JAL-629 Add --seqid for non-subval use, make arg value naming more consistent in...

[jalview.git] / help / help / html / features / clarguments-ng-summary.html

diff --git a/help/help/html/features/clarguments-ng-summary.html b/help/help/html/features/clarguments-ng-summary.html
index a85dc24..ef766b1 100644 (file)
--- a/help/help/html/features/clarguments-ng-summary.html
+++ b/help/help/html/features/clarguments-ng-summary.html
@@ -30,7 +30,7 @@
   <tr>
   <td><code>--open&nbsp;<em>filename/URL ...</em></code></td>
   <td>
-  Opens one or more alignment files in new alignment windows.
+  Opens one or more alignment files <em>filename</em> or URLs <em>URL</em> in new alignment windows.
   <a href="clarguments-ng.html#open">Examples</a>.
   </td>
   <td>
@@ -51,10 +51,10 @@
   
   <tr>
   <td><code>--append&nbsp;<em>filename/URL ...</em></code></td>
-  <td>Appends one or more alignment files to an open alignment window (or opens a new alignment if none already open).</td>
+  <td>Appends one or more alignment files <em>filename</em> or URLs <em>URL</em> to the open alignment window (or opens a new alignment if none already open).</td>
   <td>
    <code>
-      colour=<em>colourscheme</em>,
+      colour=<em>name</em>,
       title=<em>title</em>,
       features=<em>featurefile</em>,
       annotations=<em>annotationfile</em>,
@@ -70,15 +70,15 @@
   </tr>
   
   <tr>
-  <td><code>--title&nbsp;<em>"title"</em></code></td>
-  <td>Specifies the title for the open alignment window.</td>
+  <td><code>--title&nbsp;<em>"string""</em></code></td>
+  <td>Specifies the title for the open alignment window as <em>string</em>.</td>
   <td></td>
   <td align="center">&#x2713;</td>
   </tr>
   
   <tr>
-  <td><code>--colour&nbsp;<em>colourscheme</em></code></td>
-  <td>Applies the given colour scheme to the open alignment window.  Valid values are:
+  <td><code>--colour&nbsp;<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:
   <code>clustal</code>,
   <code>blosum62</code>,
   <code>pc-identity</code>,
@@ -106,7 +106,7 @@
   
   <tr>
   <td><code>--features&nbsp;<em>filename/URL</em></code></td>
-  <td>Add a feature file to the open alignment.</td>
+  <td>Add a feature file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
   <td></td>
   <td align="center">&#x2713;</td>
   </tr>
@@ -115,7 +115,7 @@
   
   <tr>
   <td><code>--tree&nbsp;<em>filename/URL</em></code></td>
-  <td>Add a tree file to the open alignment.</td>
+  <td>Add a tree file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
   <td></td>
   <td align="center">&#x2713;</td>
   </tr>
@@ -130,25 +130,32 @@
   
   <tr>
   <td><code>--annotations&nbsp;<em>filename/URL</em></code></td>
-  <td>Add an annotations file to the open alignment.</td>
+  <td>Add an annotations file <em>filename</em> or URL <em>URL</em> to the open alignment.</td>
   <td></td>
   <td align="center">&#x2713;</td>
   </tr>
-  
+
   <tr>
   <td><code>--showannotations / --noshowannotations</code></td>
   <td>Enforces showing (or not showing) alignment annotations.</td>
   <td></td>
   <td align="center">&#x2713;</td>
   </tr>
-  
+
+  <tr>
+  <td><code>--wrap / --nowrap</code></td>
+  <td>Enforces wrapped (or not wrapped) alignment formatting.</td>
+  <td></td>
+  <td align="center">&#x2713;</td>
+  </tr>
+
   
   <tr>
   <td><code>--structure&nbsp;<em>filename/URL</em></code></td>
-  <td>Load a structure file attached to a sequence in the open alignment.</td>
+  <td>Load a structure file <em>filename</em> or URL <em>URL</em> associated with a sequence in the open alignment.  The sequence to be associated with can be specified with a following <code>--seqid</code> argument, or the subval modifier <code>seqid=<em>ID</em></code> can be used.  A subval <em>INDEX</em> can also be used to specify the <em>INDEX-th</em> sequence in the open alignment.</td>
   <td>
     <code>
-      seqid=<em>sequenceid</em></code> or <code><em>sequence index</em>,
+      seqid=<em>sequenceid</em></code> or <code><em>INDEX</em>,
       paefile=<em>paefilename</em>,
       tempfac=<em>temperature factor type</em>,
       ssannotations,
@@ -157,19 +164,27 @@
     </code></td>
   <td align="center">&#x2713;</td>
   </tr>
-  
-  
+
+
+  <tr>
+  <td><code>--seqid&nbsp;<em>ID</em></code></td>
+  <td>Specify the sequence name for the preceding <code>--structure</code> to be associated with.</td>
+  <td></td>
+  <td align="center">&#x2713;</td>
+  </tr>
+
+
   <tr>
   <td><code>--paematrix&nbsp;<em>filename</em></code></td>
-  <td>Add a PAE file to the preceding <code>--structure</code></td>
+  <td>Add a PAE json matrix file <em>filename</em> to the preceding <code>--structure</code>.</td>
   <td></td>
   <td align="center">&#x2713;</td>
   </tr>
-  
+
   
   <tr>
-  <td><code>--tempfac&nbsp;<em>temperature factor type</em></code></td>
-  <td>Set the type of temperature factor.  Possible values are
+  <td><code>--tempfac&nbsp;<em>name</em></code></td>
+  <td>Set the type of temperature factor.  Possible values for <em>name</em> are
     <code>default</code>,
     <code>plddt</code>
   </td>
@@ -179,8 +194,8 @@
   
   
   <tr>
-  <td><code>--structureviewer&nbsp;<em>structure viewer</em></code></td>
-  <td>Set the structure viewer to use to open the 3d structure file specified in previous <code>--structure</code>.  Possible values are:
+  <td><code>--structureviewer&nbsp;<em>name</em></code></td>
+  <td>Set the structure viewer to use to open the 3d structure file specified in previous <code>--structure</code> to <em>name</em>.  Possible values of <em>name</em> are:
   <br/>
     <code>none</code>,
     <br/>