From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 20 Sep 2023 10:41:27 +0000 (+0100)
Subject: JAL-629 Explanation of \{m\} in case anyone actually wants it
X-Git-Tag: Release_2_11_4_0~174^2~8
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a5ef7bc19bcd58a33bb385db729fd62c88e64b09;p=jalview.git

JAL-629 Explanation of \{m\} in case anyone actually wants it
---

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>