@@ -59,7+59,7 @@ JABAWS 2.0.1 includes several bug fixes and minor updates for JABAWS Version 2.0
* Disembl returned swapped strings for HOTLOOPS and REM465
* Jronn failed to process jobs with more than 3 sequences
* JABAWS could not deal with FASTA records with '>' symbols in the record identificator
* Disembl returned swapped strings for HOTLOOPS and REM465
* Jronn failed to process jobs with more than 3 sequences
* JABAWS could not deal with FASTA records with '>' symbols in the record identificator
-* Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores in one call
+* Change of parameter description for AACon: parameters have been replaced with options for calculation methods. This allows a user to get several AACon's conservation scores in one call
* JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties
* Default web security has been incompatible with Tomcat 7.0.31 and newer
* Documentation has been updated
* JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties
* Default web security has been incompatible with Tomcat 7.0.31 and newer
@@ -7,7+7,7 @@ If you are using JABAWS VA (Virtual Appliance) then the username is *jabaws* and
If you have deployed a JABAWS WAR file, then please see the `configuring privileged access`_ for Tomcat web application server section for further details.
If you have deployed a JABAWS WAR file, then please see the `configuring privileged access`_ for Tomcat web application server section for further details.
Please note that if you deployed JABAWS WAR, in order to be able to navigate to the job directory from this view, the application server may need to be configured. Please see the `Configuring JABAWS execution statistics`_ section for further details.
Please note that if you deployed JABAWS WAR, in order to be able to navigate to the job directory from this view, the application server may need to be configured. Please see the `Configuring JABAWS execution statistics`_ section for further details.
By default, the JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for the JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory lets your VM deal with larger tasks, e.g. work with large alignments.
By default, the JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for the JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory lets your VM deal with larger tasks, e.g. work with large alignments.
@@ -59,7+59,7 @@ JABAWS 2.0.1 includes several bug fixes and minor updates for JABAWS Version 2.0
* Disembl returned swapped strings for HOTLOOPS and REM465
* Jronn failed to process jobs with more than 3 sequences
* JABAWS could not deal with FASTA records with '>' symbols in the record identificator
* Disembl returned swapped strings for HOTLOOPS and REM465
* Jronn failed to process jobs with more than 3 sequences
* JABAWS could not deal with FASTA records with '>' symbols in the record identificator
-* Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores in one call
+* Change of parameter description for AACon: parameters have been replaced with options for calculation methods. This allows a user to get several AACon's conservation scores in one call
* JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties
* Default web security has been incompatible with Tomcat 7.0.31 and newer
* Documentation has been updated
* JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties
* Default web security has been incompatible with Tomcat 7.0.31 and newer
@@ -7,7+7,7 @@ If you are using JABAWS VA (Virtual Appliance) then the username is *jabaws* and
If you have deployed a JABAWS WAR file, then please see the `configuring privileged access`_ for Tomcat web application server section for further details.
If you have deployed a JABAWS WAR file, then please see the `configuring privileged access`_ for Tomcat web application server section for further details.
Please note that if you deployed JABAWS WAR, in order to be able to navigate to the job directory from this view, the application server may need to be configured. Please see the `Configuring JABAWS execution statistics`_ section for further details.
Please note that if you deployed JABAWS WAR, in order to be able to navigate to the job directory from this view, the application server may need to be configured. Please see the `Configuring JABAWS execution statistics`_ section for further details.
By default, the JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for the JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory lets your VM deal with larger tasks, e.g. work with large alignments.
By default, the JABAWS virtual appliance is configured with 512M of memory and 1 CPU, but you are free to change these settings. If you have more than one CPU or CPU core on your computer you can make them available for the JABAWS virtual machine by editing virtual machine settings. Please bear in mind that more CPU power will not make a single calculation go faster, but it will enable the VM to do calculations in parallel. Similarly, you can add more memory to the virtual machine. More memory lets your VM deal with larger tasks, e.g. work with large alignments.
