X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments.html;h=6df40b525556a8817b8c3acd7ab712114003f481;hb=9c970ce520ca5480fcd289c8ef32ed78284cde29;hp=7c2e9d5bc9f0a5c2a98ac89f136ac2ea3cf572cf;hpb=33a18c18d0ec58e651de30890437cdf4e6eb542d;p=jalview.git

diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index 7c2e9d5..6df40b5 100644
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -44,7 +44,7 @@
   </p>
 
   <p>
-  These new arguments are all accessed with a <code>--doubledash</code> form of
+  These new arguments are all accessed with a <code>&#8209;&#8209;doubledash</code> form of
   command line argument (with the one exception where simply opening one or more
   files can be performed without any arguments other than the filenames).
   </p>
@@ -60,7 +60,7 @@
   <p>
   However, you cannot mix old and new style arguments, so if you use any
   <code>-singledash</code> arguments (with the exception of <code>-help</code> or <code>-h</code>), they will all be interpreted as
-  old style arguments with the new <code>--doubledash</code>
+  old style arguments with the new <code>&#8209;&#8209;doubledash</code>
   arguments being ignored.  If you have a script
   that uses the old arguments without any dashes, and uses the bare-word
   <code>open</code> then these will also be interpreted as old style arguments.
@@ -97,52 +97,52 @@
     <li>
         For arguments that require a value, the value can be given after an equals-sign ('=') or a space (' ').
         <br/>
-        <code>--arg value</code>
+        <code>&#8209;&#8209;arg value</code>
         <br/>
-        <code>--arg=value</code>
+        <code>&#8209;&#8209;arg=value</code>
     </li>
     <li>
         For arguments that can take multiple values (these will be filenames), the multiple filenames should appear after a space. If you use a filename wildcard you can put this after a space (which will be expanded by the shell unto multiple filenames before they reach Jalview), or you can put it after an equals-sign, which will be used by Jalview to find a list of files.  You cannot use an equals-sign and value followed by further values.
         <br/>
-        <code>--arg file1.fa otherfile.stk</code>
+        <code>&#8209;&#8209;arg file1.fa otherfile.stk</code>
         <br/>
-        <code>--arg filename*.fa</code> <em>(filenames expanded by shell)</em>
+        <code>&#8209;&#8209;arg filename*.fa</code> <em>(filenames expanded by shell)</em>
         <br/>
-        <code>--arg=filename*.fa</code> <em>(filenames expanded by Jalview)</em>
+        <code>&#8209;&#8209;arg=filename*.fa</code> <em>(filenames expanded by Jalview)</em>
     </li>
     <li>
         For arguments that act as a switch, most can be negated by preceding the argument name with <code>no</code>.
         <br/>
-        <code>--switch</code>
+        <code>&#8209;&#8209;switch</code>
         <br/>
-        <code>--noswitch</code>
+        <code>&#8209;&#8209;noswitch</code>
     </li>
     <li>
-        Some values can be modified, or may need additional information (for instance an <code>--image</code> output can be modified with a <code>--scale=number</code> factor, or a <code>--structure</code> can refer to a sequence with a <code>--seqid=ID</code>).  This additional information can be added in a number of different ways.
+        Some values can be modified, or may need additional information (for instance an <code>&#8209;&#8209;image</code> output can be modified with a <code>&#8209;&#8209;scale=number</code> factor, or a <code>&#8209;&#8209;structure</code> can refer to a sequence with a <code>&#8209;&#8209;seqid=ID</code>).  This additional information can be added in a number of different ways.
         <ul>
           <li>
               An argument immediately following the main argument.
               <br/>
-              <code>--image output.png --scale 2.5</code>
+              <code>&#8209;&#8209;image output.png --scale 2.5</code>
           </li>
           <li>
               A <em>sub-value modifier</em>, which is where one or more (comma-separated) values are added to the start of the main value, placed in square brackets.
               <br/>
-              <code>--open=[nowrap,colour=gecos-blossom]uniref50.fa</code>
+              <code>&#8209;&#8209;open=[nowrap,colour=gecos-blossom]uniref50.fa</code>
               <br/>
               Sub-value modifiers with a value must use an equals-sign separator, and those that act as a switch can simply be included without an equals-sign or value, and can be preceded with <code>no</code> to negate the value, as with the argument name.
           </li>
           <li>
               Another argument with the same <em>linked ID</em>.  A linked ID is an optional identifier for a particular open alignment, placed in square brackets immediately following the argument name (before the equals-sign or space).  If linked IDs are specified they do not need to be near to each other.
               <br/>
-              <code>--image[MYID]=output.png --other --args --scale[MYID]=2.5</code>
+              <code>&#8209;&#8209;image[MYID]=output.png --other --args --scale[MYID]=2.5</code>
           </li>
           <li>
               An argument that is designated as applying to <em>all linked IDs</em>
               <br/>
-              <code>--image=output.png --other --args --all --scale=2.5</code>
+              <code>&#8209;&#8209;image=output.png --other --args --all --scale=2.5</code>
               <br/>
-              <code>--image=output.png --other --args --scale[*]=2.5</code>
+              <code>&#8209;&#8209;image=output.png --other --args --scale[*]=2.5</code>
           </li>
         </ul>
     </li>
@@ -157,13 +157,13 @@
   <h2><a name="headlessmode"></a>Headless mode</h2>
 
   <p>
-  Jalview can be run in headless mode, i.e. without the usual graphical user interface (GUI), by specifying the <code>--headless</code> argument.  With command line arguments you can specify operations for Jalview to perform on one or more files and then stop running.  Most likely you will want to output another file, either an alignment for image file.
+  Jalview can be run in headless mode, i.e. without the usual graphical user interface (GUI), by specifying the <code>&#8209;&#8209;headless</code> argument.  With command line arguments you can specify operations for Jalview to perform on one or more files and then stop running.  Most likely you will want to output another file, either an alignment for image file.
   </p>
   <p>
-  <strong>If you specify an argument for an output file</strong> (one or more of <code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then it will be assumed that you wish to <strong>run in headless mode</strong>.
+  <strong>If you specify an argument for an output file</strong> (one or more of <code>&#8209;&#8209;output</code>, <code>&#8209;&#8209;image</code> or <code>&#8209;&#8209;structureimage</code>) then it will be assumed that you wish to <strong>run in headless mode</strong>.
   </p>
   <p>
-  You can force Jalview to run in graphical mode using the <code>--gui</code> argument.
+  You can force Jalview to run in graphical mode using the <code>&#8209;&#8209;gui</code> argument.
   </p>
 
   <p>