+ <p>
+ One such PathMatcher addition to shell file globs is the use of <code>**</code> to match any number of directories and sub-directories (matching across file separator). So to convert every Fasta file under the current working directory to BLC format you can do:
+ <pre>
+ jalview --open=./**/*.fa --output=*.blc --close --headless
+ </pre>
+ or to find every Stockholm and Pfam file under </code>/tmp</code> and convert to Fasta and save in your own folder, do
+ <pre>
+ jalview --open=/tmp/**/*.{stk,pfam} --all --output=~/rescued/{basenamedir}.fa --close --headless
+ </pre>
+ </p>
+
+ <h2><a name="subvaluemodifiers"></a>Sub-value modifiers</h2>
+
+ <p>
+ Sub-value modifiers are given in square brackets ('[', ']') <em>immediately before the value</em> (i.e. after any space or equals sign, and with no space between it and the value) like this:
+ <pre>
+ jalview --open=examples/uniref50.fa --image=[scale=1.414]picture.png
+ </pre>
+ </p>
+
+ <p>
+ Some arguments (such as <code>‑‑scale=<em>n</em></code>) are used to modify the behaviour of other "primary" arguments (such as <code>‑‑image=filename</code>). These arguments can alternatively be specifed as <em>sub-value modifiers</em> of the values given to the primary argument. If specified as a sub-value modifier, this modifier takes precedence over any following linked argument if given. e.g
+ <pre>
+ jalview --open=[colour=zappo]examples/*.fa
+ </pre>
+ Notice also that if a sub-value modifier is used for a value that is expanded by the application (i.e. using an equals sign ('=') to separate argument and value) then that modifier is applied to all of the values.
+ </p>
+
+ <p>
+ For shell expanded globs this is more problematic since the presence of a sub-value modifier will almost certainly prevent the shell from recognising the file glob, so
+ <pre>
+ jalview --open [colour=zappo]examples/*.fa
+ </pre>
+ will <em>NOT</em> work the same as above. If you need to use sub-value modifiers on a file glob you should use an equals sign ('=') to separate it from the argument.
+ </p>
+
+ <p>
+ You can specify multiple sub-value modifiers separating them with a comma (','). If you wish to specify a "boolean" argument, such as <code>‑‑wrap</code> or <code>‑‑nowrap</code> then simply use the argument name without a value, like this:
+ <pre>
+ jalview --open=[colour=gecos-flower,wrap,noannotations,features=examples/plantfdx.features]examples/plantfdx.fa
+ </pre>