Merge branch 'develop' into releases/Release_2_10_Branch

diff --git a/examples/groovy/featureCounter.groovy b/examples/groovy/featureCounter.groovy
index a16d8bb..9059dd0 100644 (file)
--- a/examples/groovy/featureCounter.groovy
+++ b/examples/groovy/featureCounter.groovy
@@ -1,3 +1,24 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+ 
 import jalview.workers.FeatureCounterI;
 import jalview.workers.AlignmentAnnotationFactory;
 

diff --git a/help/help.jhm b/help/help.jhm
index 53b09e5..1760d43 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -130,6 +130,7 @@
    
    <mapID target="memory" url="html/memory.html" />
    <mapID target="groovy" url="html/features/groovy.html" />
+   <mapID target="groovy.featurecounter" url="html/groovy/featureCounter.html" />
    <mapID target="privacy" url="html/privacy.html" />
    <mapID target="vamsas" url="html/vamsas/index.html"/>
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index c4476fd..ed95a61 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -156,9 +156,11 @@
                </tocitem>
                <tocitem text="Preferences" target="preferences" />
                <tocitem text="Memory Settings" target="memory" expand="false"/>
+               <tocitem text="Scripting with Groovy" target="groovy">
+                       <tocitem text="Groovy Feature Counter example" target="groovy.featurecounter"/>
+               </tocitem>
                <tocitem text="Command Line" target="commandline" expand="false">
                        <tocitem text="Command Line Arguments" target="clarguments" />
-                       <tocitem text="Groovy Shell" target="groovy" />
                </tocitem>
                <tocitem text="Privacy" target="privacy" />
        </tocitem>

diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html
index 200fc8f..b7738cd 100755 (executable)
--- a/help/html/features/featuresettings.html
+++ b/help/html/features/featuresettings.html
@@ -72,13 +72,13 @@
   </p>
   <p>
     <strong><em>Feature settings pop-up menu</em></strong><br> <strong>Right-click</strong>
-    on a feature to open a pop-up menu that allows you to sort the
-    alignment or current selection using that feature type (see below),
-    or toggle the type of colouring used for the feature. Features may
-    be highlighted with either a single colour or a <a
-      href="featureschemes.html"
-    >feature colourscheme</a> based on either the scores associated with
-    that feature or from the feature's description (e.g. to distinguish
+    on a feature to open a pop-up menu that allows you to<ul><li>Hide, show and
+    select columns containing that feature</li><li>Sort the alignment or
+    current selection using that feature type (see below)</li><li>Toggle the
+    type of colouring used for the feature</li></ul><p>Features may be highlighted
+    with either a single colour or a <a href="featureschemes.html">feature
+      colourscheme</a> based on either the scores associated with that
+    feature or from the feature's description (e.g. to distinguish
     different names associated with a DOMAIN feature).
   </p>
   <p>