<li>Disembl returned swapped strings for HOTLOOPS and REM465</li>
<li>Jronn failed to process jobs with more than 3 sequences</li>
<li>JABAWS could not deal with FASTA records with ‘>’ symbols in the record identificator</li>
<li>Disembl returned swapped strings for HOTLOOPS and REM465</li>
<li>Jronn failed to process jobs with more than 3 sequences</li>
<li>JABAWS could not deal with FASTA records with ‘>’ symbols in the record identificator</li>
-<li>Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon’s conservation scores in one call</li>
+<li>Change of parameter description for AACon: parameters have been replaced with options for calculation methods. This allows a user to get several AACon’s conservation scores in one call</li>
<li>JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties</li>
<li>Default web security has been incompatible with Tomcat 7.0.31 and newer</li>
<li>Documentation has been updated</li>
<li>JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties</li>
<li>Default web security has been incompatible with Tomcat 7.0.31 and newer</li>
<span id="jabaws-api"></span><h2>The API<a class="headerlink" href="#the-api" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="the-api">
<span id="jabaws-api"></span><h2>The API<a class="headerlink" href="#the-api" title="Permalink to this headline">¶</a></h2>
-<p><a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html">Data Model JavaDoc</a> - read this if your are coding against JABA Web Services</p>
-<p><a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/index.html">Complete JavaDoc</a> - for developers who want to use JABAWS framework and use Engines and Executables directly</p>
+<p><a class="reference external" href="../dm_javadoc/index.html">Data Model JavaDoc</a> - read this if your are coding against JABA Web Services</p>
+<p><a class="reference external" href="../full_javadoc/index.html">Complete JavaDoc</a> - for developers who want to use JABAWS framework and use Engines and Executables directly</p>
@@ -337,7+337,7 @@ JABAWS uses TestNG for testing. There is a TestNG plugin available for Eclipse w
</tbody>
</table>
<p>Additional utility libraries that this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.</p>
</tbody>
</table>
<p>Additional utility libraries that this client depend upon is the compbio-util-1.3.jar and compbio-annotation-1.0.jar.</p>
-<p>Please refer to a <a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html">Data Model JavaDoc</a> for a detailed description of each class and its methods.</p>
+<p>Please refer to a <a class="reference external" href="../dm_javadoc/index.html">Data Model JavaDoc</a> for a detailed description of each class and its methods.</p>
<hr class="docutils" />
</div>
<div class="section" id="connecting-to-jabaws">
<hr class="docutils" />
</div>
<div class="section" id="connecting-to-jabaws">
@@ -587,7+587,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
<span class="o">}</span>
</pre></div>
</div>
<span class="o">}</span>
</pre></div>
</div>
-<p>For a more detailed description of all available types and their functions please refer to the <a class="reference external" href="http://www.compbio.dundee.ac.uk/jabaws/dm_javadoc/index.html">Data Model JavaDoc</a>.</p>
+<p>For a more detailed description of all available types and their functions please refer to the <a class="reference external" href="../dm_javadoc/index.html">Data Model JavaDoc</a>.</p>
<hr class="docutils" />
</div>
</div>
<hr class="docutils" />
</div>
</div>
@@ -695,7+695,7 @@ Methods and classes mentioned in the excerpt are available from the JABAWS clien
<h1>Welcome to JABAWS’s documentation!<a class="headerlink" href="#welcome-to-jabaws-s-documentation" title="Permalink to this headline">¶</a></h1>
<h1>Welcome to JABAWS’s documentation!<a class="headerlink" href="#welcome-to-jabaws-s-documentation" title="Permalink to this headline">¶</a></h1>
-<p>Read on these documentation pages or go back to the <a class="reference external" href="../">JABAWS homepage</a>!</p>
+<p>Read on these documentation pages or go back to the <a class="reference external" href="../../">JABAWS homepage</a>!</p>
<p>JABAWS documentation is also available in <em>pdf</em>. <a class="reference external" href="./jabaws_manual.pdf">Download it here</a>!</p>