jalview 2.5 documentation (still)

diff --git a/help/help.jhm b/help/help.jhm
index c575a5f..865013b 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -17,6 +17,7 @@
    <mapID target="mafft" url="html/webServices/mafft.html"/>
    <mapID target="jnet" url="html/webServices/jnet.html"/>
    <mapID target="seqfetch" url="html/features/seqfetch.html"/>
+   <mapID target="dbreffetcher" url="html/webservices/dbreffetcher.html"/>
    <mapID target="seqmappings" url="html/features/seqmappings.html"/>
    <mapID target="cdnafeatures" url="html/features/codingfeatures.html"/>
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index feafc0f..f0403e7 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -20,9 +20,10 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
        <tocitem text="What's new" target="new" expand="true">
+      <tocitem text="Graduated Feature Colours" target="features.featureschemes"/>
+      <tocitem text="Sort by Features" target="seqfeatures.settings"/>
+      <tocitem text="Envision2 Service" target="webservice"/>
       <tocitem text="Release History" target="release"/>
-               <tocitem text="Sequence Retrieval" target="seqfetch"/>
-               <tocitem text="VAMSAS Interoperation" target="vamsas"/>
        </tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>        
     <tocitem text="Cursor Mode" target="cursor"/>
@@ -51,6 +52,7 @@
             </tocitem>
           <tocitem text="Secondary Structure Prediction" target="jnet"/>
                <tocitem text="Sequence Retrieval" target="seqfetch"/>
+               <tocitem text="Database Reference Retrieval" target="dbreffetcher"/>
                <tocitem text="DAS Feature Retrieval" target="das.viewing"/>
        </tocitem>
        <tocitem text="Colour Schemes" target="colours" expand="false">

diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html
index 95e233b..00beb2f 100755 (executable)
--- a/help/html/features/annotation.html
+++ b/help/html/features/annotation.html
@@ -98,7 +98,7 @@ User defined annotation is stored and retrieved using <a
 href="../features/jalarchive.html">Jalview Archives</a>.
 </p>
 <p><em>Current Limitations</em></p>
-<p>As of version 2.4, the Jalview user interface does not support the 
+<p>As of version 2.5, the Jalview user interface does not support the 
 creation and editing quantitative annotation (histograms and line graphs), or 
 to create annotation associated with a specific sequence. It is also incapable of
 annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an 

diff --git a/help/html/features/featuresFormat.html b/help/html/features/featuresFormat.html
index b802c63..93ce408 100755 (executable)
--- a/help/html/features/featuresFormat.html
+++ b/help/html/features/featuresFormat.html
@@ -105,7 +105,7 @@ in order to attach it to the whole sequence. Non-positional features are
 shown in a tooltip when the mouse hovers over the sequence ID panel, and
 any embedded links can be accessed from the popup menu.
 <em>Scores</em><br>
-Scores can be associated with sequence features, and used to sort sequences or shade the alignment (this was added in jalview 2.4.X). The score field is optional, and malformed scores will be ignored.
+Scores can be associated with sequence features, and used to sort sequences or shade the alignment (this was added in jalview 2.5). The score field is optional, and malformed scores will be ignored.
 </p>
 <p>Feature annotations can be collected into named groups by
 prefixing definitions with lines of the form:<strong><pre>startgroup&#9;groupname</pre></strong>..