diff --git a/help/html/features/groovy.html b/help/html/features/groovy.html
index a2bc627..079cf9e 100644 (file)
--- a/help/html/features/groovy.html
+++ b/help/html/features/groovy.html
@@ -27,21 +27,23 @@
     <strong>The Groovy Shell</strong>
   </p>
   <p>
-    <a href="http://www.groovy-lang.org/">Groovy</a> is an &quot;<em>agile
-      and dynamic language for the Java platform</em>&quot;. The groovy
-    scripting language makes it extremely easy to programmatically
-    interact with Java programs, in much the same way that Javascript is
-    used to generate and interact with applets and other objects on the
-    page.
+    Groovy (<a href="http://www.groovy-lang.org/">www.groovy-lang.org</a>)
+    is an &quot;<em>agile and dynamic language for the Java
+      platform</em>&quot;. The groovy scripting language makes it extremely
+    easy to programmatically interact with Java programs, in much the
+    same way that Javascript is used to generate and interact with
+    applets and other objects on the page.
   </p>
   <p>
-    <strong><em>Getting Groovy...</em> </strong><br> Jalview comes with
-    an embedded installation of Groovy. All you need is to select <strong>Tools&#8594;Groovy
-      Console...</strong> menu option from the Jalview Desktop's
-    drop-down menu. After a short pause, you should then see the <a
-      href="http://groovy-lang.org/groovyconsole.html"
-    >Groovy Console</a> appear. This allows you to interactively execute Groovy
-    scripts within the Jalview run-time environment.
+    <em>Getting Groovy...</em><br> Jalview comes with an embedded
+    installation of Groovy. Just select <strong>Tools&#8594;Groovy
+      Console...</strong> from the Jalview Desktop's drop-down menu. After a
+    short pause, you should then see the <a
+      href="http://groovy-lang.org/groovyconsole.html">Groovy
+      Console</a> appear. This allows you to interactively execute Groovy
+    scripts whilst Jalview is running. We've also provided a <strong>Calculations&#8594;Execute
+      Groovy Script</strong> button so you can execute the currently loaded
+    groovy script whilst viewing an alignment.
   </p>
   <p>
     <strong>Executing groovy scripts on Jalview startup</strong><br>
@@ -56,18 +58,29 @@
     </em>
   </p>
   <p>
-    <strong>Executing a groovy script on a particular alignment</strong><br/>
-    
-  <p>
     <strong>Access to Jalview's functions from Groovy Scripts</strong><br>
-    There is as yet no properly defined scripting interface to Jalview,
-    but all the public methods of the jalview class hierarchy can be
-    called from Groovy scripts. The access point for this is the <strong>Jalview</strong>
-    object defined in the groovy environment which corresponds to the
-  <pre>jalview.gui.Desktop</pre>
-  object which manages all the Jalview windows. Here's an example to get
-  you started:
-  <br>
+    The scripting interface to Jalview is still a work in progress, so
+    we recommend you also take a look at Jalview's source, since all the
+    public methods of the jalview class hierarchy can be called from
+    Groovy scripts. In addition, the following objects are also defined:
+
+  
+  <ul>
+    <li><strong>Jalview</strong> - this is bound to <code>jalview.bin.Jalview</code>.<br />Useful
+      methods include:
+      <ul>
+        <li>Jalview.getAlignFrames() - returns a list of
+          jalview.gui.AlignFrame objects</li>
+        <li>Jalview.getCurrentAlignFrame() - returns the alignment
+          window which is currently being looked at by the user</li>
+      </ul></li>
+    <li><strong>currentAlFrame</strong> - this is only defined when
+      running a Groovy script via the -groovy command line argument. It
+      returns the first alignment window created after acting on the
+      other arguments passed on the command line.</li>
+  </ul>
+  <p>
+    <em>A simple script</em><br />
   <ul>
     <li>Getting the title, alignment and first sequence from the
       current alignFrame<br> <pre>
@@ -77,13 +90,26 @@ def alignment = alf[0].viewport.alignment;
 def seq = alignment.getSequenceAt(0);
 </pre>
     </li>
-    <li>When running a groovy script from the command line, the
-      alignment that was just loaded can be referred to like so:<br>
-    <pre>
+    <li>If you wanted to do the same thing from the command line, you can refer to
+      alignment that was just loaded with currentAlFrame:<br>
+      <pre>
 print currentAlFrame.getTitle();</pre>
   </ul>
-  If you have downloaded the InstallAnywhere version of Jalview, you can
-  find additional groovy scripts in the examples/groovy subfolder of the
-  installation directory.
+  <p>
+    <em>Example scripts</em><br />If you have downloaded the
+    InstallAnywhere version of Jalview, you can find additional groovy
+    scripts in the examples/groovy subfolder of the installation
+    directory. The examples are also available at <a
+      href="http://www.jalview.org/examples/groovy">http://www.jalview.org/examples/groovy</a>.
+  </p>
+  <p>
+    <em>Using Groovy to add new Alignment Calculations</em><br />We've
+    simplified the alignment analysis programming interface in Jalview
+    2.10 to make it easy for you to add your own dynamic annotation
+    tracks with Groovy. Have a look at the <a
+      href="../groovy/featureCounter.html">featureCounter.groovy</a>
+    example for more information.
+  </p>
+
 </body>
 </html>

