
-{\sl Format $\Rightarrow$ Show Gaps}, respectively. The {\sl Text} and {\sl Colour Text} option controls the display of sequence text and the application of alignment and group colouring to it. {\sl Boxes } controls the display of the background area behind each residue that is coloured by the applied coloursheme.
+{\sl Format $\Rightarrow$ Show Gaps}, respectively. The {\sl Text} and {\sl Colour Text} option controls the display of sequence
+text and the application of alignment and group colouring to it. {\sl Boxes } controls the display of the background area
+behind each residue that is coloured by the applied colourscheme.
\subsubsection{Highlighting Nonconserved Symbols}
The alignment layout and group sub-menu both contain an option to hide
dialog box. Then, adjust the slider or enter a value in the text box to set the
threshold for displaying this type of feature.
-When a filters and complex colourschemes are applied, the configuration column will show coloured blocks or text to indicate the colouring
+When filters and complex colourschemes are applied, the configuration column will show coloured blocks or text to indicate the colouring
style and any attribute filters.
git://source.jalview.org / jalview-manual.git / blobdiff