Merge branch 'develop' into improvement/JAL-3830_remove_dock_icon_in_headless_mode

[jalview.git] / help / help / html / features / groovy.html

diff --git a/help/help/html/features/groovy.html b/help/help/html/features/groovy.html
index ead4436..cb0b10c 100644 (file)
--- a/help/help/html/features/groovy.html
+++ b/help/help/html/features/groovy.html
@@ -39,7 +39,7 @@
     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
+      href="https://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
@@ -47,7 +47,7 @@
   </p>
   <p>
     <strong>Executing groovy scripts on Jalview startup</strong><br>
-    The -groovy &lt;script&gt; option on the <a href="commandline.html">
+    The --groovy &lt;script&gt; option on the <a href="commandline.html">
       Jalview command line</a> will execute the contents of &lt;script&gt;.
     &lt;script&gt; may be a file, a URL, or alternatively if it is
     &quot;STDIN&quot; then the standard input will be used.<br> <em>Note:
@@ -76,7 +76,7 @@
           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
+      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>
@@ -101,7 +101,7 @@ print currentAlFrame.getTitle();</pre>
     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>.
+      href="https://www.jalview.org/examples/groovy">https://www.jalview.org/examples/groovy</a>.
   </p>
   <p>
     <em>Using Groovy to add new Alignment Calculations</em><br />We've
@@ -115,8 +115,8 @@ print currentAlFrame.getTitle();</pre>
     <em>Creating custom colourschemes</em><br/>
     You can create your own alignment colourschemes with a groovy script. We've provided two examples:<br/>
     <ul>
-    <li><a href="http://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
-    <li><a href="http://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
+    <li><a href="https://www.jalview.org/examples/groovy/colourConserved.groovy">colourConserved.groovy</a> creates an 'Conserved' colourscheme - similar to the classic <a href="http://www.nrbsc.org/old/gfx/genedoc/">GeneDOC</a> shading model.</li>
+    <li><a href="https://www.jalview.org/examples/groovy/colourUnconserved.groovy">colourUnconserved.groovy</a> creates an 'Unconserved' colourscheme, where any unconserved residues are coloured pink.</li>
     
     </ul>
   </p>