diff --git a/help/html/groovy/featureCounter.html b/help/html/groovy/featureCounter.html
new file mode 100644 (file)
index 0000000..fe848a9
--- /dev/null
+++ b/help/html/groovy/featureCounter.html
@@ -0,0 +1,262 @@
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Extending Jalview with Groovy - Feature Counter Example</title>
+</head>
+<body>
+  <p>
+    <strong>Extending Jalview with Groovy - A customisable
+      feature counter</strong><br /> 
+    <br />The groovy script below shows how to add a new calculation
+    track to a Jalview alignment window.</p><p>As currently written, it will
+    add two tracks to a protein alignment view which count Pfam features
+    in each column, and ones where a charge residue also occur.</p><p>To try
+    it for yourself:</p><ol><li>Copy and paste it into the groovy script
+    console</li><li>Load the example Feredoxin project (the one that opens
+    by default when you first launched Jalview)</li><li>Select <strong>Calculations&#8594;Execute
+      Groovy Script</strong> from the alignment window's menu bar to run the script on
+    the current view.</li></ol>
+  <em><a
+      href="http://www.jalview.org/examples/groovy/featureCounter.groovy">http://www.jalview.org/examples/groovy/featureCounter.groovy</a> - rendered with <a href="http://hilite.me">hilite.me</a></em>
+  <!-- HTML generated using hilite.me -->
+  <div
+    style="background: #ffffff; overflow: auto; width: auto; border: solid gray; border-width: .1em .1em .1em .8em; padding: .2em .6em;">
+    <pre style="margin: 0; line-height: 125%">
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Jalview - A Sequence Alignment Editor and Viewer (Version 2.10)</span>
+<span style="color: #888888"> * Copyright (C) 2016 The Jalview Authors</span>
+<span style="color: #888888"> * </span>
+<span style="color: #888888"> * This file is part of Jalview.</span>
+<span style="color: #888888"> * </span>
+<span style="color: #888888"> * Jalview is free software: you can redistribute it and/or</span>
+<span style="color: #888888"> * modify it under the terms of the GNU General Public License </span>
+<span style="color: #888888"> * as published by the Free Software Foundation, either version 3</span>
+<span style="color: #888888"> * of the License, or (at your option) any later version.</span>
+<span style="color: #888888"> *  </span>
+<span style="color: #888888"> * Jalview is distributed in the hope that it will be useful, but </span>
+<span style="color: #888888"> * WITHOUT ANY WARRANTY; without even the implied warranty </span>
+<span style="color: #888888"> * of MERCHANTABILITY or FITNESS FOR A PARTICULAR </span>
+<span style="color: #888888"> * PURPOSE.  See the GNU General Public License for more details.</span>
+<span style="color: #888888"> * </span>
+<span style="color: #888888"> * You should have received a copy of the GNU General Public License</span>
+<span style="color: #888888"> * along with Jalview.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
+<span style="color: #888888"> * The Jalview Authors are detailed in the &#39;AUTHORS&#39; file.</span>
+<span style="color: #888888"> */</span>
+ 
+<span style="color: #008800; font-weight: bold">import</span> <span
+        style="color: #0e84b5; font-weight: bold">jalview.workers.FeatureCounterI</span><span
+        style="color: #333333">;</span>
+<span style="color: #008800; font-weight: bold">import</span> <span
+        style="color: #0e84b5; font-weight: bold">jalview.workers.AlignmentAnnotationFactory</span><span
+        style="color: #333333">;</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Example script that registers two alignment annotation calculators</span>
+<span style="color: #888888"> * - one that counts residues in a column with Pfam annotation</span>
+<span style="color: #888888"> * - one that counts only charged residues with Pfam annotation</span>
+<span style="color: #888888"> *</span>
+<span style="color: #888888"> * To try:</span>
+<span style="color: #888888"> * 1. load uniref50.fa from the examples folder</span>
+<span style="color: #888888"> * 2. load features onto it from from examples/exampleFeatures.txt</span>
+<span style="color: #888888"> * 3. Open this script in the Groovy console.</span>
+<span style="color: #888888"> * 4. Either execute this script from the console, or via Calculate-&gt;Run Groovy Script</span>
+<span style="color: #888888"> </span>
+<span style="color: #888888"> * To explore further, try changing this script to count other kinds of occurrences of </span>
+<span style="color: #888888"> * residue and sequence features at columns in an alignment.</span>
+<span style="color: #888888"> */</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * A closure that returns true for any Charged residue</span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> isCharged <span
