JAL-1628 tweak signature of core annotation printer for outputting hidden columns...

[jalview.git] / help / html / features / annotationsFormat.html

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index 90dfd9b..72691ce 100755 (executable)
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -60,7 +60,7 @@ ignored. The sections below describe the structure of an annotation file.
 <li><a href="#groupdefs">SEQUENCE_GROUP</a> to define groups of sequences for further annotation</li>
 <li><a href="#groupprops">PROPERTIES</a> to set visualisation properties for sequence groups</li>
 <li><a href="#seqgrprefs">SEQUENCE_REF and GROUP_REF</a> for attaching annotation to sequences and groups</li>
 <li><a href="#groupdefs">SEQUENCE_GROUP</a> to define groups of sequences for further annotation</li>
 <li><a href="#groupprops">PROPERTIES</a> to set visualisation properties for sequence groups</li>
 <li><a href="#seqgrprefs">SEQUENCE_REF and GROUP_REF</a> for attaching annotation to sequences and groups</li>

-               <li><a href="#refsandviews">VIEW_SETREF and HIDE_INSERTIONS</a>
+               <li><a href="#refsandviews">VIEW_SETREF, VIEW_HIDECOLS and HIDE_INSERTIONS</a>

                        for defining a reference sequence on the alignment and hiding regions
                        based on gaps in a reference sequence</li>
        </ul>
                        for defining a reference sequence on the alignment and hiding regions
                        based on gaps in a reference sequence</li>
        </ul>

@@ -168,7 +168,7 @@ of sequence IDs. </p>
 <tr><td width="50%">idColour</td><td>Colour for highlighting the Sequence ID labels for this group<br/>If <em>idColour</em> is given but <em>colour</em> is not, then idColor will also be used for the group background colour.</td></tr>
 <tr><td width="50%">showunconserved</td><td>Boolean (default false) indicating whether residues should only be shown that are different from current reference or consensus sequence</td></tr>
 <tr><td width="50%">hide</td><td>Boolean (default false) indicating whether the rows in this group should be marked as hidden.<br/><em>Note:</em> if the group is sequence associated (specified by SEQUENCE_REF), then all members will be hidden and marked as represented by the reference sequence.</td></tr>
 <tr><td width="50%">idColour</td><td>Colour for highlighting the Sequence ID labels for this group<br/>If <em>idColour</em> is given but <em>colour</em> is not, then idColor will also be used for the group background colour.</td></tr>
 <tr><td width="50%">showunconserved</td><td>Boolean (default false) indicating whether residues should only be shown that are different from current reference or consensus sequence</td></tr>
 <tr><td width="50%">hide</td><td>Boolean (default false) indicating whether the rows in this group should be marked as hidden.<br/><em>Note:</em> if the group is sequence associated (specified by SEQUENCE_REF), then all members will be hidden and marked as represented by the reference sequence.</td></tr>

-<tr><td width="50%">hidecols</td><td>Boolean (default false) indicating whether columns in this groushould be marked as hidden</td></tr></tbody>
+<!-- <tr><td width="50%">hidecols</td><td>Boolean (default false) indicating whether columns in this groushould be marked as hidden</td></tr> --></tbody>

 </table>
 
 <p><strong>Specifying colours in PROPERTIES key-value pairs</strong><br/>
 </table>
 
 <p><strong>Specifying colours in PROPERTIES key-value pairs</strong><br/>

@@ -206,7 +206,7 @@ Group association is turned off for subsequent annotation rows by:
 <pre>GROUP_REF&#9;<em>ALIGNMENT</em></pre>
 </p>
 <hr/>
 <pre>GROUP_REF&#9;<em>ALIGNMENT</em></pre>
 </p>
 <hr/>

-<p><strong><a name="refsandviews">VIEW_SETREF, and HIDE_INSERTIONS</a></strong><br/>
+<p><strong><a name="refsandviews">VIEW_SETREF, VIEW_HIDECOL and HIDE_INSERTIONS</a></strong><br/>

 Since Jalview 2.9, the Annotations file has also supported the definition of views on the alignment, and definition of hidden regions.</p>
 <!--   <p>
                <em>VIEW_DEF</em> allows the current view to be named according to the
 Since Jalview 2.9, the Annotations file has also supported the definition of views on the alignment, and definition of hidden regions.</p>
 <!--   <p>
                <em>VIEW_DEF</em> allows the current view to be named according to the

@@ -220,6 +220,12 @@ Since Jalview 2.9, the Annotations file has also supported the definition of vie
                corresponding sequence as the <a href="../features/refsequence.html">reference
                        sequence</a> for the alignment.
        </p>
                corresponding sequence as the <a href="../features/refsequence.html">reference
                        sequence</a> for the alignment.
        </p>

+       <em>VIEW_HIDECOLS</em> takes either a single argument consisting of a
+       comma separated series of integer pairs like
+       <em>3-4</em>. These integer pairs define columns (starting from the
+       left-hand column 0) that should be marked as hidden in the alignment
+       view.
+       </p>

        <p>
                <em>HIDE_INSERTIONS</em> takes a either a single sequence ID or a
                numeric index, or no arguments. This command marks all gapped
        <p>
                <em>HIDE_INSERTIONS</em> takes a either a single sequence ID or a
                numeric index, or no arguments. This command marks all gapped