JAL-4153 avoid use of invokeAndWait, increase wait time and add timeout for the cache...

[jalview.git] / help / help / html / features / clarguments-basic.html

diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html
index 44c3459..238366c 100644 (file)
--- a/help/help/html/features/clarguments-basic.html
+++ b/help/help/html/features/clarguments-basic.html
@@ -315,11 +315,11 @@
   <br/>
   The value can also be specified as a sub-value:
   <pre>
-  jalview --open examples/uniref50.fa --structure [seqid=FER1+SPIOL,structureviewer=jmol,tempfac=plddt]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
+  jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL,structureviewer=jmol,tempfac=plddt]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
   </pre>
   which is equivalent to
   <pre>
-  jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --tempfac plddt --seqid FER1+SPIOL
+  jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --tempfac plddt --seqid FER1_SPIOL
    --structureviewer jmol
   </pre>
 
@@ -540,7 +540,7 @@
   <h3><a name="bgcolour"></a><code>&#8209;&#8209;bgcolour</code></h3>
 
   <p>
-  <strong>Only applies to <code>&#8209;&#8209;structureimage</code>.</strong> Specify a background colour for a structure image.  The colour can be specified as a named colour recognised by Java (e.g. <code>"white"</code>, <code>"cyan"</code>) or as a #RRGGBB hash-6-digit-hex-string as used in web pages (e.g. <code>"#ffffff"</code>, <code>"#00ffff"</code>).  Note that if you're using a hash in a bash-like shell then you should quote the string to avoid problems with it being interpreted as a comment character.
+  <strong>Only applies to <code>&#8209;&#8209;structureimage</code>.</strong> Specify a background colour for a structure image.  The colour can be specified as a named colour recognised by Java (e.g. <code>"white"</code>, <code>"cyan"</code>) or as a RRGGBB 6 digit hex string (e.g. <code>ffffff</code>, <code>00ffff</code>).
   </p>
   <p>
   E.g.
@@ -556,7 +556,7 @@
   <h3><a name="vector"></a>Vector image export (<code>svg</code>, <code>eps</code>, <code>html</code>, <code>biojs</code>)</h3>
 
   <p>
-  Jalview can export an alignment in Encapsulated PostScript (<code>eps</code>), Scalable Vector Graphics (<code>svg</code>), HTML (<code>html</code>) or BioJSON -- another HTML format (<code>biojs</code>), by using, e.g.
+  Jalview can export an alignment in Encapsulated PostScript (<code>eps</code>), Scalable Vector Graphics (<code>svg</code>), HTML (<code>html</code>) or <a href="biojsmsa.html">BioJSON</a> -- another HTML format with an interactive MSA viewer (<code>biojs</code>), by using, e.g.
   <pre>
   jalview --open examples/uniref50.fa --colour gecos-flower --image printable.eps
   </pre>
@@ -565,6 +565,7 @@
   jalview --open examples/uniref50.fa --colour gecos-flower --image printable.eps
   jalview --open examples/uniref50.fa --colour gecos-flower --image printable.postscript --type eps
   jalview --open examples/uniref50.fa --colour gecos-flower --image [type=eps]printable.postscript
+  jalview --open examples/uniref50.fa --colour gecos-flower --image [type=biojs]printable.html
   </pre>
   </p>