+        style="color: #333333">=</span> <span style="color: #333333">{</span> residue <span
+        style="color: #333333">-&gt;</span>
+    <span style="color: #008800; font-weight: bold">switch</span><span
+        style="color: #333333">(</span>residue<span
+        style="color: #333333">)</span> <span style="color: #333333">{</span>
+        <span style="color: #008800; font-weight: bold">case</span> <span
+        style="color: #333333">[</span><span
+        style="background-color: #fff0f0">&#39;D&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;d&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;E&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;e&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;H&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;h&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;K&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;k&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;R&#39;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&#39;r&#39;</span><span
+        style="color: #333333">]:</span>
+            <span style="color: #008800; font-weight: bold">return</span> <span
+        style="color: #008800; font-weight: bold">true</span>
+    <span style="color: #333333">}</span>
+    <span style="color: #008800; font-weight: bold">false</span>
+<span style="color: #333333">}</span> 
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * A closure that returns 1 if sequence features include type &#39;Pfam&#39;, else 0</span>
+<span style="color: #888888"> * Argument should be a list of SequenceFeature </span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> hasPfam <span
+        style="color: #333333">=</span> <span style="color: #333333">{</span> features <span
+        style="color: #333333">-&gt;</span> 
+    <span style="color: #008800; font-weight: bold">for</span> <span
+        style="color: #333333">(</span>sf <span
+        style="color: #008800; font-weight: bold">in</span> features<span
+        style="color: #333333">)</span>
+    <span style="color: #333333">{</span>
+        <span style="color: #888888">/*</span>
+<span style="color: #888888">         * Here we inspect the type of the sequence feature.</span>
+<span style="color: #888888">         * You can also test sf.description, sf.score, sf.featureGroup,</span>
+<span style="color: #888888">         * sf.strand, sf.phase, sf.begin, sf.end</span>
+<span style="color: #888888">         * or sf.getValue(attributeName) for GFF &#39;column 9&#39; properties</span>
+<span style="color: #888888">         */</span>
+        <span style="color: #008800; font-weight: bold">if</span> <span
+        style="color: #333333">(</span><span
+        style="background-color: #fff0f0">&quot;Pfam&quot;</span><span
+        style="color: #333333">.</span><span style="color: #0000CC">equals</span><span
+        style="color: #333333">(</span>sf<span style="color: #333333">.</span><span
+        style="color: #0000CC">type</span><span style="color: #333333">))</span>
+        <span style="color: #333333">{</span>
+            <span style="color: #008800; font-weight: bold">return</span> <span
+        style="color: #008800; font-weight: bold">true</span>
+        <span style="color: #333333">}</span>
+    <span style="color: #333333">}</span>
+    <span style="color: #008800; font-weight: bold">false</span>
+<span style="color: #333333">}</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Closure that computes an annotation based on </span>
+<span style="color: #888888"> * presence of particular residues and features</span>
+<span style="color: #888888"> * Parameters are</span>
+<span style="color: #888888"> * - the name (label) for the alignment annotation</span>
+<span style="color: #888888"> * - the description (tooltip) for the annotation</span>
+<span style="color: #888888"> * - a closure (groovy function) that tests whether to include a residue</span>
+<span style="color: #888888"> * - a closure that tests whether to increment count based on sequence features  </span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> getColumnCounter <span
+        style="color: #333333">=</span> <span style="color: #333333">{</span> name<span
+        style="color: #333333">,</span> desc<span style="color: #333333">,</span> acceptResidue<span
+        style="color: #333333">,</span> acceptFeatures <span
+        style="color: #333333">-&gt;</span>
+    <span style="color: #333333">[</span>
+     <span style="color: #997700; font-weight: bold">getName:</span> <span
+        style="color: #333333">{</span> name <span
+        style="color: #333333">},</span> 
+     <span style="color: #997700; font-weight: bold">getDescription:</span> <span
+        style="color: #333333">{</span> desc <span
+        style="color: #333333">},</span>
