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
Java Web Start version of Jalview fails with error 'Unable to Launch - because JAR resources in JNLP are not signed by same certificate'
Warning about invalid or out of date certificate when launching Jalview via Java Webstart
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:
-nodisplay |
Run Jalview without User Interface. (automatically disables questionnaire, version and usage stats checks) |
-props FILE |
Use the given Jalview properties file instead
of users default. |
-features FILE |
Use the given file to add sequence features to an alignment.
See Features
File (Known as Groups file prior to 2.08) description.
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-annotations FILE
|
Add precalculated annotations to the alignment. See Annotation File
description. |
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-tree FILE
|
Load the given newick format tree file onto
the alignment
|
|
-questionnaire URL
|
Queries the given URL for information about
any Jalview user questionnaires
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-noquestionnaire
|
Turn off questionnaire check
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-nousagestats
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Turn off google analytics usage tracking
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-dasserver nickname=URL
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Add and enable a das server with given
nickname (alphanumeric or underscores only) for retrieval of features
for all alignments
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-fetchfrom nickname
|
Query nickname for features for the alignments
and display them
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-groovy FILE
|
Execute groovy script in FILE (where FILE may be 'STDIN' to read from the standard input) after all other
arguments have been processed
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|
-fasta FILE
|
Create alignment file FILE in Fasta format.
|
-clustal FILE |
Create alignment file FILE in Clustal format. |
-msf FILE |
Create alignment file FILE in MSF format. |
-pileup FILE |
Create alignment file FILE in Pileup format. |
-pir FILE |
Create alignment file FILE in PIR format. |
-pfam FILE |
Create alignment file FILE in PFAM format. |
-blc FILE |
Create alignment file FILE in BLC format. |
-jalview FILE |
Create alignment file FILE in Jalview format. |
-png FILE |
Create PNG image FILE from alignment. |
-imgMap FILE |
Create HTML file FILE with image map of PNG
image. |
-eps FILE |
Create EPS file FILE from alignment. |
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 the Jalview Discussion list 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));
Java Web Start version of Jalview fails with error 'Unable to Launch - because JAR resources in JNLP are not signed by same certificate'
This error (and others like it) is raised when an old version of the Jalview Webstart JNLP is being used to launch the latest version of the application (for instance, because you have created your own JNLP file in order to increase the memory available to Jalview).
To fix, simply make sure that you are using the latest version of the Jalview JNLP file (right-click or apple-click to save this link to a file) to launch jalview.
Warning about untrusted or out of date certificate when launching Jalview via Java Webstart
We publish Jalview using our own X.509 certificates. When launching Jalview for the first time, you will be asked if you would like to accept the signing certificate. Certificates are usually signed by the Barton Group (this information is in the technical details panel), and also include an expiry date. If you use a version of Jalview with an expired certificate you will get a 'Signer's certificate has expired' warning, but if you press 'OK' or 'Accept', you should still be able to launch Jalview.
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