diff --git a/help/html/jalviewjnlp.html b/help/html/jalviewjnlp.html
index 0eacdb4..0c68bfb 100755 (executable)
--- a/help/html/jalviewjnlp.html
+++ b/help/html/jalviewjnlp.html
@@ -47,7 +47,7 @@
   &lt;!-- <em>the additional memory parameters are here</em> --&gt;
   &lt;j2se version="1.4+" initial-heap-size="500M" max-heap-size="1000M"/&gt;
     &lt;jar href="jalview.jar"/&gt;
-               &lt;jar href="JGoogleAnalytics_0.2.jar"/&gt;
+               &lt;jar href="JGoogleAnalytics-0.2.1-SNAPSHOT.jar"/&gt;
                &lt;jar href="Jmol-11.0.2.jar"/&gt;
                &lt;jar href="activation.jar"/&gt;
                &lt;jar href="axis.jar"/&gt;
@@ -64,7 +64,7 @@
                &lt;jar href="wsdl4j.jar"/&gt;
                &lt;jar href="xercesImpl.jar"/&gt;
                &lt;jar href="xml-apis.jar"/&gt;
-               &lt;property name="jalview.version" value="2.4.0.b2"/&gt;
+               &lt;property name="jalview.version" value="2.5"/&gt;
   &lt;/resources&gt;
   &lt;application-desc main-class="jalview.bin.Jalview"/&gt;
 &lt;/jnlp&gt;

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 8f03c9a..30d9033 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -88,7 +88,8 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
        </em></li>
                    </ul>
       </li>
-      <li><strong>Group Links<br>
+<!-- not available in 2.5 yet
+    <li><strong>Group Links<br>
     </strong><em>This menu is only visible if there are group links available for the current selection.
     </em> 
     <ul>
@@ -97,7 +98,7 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).</em></p>
     <li><em>Sequence and ID links</em> allow you to send sets of IDs and sequences associated with the current selection to a web server.</li>
     </ul>
     <em>Group Links were added in Jalview 2.5</em></li>
-    </ul>
+-->    </ul>
   </li>
   <li><strong>Sequence Id<br>
     </strong><em>This menu is only visible if you right-click on a sequence name. 

diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index 6425e9c..8e785dc 100755 (executable)
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -26,12 +26,16 @@
 <p>Jalview includes clients for a variety of web services for both
 bioinformatic data retrieval and analysis.
 <ul>
-       <li>The <a href="../features/seqfetcher.html">Sequence Fetcher</a>
+       <li>The <a href="../features/seqfetch.html">Sequence Fetcher</a>
        utilises web services for sequence, alignment and structure retrieval
        provided by the European Bioinformatics Institute (EBI) and Distributed
        Annotation System servers that are capable of serving sequences.</li>
-       <li>The DAS Feature Fetcher enables the retrieval and
-       visualization of features from DAS annotation sources</li>
+       <li>The <a href="../features/dasfeatures.html">DAS Feature
+       Fetcher</a> enables the retrieval and visualization of features from DAS
+       annotation sources</li>
+       <li>The <a href="dbreffetcher.html">Database Reference Fetcher</a>
+       transfers database references from records available from DAS or the
+       public sequence databases.</li>
        <li>Jalview SOAP Web Services for sequence and alignment analysis
        are provided by the University of Dundee, and are available from the
        Alignment window's <strong> Web Service</strong> menu.</li>
@@ -43,12 +47,13 @@ programs. These services actually run on the cluster based in the School
 of Life Sciences, University of Dundee, and are maintained by the Barton
 group.</p>
 <p><strong><a name="envision2">Envision2 Services</a></strong></p>
-<p>Jalview 2.5 includes a client to enable the user to
-submit one or more sequences or sequence IDs to analysis workflows provided 
-by the <a href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2
-web application</a>. This allows Jalview users to easily access the EnCore network of
-databases and analysis services developed by members of <a href="http://www.enfin.org">ENFIN</a>.</p>
-<br/>
+<p>Jalview 2.5 includes a client to enable the user to submit one or
+more sequences or sequence IDs to analysis workflows provided by the <a
+       href="http://www.ebi.ac.uk/enfin-srv/envision2">EnVision2 web
+application</a>. This allows Jalview users to easily access the EnCore
+network of databases and analysis services developed by members of <a
+       href="http://www.enfin.org">ENFIN</a>.</p>
+<br />
 <p><strong>Web Service Dialog Box</strong></p>
 <img src="clwqueued.gif">
 <p>This dialog box is displayed when a web service job is submitted.