+     <span style="color: #997700; font-weight: bold">getMinColour:</span> <span
+        style="color: #333333">{</span> <span style="color: #333333">[</span><span
+        style="color: #0000DD; font-weight: bold">0</span><span
+        style="color: #333333">,</span> <span
+        style="color: #0000DD; font-weight: bold">255</span><span
+        style="color: #333333">,</span> <span
+        style="color: #0000DD; font-weight: bold">255</span><span
+        style="color: #333333">]</span> <span style="color: #333333">},</span> <span
+        style="color: #888888">// cyan</span>
+     <span style="color: #997700; font-weight: bold">getMaxColour:</span> <span
+        style="color: #333333">{</span> <span style="color: #333333">[</span><span
+        style="color: #0000DD; font-weight: bold">0</span><span
+        style="color: #333333">,</span> <span
+        style="color: #0000DD; font-weight: bold">0</span><span
+        style="color: #333333">,</span> <span
+        style="color: #0000DD; font-weight: bold">255</span><span
+        style="color: #333333">]</span> <span style="color: #333333">},</span> <span
+        style="color: #888888">// blue</span>
+     <span style="color: #997700; font-weight: bold">count:</span> 
+         <span style="color: #333333">{</span> res<span
+        style="color: #333333">,</span> feats <span
+        style="color: #333333">-&gt;</span> 
+            <span style="color: #333399; font-weight: bold">def</span> c <span
+        style="color: #333333">=</span> <span
+        style="color: #0000DD; font-weight: bold">0</span>
+            <span style="color: #008800; font-weight: bold">if</span> <span
+        style="color: #333333">(</span>acceptResidue<span
+        style="color: #333333">.</span><span style="color: #0000CC">call</span><span
+        style="color: #333333">(</span>res<span style="color: #333333">))</span>
+            <span style="color: #333333">{</span>
+                <span style="color: #008800; font-weight: bold">if</span> <span
+        style="color: #333333">(</span>acceptFeatures<span
+        style="color: #333333">.</span><span style="color: #0000CC">call</span><span
+        style="color: #333333">(</span>feats<span style="color: #333333">))</span>
+                <span style="color: #333333">{</span>
+                    c<span style="color: #333333">++</span>
+                <span style="color: #333333">}</span>
+            <span style="color: #333333">}</span>
+            c
+         <span style="color: #333333">}</span>
+     <span style="color: #333333">]</span> <span
+        style="color: #008800; font-weight: bold">as</span> FeatureCounterI
+<span style="color: #333333">}</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Define an annotation row that counts any residue with Pfam domain annotation</span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> pfamAnnotation <span
+        style="color: #333333">=</span> getColumnCounter<span
+        style="color: #333333">(</span><span
+        style="background-color: #fff0f0">&quot;Pfam&quot;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&quot;Count of residues with Pfam domain annotation&quot;</span><span
+        style="color: #333333">,</span> <span style="color: #333333">{</span><span
+        style="color: #008800; font-weight: bold">true</span><span
+        style="color: #333333">},</span> hasPfam<span
+        style="color: #333333">)</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Define an annotation row that counts charged residues with Pfam domain annotation</span>
+<span style="color: #888888"> */</span>
+<span style="color: #333399; font-weight: bold">def</span> chargedPfamAnnotation <span
+        style="color: #333333">=</span> getColumnCounter<span
+        style="color: #333333">(</span><span
+        style="background-color: #fff0f0">&quot;Pfam charged&quot;</span><span
+        style="color: #333333">,</span> <span
+        style="background-color: #fff0f0">&quot;Count of charged residues with Pfam domain annotation&quot;</span><span
+        style="color: #333333">,</span> isCharged<span
+        style="color: #333333">,</span> hasPfam<span
+        style="color: #333333">)</span>
+
+<span style="color: #888888">/*</span>
+<span style="color: #888888"> * Register the annotations</span>
+<span style="color: #888888"> */</span>
+AlignmentAnnotationFactory<span style="color: #333333">.</span><span
+        style="color: #0000CC">newCalculator</span><span
+        style="color: #333333">(</span>pfamAnnotation<span
+        style="color: #333333">)</span> 
+AlignmentAnnotationFactory<span style="color: #333333">.</span><span
+        style="color: #0000CC">newCalculator</span><span
+        style="color: #333333">(</span>chargedPfamAnnotation<span
+        style="color: #333333">)</span>
+</pre>
+  </div>
+</body>
+</html>

