-<h2>
- <center>
- <strong>Memory Usage Settings for Jalview</strong>
- </center>
-</h2>
-<p>Jalview sometimes runs out of memory. This is because of the way that Java
- runs on a computer - what is actually run is a program called a virtual machine
- (the JVM) which executes the java instructions. The JVM has limits on the memory
- that can be allocated to the java program - and you might need to increase them
- if you are working with particularly large datasets.<br>
- If Jalview has not explicitly told you that it has run out of memory, then a
- common sign is that a function that normally works seems to have no effect when
- working with a larger set of sequences (this might include open dialog boxes
- for saving PNG files, or when interpreting the result of a web service calculation).</p>
- <p><em>Jalview Memory Usage Monitor</em>: If you are concerned about memory, or think that things might be behaving
- strangely because of a shortage of memory, then you can check this by enabling the
- memory usage monitor. This is done by selecting the <strong>Tools→Show Memory Usage</strong>
- option. Once enabled, the memory usage monitor displays the currently
- available memory, the total memory, and the percentage free at the
- bottom left hand side of the Jalview Desktop window's background.</p>
-<p><em>Increasing the memory available to Jalview</em><br>
-The way you increase the memory settings for the JVM depends on which installation
- of Jalview you use:</p>
-<ul>
- <li><em><font size="3">Web Start Version</font></em>
- <p>
- JavaWS sets the JVM parameters through special tags in the JNLP
- file. You can obtain a JNLP file with modified memory settings from
- our service with the following link (replace 2G with desired memory
- in G or M):<br /> <a
- href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G">http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
- </p>
- <p>
- Alternatively, if you want to create your own JNLP file then please
- download the latest JNLP file from <a
- href="http://www.jalview.org/webstart/jalview.jnlp">http://www.jalview.org/webstart/jalview.jnlp</a>
- and modify the max-heap-size parameter for the j2se tag in the
- <resources> element. e.g.
- <pre>
+ <h2>
+ <center>
+ <strong>Memory Usage Settings for Jalview</strong>
+ </center>
+ </h2>
+ <p>
+ Jalview sometimes runs out of memory. This is because of the way
+ that Java runs on a computer - what is actually run is a program
+ called a virtual machine (the JVM) which executes the java
+ instructions. The JVM has limits on the memory that can be allocated
+ to the java program - and you might need to increase them if you are
+ working with particularly large datasets.<br> If Jalview has
+ not explicitly told you that it has run out of memory, then a common
+ sign is that a function that normally works seems to have no effect
+ when working with a larger set of sequences (this might include open
+ dialog boxes for saving PNG files, or when interpreting the result
+ of a web service calculation).
+ </p>
+ <p>
+ <em>Jalview Memory Usage Monitor</em>: If you are concerned about
+ memory, or think that things might be behaving strangely because of
+ a shortage of memory, then you can check this by enabling the memory
+ usage monitor. This is done by selecting the <strong>Tools→Show
+ Memory Usage</strong> option. Once enabled, the memory usage monitor
+ displays the currently available memory, the total memory, and the
+ percentage free at the bottom left hand side of the Jalview Desktop
+ window's background.
+ </p>
+ <p>
+ <em>Increasing the memory available to Jalview</em><br> The way
+ you increase the memory settings for the JVM depends on which
+ installation of Jalview you use:
+ </p>
+ <ul>
+ <li><em><font size="3">Web Start Version</font></em>
+ <p>
+ JavaWS sets the JVM parameters through special tags in the JNLP
+ file. You can obtain a JNLP file with modified memory settings
+ from our service with the following link (replace 2G with
+ desired memory in G or M):<br /> <a
+ href="http://www.jalview.org/services/launchApp?jvm-max-heap=2G"
+ >http://www.jalview.org/services/launchApp?jvm-max-heap=2G</a>
+ </p>
+ <p>
+ Alternatively, if you want to create your own JNLP file then
+ please download the latest JNLP file from <a
+ href="http://www.jalview.org/webstart/jalview.jnlp"
+ >http://www.jalview.org/webstart/jalview.jnlp</a> and modify the
+ max-heap-size parameter for the j2se tag in the
+ <resources> element. e.g.
+ <pre>