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Merge branch 'develop' into features/r2_11_2_alphafold/JAL-629
[jalview.git]
/
help
/
help
/
html
/
features
/
clarguments-reference.html
diff --git
a/help/help/html/features/clarguments-reference.html
b/help/help/html/features/clarguments-reference.html
index
fc4f0a0
..
dd0bd52
100644
(file)
--- a/
help/help/html/features/clarguments-reference.html
+++ b/
help/help/html/features/clarguments-reference.html
@@
-103,6
+103,11
@@
</tr>
<tr valign="top">
</tr>
<tr valign="top">
+ <td><code>‑‑nostartupfile</code></td>
+ <td>Don't show the default startup file.</td>
+ </tr>
+
+ <tr valign="top">
<td><code>‑‑webservicediscovery / ‑‑nowebservicediscovery</code></td>
<td>Attempt (/ or don't attempt) to connect to JABAWS web services.</td>
</tr>
<td><code>‑‑webservicediscovery / ‑‑nowebservicediscovery</code></td>
<td>Attempt (/ or don't attempt) to connect to JABAWS web services.</td>
</tr>
@@
-124,6
+129,13
@@
<!--
<tr valign="top">
<!--
<tr valign="top">
+ <td><code>‑‑P<em>PREFERENCE=VALUE</em></code></td>
+ <td>Set a Jalview preference for this session only. Experimental.</td>
+ </tr>
+-->
+
+<!--
+ <tr valign="top">
<td><code>‑‑initsubstitutions / ‑‑noinitsubstitutions</code></td>
<td>Set <code>‑‑substitutions</code> to be initially enabled (or initially disabled).</td>
</tr>
<td><code>‑‑initsubstitutions / ‑‑noinitsubstitutions</code></td>
<td>Set <code>‑‑substitutions</code> to be initially enabled (or initially disabled).</td>
</tr>
@@
-232,7
+244,7
@@
</tr>
<tr valign="top">
</tr>
<tr valign="top">
- <td><code>‑‑title <em>"string""</em></code></td>
+ <td><code>‑‑title <em>"string"</em></code></td>
<td>Specifies the title for the open alignment window as <em>string</em>.</td>
<td></td>
<td align="center">✓</td>
<td>Specifies the title for the open alignment window as <em>string</em>.</td>
<td></td>
<td align="center">✓</td>
@@
-240,7
+252,7
@@
<tr valign="top">
<td><code>‑‑colour <em>name</em></code></td>
<tr valign="top">
<td><code>‑‑colour <em>name</em></code></td>
- <td>Applies the colour scheme <em>name</em> to the open alignment window. Valid values for <em>name</em> are:
+ <td>Applies the colour scheme <em>name</em> to the open alignment window. Valid values for <em>name</em> include:
<br/>
<code>clustal</code>,
<br/>
<br/>
<code>clustal</code>,
<br/>
@@
-281,6
+293,11
@@
<code>t-coffee-scores</code>,
<br/>
<code>sequence-id</code>.
<code>t-coffee-scores</code>,
<br/>
<code>sequence-id</code>.
+ <br/>
+ <br/>
+ Names of user defined schemes will also work, and jalview colour scheme specifications like:
+ <br/>
+ <code>‑‑colour "D,E=red; K,R,H=0022FF; C,c=yellow"</code>
<td></td>
<td align="center">✓</td>
</tr>
<td></td>
<td align="center">✓</td>
</tr>