diff --git a/help/html/menus/alwannotation.html b/help/html/menus/alwannotation.html
index f8f4889..6f91d2f 100755 (executable)
--- a/help/html/menus/alwannotation.html
+++ b/help/html/menus/alwannotation.html
@@ -25,8 +25,8 @@
 
 <body>
   <p>
-    <strong>Alignment Window Annotations Menu</strong> (Since Jalview
-    2.8.2)
+    <strong>Alignment Window Annotations Menu</strong> <em>Since Jalview
+    2.8.2</em>
   </p>
   <ul>
     <li><strong>Show Alignment Related</strong><em><br>

diff --git a/help/html/menus/alwannotationpanel.html b/help/html/menus/alwannotationpanel.html
index ad9596a..7d07595 100755 (executable)
--- a/help/html/menus/alwannotationpanel.html
+++ b/help/html/menus/alwannotationpanel.html
@@ -30,6 +30,10 @@
     <li><strong>Annotation Label Popup Menu</strong><br> <em>This
         menu is opened by clicking anywhere on the annotation row labels
         area (below the sequence ID area).</em>
+        <br/><em><strong>Mac Users:</strong> pressing CTRL whilst clicking
+      the mouse/track pad is the same as a right-click. See your
+      system's settings to configure your track-pad's corners to
+      generate right-clicks.</em>
       <ul>
         <li><strong>Add New Row</strong><br> <em>Adds a
             new, named annotation row (a dialog box will pop up for you

diff --git a/help/html/menus/index.html b/help/html/menus/index.html
index cbc4217..fcfcdae 100755 (executable)
--- a/help/html/menus/index.html
+++ b/help/html/menus/index.html
@@ -41,7 +41,11 @@
   <p>
     The <a href="popupMenu.html">Popup Menus</a> are opened by clicking
     with the right mouse button in the alignment display area or on a
-    sequence label in the alignment window.
+    sequence label in the alignment window.<br />
+    <em><strong>Mac Users:</strong> pressing CTRL whilst clicking
+      the mouse/track pad is the same as a right-click. See your
+      system's settings to configure your track-pad's corners to
+      generate right-clicks.</em>
   </p>
   <p>
     The <a href="alwannotationpanel.html">Annotations Menu</a> is opened

diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html
index 353fb41..79e7ada 100755 (executable)
--- a/help/html/menus/popupMenu.html
+++ b/help/html/menus/popupMenu.html
@@ -25,10 +25,13 @@
 
 <body>
   <p>
-    <strong>Popup Menu</strong><br> <em>This menu is visible
-      when right clicking either within a selected region on the
-      alignment or on a selected sequence name. It may not be accessible
-      when in 'Cursor Mode' (toggled with the F2 key).</em>
+    <strong>Popup Menu</strong><br> <em>This menu is visible when
+      right clicking either within a selected region on the alignment or
+      on a selected sequence name. It may not be accessible when in
+      'Cursor Mode' (toggled with the F2 key).</em><br /> <em><strong>Mac Users:</strong> pressing CTRL whilst clicking
+        the mouse/track pad is the same as a right-click. See your
+        system's settings to configure your track-pad's corners to
+        generate right-clicks.</em>
   </p>
   <ul>
     <li><strong>Selection</strong>
@@ -171,13 +174,11 @@
       </ul></li>
     <li><strong>3D Structure Data...</strong> </strong><em>This menu is
         visible when you right-click on a sequence name. When this
-        option is clicked, Jalview will open a <a
-        href="../features/structurechooser.html"
-      >'Structure Chooser' </a> dialogue with options to select the
-        structure which will eventually be opened in a 3D interactive
-        view.<br> These entries will only be present if the
-        sequence has <a href="../features/viewingpdbs.html">associated
-          PDB structures</a>.
+        option is clicked, Jalview will open the <a
+        href="../features/structurechooser.html">'Structure
+          Chooser' </a>, which allows you to discover and view 3D structures
+        for the current selection. For more info, see <a
+        href="../features/viewingpdbs.html">viewing PDB structures</a>.
     </em></li>
     <li><strong>VARNA 2D Structure</strong><br />
     <em> If the sequence or alignment has RNA structure, then <strong>VARNA

