<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<li><a href="#annrowprops">ROWPROPERTIES</a> control the display of individual annotation rows</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="#seqgrprefs">SEQUENCE_REF and GROUP_REF</a> for specifying target sequences and groups for annotation, reference sequence and column visibilty commands.</li>
<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>
+ for assigning the reference sequence on the alignment and hiding columns.</li>
</ul>
<p>
At the end of this document, you can also find notes on <a
<ul><em>Please note: URL links embedded in HTML descriptions are not yet supported.</em>
</ul>
</p>
- <p>The final <em>Values</em>
- field contains a series of "|" separated value fields. Each
- value field is itself a comma separated list of fields of a particular
- type defined by the annotation row's <em>GRAPH_TYPE</em>. The allowed values of
- <em>GRAPH_TYPE</em> and corresponding interpretation of each <em>Value</em> are shown below:
+ <p>
+ The final <em>Values</em> field contains a series of "|"
+ separated value fields. Each value field is itself a comma separated
+ list of fields of a particular type defined by the annotation row's <em>GRAPH_TYPE</em>.
+ The allowed values of <em>GRAPH_TYPE</em> and corresponding
+ interpretation of each <em>Value</em> are shown below:
<ul>
- <li><strong>BAR_GRAPH</strong><br> Plots a histogram with labels below each
- bar.<br> <em>number</em>,<em>text character</em>,<em>Tooltip
- text</em>
- </li>
- <li><strong>LINE_GRAPH</strong><br> Draws a line between values on the
- annotation row.<br> <em>number</em>
- </li>
- <li><strong>NO_GRAPH</strong><br>For a row consisting of text labels and/or
- secondary structure symbols.<br><em>{Secondary Structure
- Symbol}</em>,<em>text label</em>,<em>Tooltip text</em><br/><br/>The type of secondary structure symbol depends on the alignment being annotated being either Protein or RNA. <br/>For proteins, structure symbols are <em>H</em> (for
- helix) and <em>E</em> (for strand)<br/><br/>For RNA, VIENNA, WUSS or extended notation can be used to specify positions that are paired (e.g. "(|(||)|)" or "|A|A|A|(|a|a|a|)")</li>
+ <li><strong>BAR_GRAPH</strong><br> Plots a histogram with
+ labels below each bar.<br> <em>number</em>,<em>text
+ character</em>,<em>Tooltip text</em></li>
+ <li><strong>LINE_GRAPH</strong><br> Draws a line between
+ values on the annotation row.<br> <em>number</em></li>
+ <li><strong>NO_GRAPH</strong><br>For a row consisting of
+ text labels and/or secondary structure symbols.<br> <em>{Secondary
+ Structure Symbol}</em>,<em>text label</em>,<em>Tooltip text</em><br /> <br />The
+ type of secondary structure symbol depends on the alignment being
+ annotated being either Protein or RNA. <br />For proteins, structure
+ symbols are <em>H</em> (for helix) and <em>E</em> (for strand)<br />
+ <br />For RNA structures, VIENNA, WUSS, and extended notations can
+ be used to specify paired positions.
+ <ul>e.g. "(|(||)|)" or "|A|A|A|(|a|a|a|)")
+ </ul></li>
</ul>
Any or all value fields may be left empty, as well as the BAR_GRAPH's
-text character field, and either or both of the text-label and secondary
-structure symbol fields of the NO_GRAPH type annotation rows.</p>
+ text character field, and either or both of the text-label and
+ secondary structure symbol fields of the NO_GRAPH type annotation rows.
+ </p>
<p>Color strings can be embedded in a value field by enclosing an RGB triplet in square brackets to colour that position in an annotation row.
</p>
<hr/>
<pre>GROUP_REF	<em>ALIGNMENT</em></pre>
</p>
<hr/>
-<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>
+ <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 reference
+ sequences and hidden regions for an alignment view.
+ </p>
+ <!-- <p>
<em>VIEW_DEF</em> allows the current view to be named according to the
first argument after the tab character. If a second argument is
provided, then a new view is created with the given name, and
properties.
</p> -->
- <p>
- <em>VIEW_SETREF</em> takes either a single sequence ID string, or a
- numeric index (second argument), and attempts to assign a
- 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
- positions in a specified sequence (either the one located by the
- arguments, the current SEQUENCE_REF, or the reference sequence for the
- view).
- <hr/>
-<p><strong><a name="compatibility">COMPATIBILITY NOTES</a></strong><br/>
+ <p>
+ <em>VIEW_SETREF</em><br />Marks the first sequence in the alignment,
+ or alternately, the one specified by the most recent <em>SEQUENCE_REF</em>
+ statement, as the <a href="../calculations/referenceseq.html">reference
+ sequence</a> for the alignment.
+ </p>
+ <p>
+ <em>HIDE_INSERTIONS</em><br />This command hides all gapped
+ positions in the current target sequence. Any columns already hidden
+ will be re-displayed.<br /> <br>The current target sequence is
+ either the one specified by the most recent <em>SEQUENCE_REF</em>
+ statement, the alignment's reference sequence, or the first sequence
+ in the alignment.
+ </p>
+ <p>
+ <em>VIEW_HIDECOLS</em><br />Modifies the visibility of columns in
+ the view. The statement is followed by a single argument consisting
+ of a comma separated series of single integers or integer pairs
+ (like <em>3-4</em>). These define columns (starting from the
+ left-hand column 0) that should be marked as hidden in the alignment
+ view.
+ </p>
+
+ <hr />
+ <p><strong><a name="compatibility">COMPATIBILITY NOTES</a></strong><br/>
The interpretation of the COMBINE statement in <em>Version 2.8.1</em> was refined
so that only annotation line graphs with the given names ands the same
<strong>SEQUENCE_REF</strong> and <strong>GROUP_REF</strong> scope are grouped.</p>
git://source.jalview.org / jalview.git / blobdiff