Frequently Asked Questions

How do I run Jalview?

How do I edit sequences in Jalview?

How do I get the consensus sequence for an alignment?

F2 key does not toggle Cursor mode on my Mac?

Is there a quick reference for Jalview?

Does Jalview work with nucleotide sequences and alignments?

Why can't I save files or images from the Applet version?

Can I run Jalview from the command line?

The old Jalview had font size and page orientation settings for its Postscript output. Where have they gone?

How do I increase the memory available to Jalview?

Something that normally works in Jalview has stopped working! What should I do?

How do I report a bug in Jalview?

Can I install Jalview on a server?

I'm having problems using InstallAnywhere on Mac OSX 10.3.9

I get "Windows Error 3" when installing with InstallAnywhere

A Jalview file I created in an earlier version of Jalview no longer loads.

InstallAnywhere on Linux fails to find shared libraries

My application doesn't like the "/start-end" sequence suffix in files saved by Jalview

Jalview Applet fails on Linux under Java 1.6 runtime

How do I run Jalview?

You need a computer that can run Java 1.4 or later to run the full Jalview application (at the moment, this excludes Mac OS 9 users and some OSX users who have not upgraded yet - sorry).
To download and run the application, go to the download area and follow the instructions there.
If you don't have Java 1.4, but do have Java turned on in your browser, then you can try the applet version of Jalview on the applets page. You can't use the web services, or save projects, but can at least edit your alignments.

How do I get the consensus sequence for an alignment?

Right-click on the consensus histogram and select "Copy consensus sequence".

F2 key does not toggle Cursor mode on my Mac?

You may be using a keyboard which has visual / audio settings mapped onto the Function keys. You must press the "Fn" key, together with F2 key to toggle Cursor Mode. Future releases of Jalview may allow the user to specify key mappings from the Preferences window.

Is there a quick reference for Jalview?

Yes. The PDF is here.

Does Jalview work with nucleotide sequences and alignments?

Jalview does not currently include any special support for scoring or visualizing nucleotide sequence alignments. It can read, write and manipulate DNA sequences, but treats each symbol as an amino-acid rather than a nucleotide. Versions prior to 2.05b will not read and write RNA sequences containing uracil (U). Support for nucleotide sequences and score models will be provided in the next major Jalview release.

Why can't I save files or images from the Applet version?

Because of security restrictions, an applet may not read or write files on the local system. This is to protect you from a malicious applet storing a virus on your computer or deleting all your files. For the moment, only the application can create and save images / alignment files.

Since Jalview 2.1, if the applet on the web page uses the "application_url" parameter, the full application can be launched from the applet by selecting "File -> View In Full Application". This will only work if you have Java 1.4 installed on your desktop. This is the quickest way to get files from the applet into the application from which images can be created.

Can I run Jalview from the command line?

If you use Java Web Start to launch Jalview, you can start up Jalview with a specific file by typing:

javaws http://www.jalview.org/webstart/jalview.jnlp -open yourFileName

If you install with InstallAnywhere you can use several more commands. However, if you call the application with the link provided by InstallAnywhere any output from the application will be sent to output.txt, not standard out.
Extra libraries are necessary to run Jalview 2+ compared to version 1+, so you must start the application with the following command:

java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE]

Current arguments are:

The old Jalview had font size and page orientation settings for its Postscript output. Where have they gone?

Jalview now exports images and graphics using the same settings as the alignment display window. Just set the font and font size, and the layout style (normal or wrapped) using the View menu.
If you do want to specify portrait or landscape, you could use the File→Print dialog box, and redirect the output to a file.

How do I increase the memory available to Jalview?

Full instructions for different operating systems and installations are here. If yours isn't listed, drop us a line at the help address.

Something that normally works in Jalview has stopped working! What should I do?

One of the commonest causes of 'strange behaviour' that our users have reported seems to be Jalview running out of memory. Memory errors can cause some operations to fail silently - with no warning, annotations may disappear from the alignment window, and web service calculations (apparently) never finish.

You should be able to see something in the error log - see the instructions for bug reporting on how to view this. If you do see 'Out of memory' or 'Cannot allocate stack' or 'HeapAllocationError' type messages, then you might be able to fix it by increasing the memory available to jalview.

How do I report a bug in Jalview?

Firstly, see if you can reproduce the bug. Then send a copy of any error report to Jalview by clicking the link under Feedback.

• If you installed Jalview using Java Webstart, locate and start the program "javaws" or "javaws.exe" on your system. Then click the "Edit" menu, select "Preferences" then click the "Advanced" tab. Make sure you check the "Java Console" option to "Show Console", then click "OK" and restart Jalview. Any problems should be output to the console window.
• If you installed Jalview with InstallAnywhere, you will find a text file in the directory in which you installed Jalview called "output.txt" Include this file with any bug report you have.

Also include a copy of the alignment file you are using when you find the bug. Then try to describe as fully as possible the steps you took before the bug occurred.

Can I install Jalview on a server?

Not in version 2.02 or below. Many environments, such as mainframe machines and dedicated servers, do not support a display, keyboard, or mouse. Versions prior to Jalview 2.03 do not run without a graphics environment.
Version 2.03 and above allow the java -Djava.awt.headless=true to be set from the command line.

I'm having problems using InstallAnywhere on Mac OSX 10.3.9

There is a Mac OS X bug that affects InstallAnywhere LaunchAnywheres on OS X 10.3.9 systems with the QuickTime 7.0.4 upgrade.
This appears to only affect systems running 10.3.9, and not 10.4. The current workaround is to revert to QuickTime 7.0.1, through a reinstaller available from Apple on the Support/Downloads page.

http://www.apple.com/support/downloads/quicktime701reinstallerforquicktime704.html

I get "Windows Error 3" when installing with InstallAnywhere

This seems to be a bug that occurs if current JDK versions are installed. You can work around this bug by moving to the directory C:\IA_Installers\Jalview and specifying the JVM location from the command line eg:

     install.exe LAX_VM <path to java executable>

A Jalview file I created in an earlier version of Jalview no longer loads.

We have tried to ensure that all files created in earlier versions of Jalview can be read in by later versions. If you have a Jalview format file which no longer loads, please let us know by emailing the file to us. Its possible other people are having the same problem!

InstallAnywhere on Linux fails to find shared libraries

Some latest versions of Linux fail to install with InstallAnywhere and will generate error messages such as "error while loading shared libraries: libm.so.6: cannot open". The problem can be fixed by modifying the install.bin script, and also the Jalview script.

cp install.bin install.bak
cat install.bak | sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > install.bin
sh install.bin

cp Jalview Jalview.bak
cat Jalview.bak | sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" > Jalview
sh Jalview

My application doesn't like the "/start-end" sequence suffix in files saved by Jalview

In the application, open the preferences dialog window (Tools -> Preferences) Open the tab labelled "Output" and then select which file formats to which you do not wish to append "/start-end"

Jalview Applet fails on Linux under Java 1.6 runtime

Certain flavours of Linux with Java 1.6 installed fail and crash the browser when running the Jalview Applet version 2.2 and earlier. There appears to be a deadlock situation when Linux is loading the font libraries. This is fixed in Jalview 2.2.1.

For developers, comment out the following line of code in jalview.appletgui.AlignFrame:

alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));