diff --git a/help/html/releases.html b/help/html/releases.html
index 51f86e1..74be08e 100755 (executable)
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,7 +47,7 @@
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>20/9/2016</em></strong>
+          <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>27/9/2016</em></strong>
         </div>
       </td>
       <td><em>General</em>
@@ -57,26 +57,30 @@
             <li><!-- JAL-2202 -->Position/residue shown in status bar when mousing over sequence associated annotation</li>
             <li><!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket' for manual entry</li>
             <li><!-- JAL-2214 -->RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column</li>
+            <li><!-- JAL-2092 -->Feature settings popup menu options for showing or hiding columns containing a feature</li>
+            <li><!-- JAL-1557 -->Edit selected group by double clicking on group and sequence associated annotation labels</li>
         </ul> <em>Application</em>
         <ul>
             <li><!-- JAL---></li>
             <li><!-- JAL---></li>
             <li><!-- JAL---></li>
             <li><!-- JAL---></li>
-            <li><!-- JAL---></li>
+            <li><!-- JAL-1479 JAL-1491 -->UniProt - PDB protein structure mappings with the EMBL-EBI PDBe SIFTS database</li>
             <li><!-- JAL-2079 -->Updated download sites used for Rfam and Pfam sources to xfam.org</li>
             <li><!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher</li>
             <li><!-- JAL-2123 -->Show residue labels in Chimera when mousing over sequences in Jalview</li>
             <li><!-- JAL-2027-->Support for reverse-complement coding regions in ENA and EMBL</li>
             <li><!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2 for ENA record retrieval</li>
             <li><!-- JAL-2027 -->Support for ENA CDS records with reverse complement operator</li>
-            <li><!--  JAL 1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
-            <li><!--  JAL 1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
+            <li><!--  JAL-1812 -->New 'execute Groovy script' option in an alignment window's Calculate menu</li>
+            <li><!--  JAL-1812 -->Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode</li>
+            <li><!--  JAL-2068 -->Support for creating new alignment calculation workers from groovy scripts</li>
             <li><!-- JAL-1369 --->Store/restore reference sequence in Jalview projects</li>
-            <li><!-- JAL-1803-->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
-            <li><!-- JAL-2183-->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
-            <li><!-- JAL-1563-->Free-text search client for UniProt using the UniProt REST API</li>
-            
+            <li><!-- JAL-1803 -->Chain codes for a sequence's PDB associations are now saved/restored from project</li>
+            <li><!-- JAL-2183 -->Double click on an entry in Jalview's database chooser opens a sequence fetcher</li>
+            <li><!-- JAL-1563 -->Free-text search client for UniProt using the UniProt REST API</li>
+            <li><!-- JAL-2168 -->-nonews command line parameter to prevent the news reader opening</li>
+                    
              
         </ul> <em>Applet</em>
         <ul>
@@ -100,7 +104,9 @@
             <li><!--  JAL-1577 -->Colour by RNA Helices not enabled when user created annotation added to alignment</li>
             <li><!-- JAL-1841 -->RNA Structure consensus only computed for '()' base pair annotation</li>
             <li><!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus</li>
-            
+            <li><!-- JAL-2174-->Extend selection with columns containing feature not working</li>
+            <li><!-- JAL-2275 -->Pfam format writer puts extra space at beginning of sequence</li>            
+            <li><!-- JAL-1827 -->Incomplete sequence extracted from pdb entry 3a6s </li>
             
           </ul>
           <em>Application</em>
@@ -115,12 +121,13 @@
             <li><!--  JAL-1989  -->Hide columns not mirrored in complement view in a cDNA/Protein splitframe</li>
             <li><!--  JAL-1369 -->Cannot save/restore representative sequence from project when only one sequence is represented</li>
             <li><!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option in Structure Chooser</li>
-            <li><!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel</li>            
+            <li><!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel</li>
+                        
             <!--  may exclude, this is an external service stability issue  JAL-1941 /> RNA 3D structure not added via DSSR service</li> -->
           </ul>
           <em>Applet</em>
           <ul>
-            <li><!--  --></li>
+            <li><!-- JAL-2151 -->Incorrect columns are selected when hidden columns present before start of sequence</li>
           </ul>
         </div>
       </td>