X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments-advanced.html;h=8e4012c8487183e65b40e2b5e1ea5eea38bc0dd0;hb=1140532d01b32b648e7e5b17ea717ae790625f8f;hp=eea97fb4caa43a2b5aa3e1e645ee0b23cc74bfe1;hpb=9c970ce520ca5480fcd289c8ef32ed78284cde29;p=jalview.git

diff --git a/help/help/html/features/clarguments-advanced.html b/help/help/html/features/clarguments-advanced.html
index eea97fb..8e4012c 100644
--- a/help/help/html/features/clarguments-advanced.html
+++ b/help/help/html/features/clarguments-advanced.html
@@ -75,7 +75,7 @@
   </p>
 
 
-  <h2><a name="moresubstitutions"></a>More substitutions (<code>{n}</code>, <code>{++n}</code>, <code>[*]</code>)</h2>
+  <h2><a name="moresubstitutions"></a>More substitutions (<code>{n}</code>, <code>{++n}</code>, <code>[*]</code>, <code>{m}</code>, <code>{++m}</code>)</h2>
 
   <p>
   In the <a href="clarguments-basic.html#substitutions">basic usage document</a> we have a list of special strings that get replaced in output filename values with parts of input filename values.
@@ -97,8 +97,10 @@
   </pre>
   because all of the command line arguments are read and sorted into their linked IDs before starting to be processed, and the <code>[myId3]</code> specified linked ID takes precedence over the <code>[*]</code> wildcard linked ID.
   </p>
-  </p>
 
+  <p>
+  All of the substitutions talked about so far are evaluated in the argument parsing process.  If in some cases (almost certainly involving structure images!) you find <code>{n}</code> is not incrementing when you think it should, when specifying <code>&#8209;&#8209;structureimage</code> filenames you can also use <code>{m}</code> and <code>{++m}</code>, along with <code>{structuredirname}</code>, <code>{structurebasename}</code> and <code>{structureextension}</code> which are substituted at the point of use.  <code>{m}</code> is just a plain counter starting at 0.
+  </p>
 
   <h2><a name="equalsseparatorandfileglobs"></a>Equals separator and Java file globs</h2>