GRAPH_TYPE. The allowed values of GRAPH_TYPE and the format of their respective value fields (with the trailing "<strong>|</strong>" symbol) are shown below:<ul>
<li>BAR_GRAPH<br>
Plots a histogram with labels below each bar.<br>
- <em>number</em>,<em>text character</em></li>
+ <em>number</em>,<em>text character</em>,<em>Tooltip text</em></li>
<li>LINE_GRAPH<br>
Draws a line between values on the annotation row.<br>
<em>number</em></li>
<li>NO_GRAPH<br>
For a row consisting of text labels and/or secondary structure symbols.<br>
- <em>{Secondary Structure Symbol}</em>,<em>text label</em><br>
+ <em>{Secondary Structure Symbol}</em>,<em>text label</em>,<em>Tooltip text</em><br>
Currently supported secondary structure structure symbols are <em>H</em> (for helix) and <em>E</em> (for strand)</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.
+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>
<p>You can associate an annotation with a sequence by preceding its
definition with the line:
list will (optionally) be placed at the <em>startIndex</em>'th column.</p>
<ul><em>New in Jalview 2.4</em>: the tooltip displayed when the mouse is moved over the row
label for sequence associated annotation gives the associated
-sequence's name followed by the annotation row's description.</ul>
+sequence's name followed by the annotation row's description.<br/>
+<em>New in Jalview 2.5</em>: Clicking on a sequence or group associated annotation row's label will highlight the sequence or sequence group in the alignment, and double clicking the annotation row label will select the associated sequence or group.</ul>
<p>Sequence associations are turned off for subsequent annotation
definitions by:
<pre>SEQUENCE_REF	ALIGNMENT</pre>
</p>
+<p>Since version 2.5, Jalview allows annotation rows to be associated with a group defined on the alignment, by preceding the annotation row with the line:
+<pre>GROUP_REF	<em>group_name</em></pre>
+Group association is turned off for subsequent annotation rows by
+<pre>GROUP_REF	<em>ALIGNMENT</em></pre>
+Annotations may be associated with both a sequence and a group, however - group annotations are still experimental and unexpected behaviour may be observed when editing alignments containing both group and sequence associated annotation rows.</p>
<p><em>LINE_GRAPH</em> type annotations can be given a colour
(specified as 24 bit RGB triplet in hexadecimal or comma separated
values), combined onto the same vertical axis, and have ordinate lines
COMBINE	<em>graph_1_name</em>	<em>graph_2_name</em>
GRAPHLINE	<em>graph_name</em>	<em>value</em>	<em>label</em>	<em>colour</em><strong><em>
</em></strong></pre>
+<h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.5) ROWPROPERTIES</font></h3>
+<p>The visual display properties for a set of annotation rows can be modified using the following tab-delimited line:</p>
+<pre>ROWPROPERTIES	<em>Row label</em>	<em>centrelabs=true( or false)</em>	<em>showalllabs=true(default is false)</em>	<em>scaletofit=true (default is false)</em></pre>
+<p>This sets the visual display properties according to the given values for all the annotation rows with labels matching <em>Row label</em>. The properties mostly affect the display of multi-character column labels, and are as follows:
+<ul><li><em>centrelabs</em> Centre each label on its column.</li>
+<li><em>showalllabs</em> Show every column label rather than only the first of a run of identical labels (setting this to true can have a drastic effect on secondary structure rows).</li>
+<li><em>scaletofit</em> Shrink each label's font size so that the label fits within the column. Useful when annotating an alignment with a specific column numbering system. (<em>Not available in Jalview applet due to AWT 1.1 limitations</em>)</li>
+</ul></p>
<h3><font face="Arial, Helvetica, sans-serif">(Since Jalview 2.2.1) SEQUENCE_GROUP</font></h3>
<p>Groups of sequences can be defined using the tab delimited line</p>
<pre>SEQUENCE_GROUP Group_Name Group_Start Group_End Sequences</pre>
textCol2=black<br>
textColThreshold=0<br>
idColour=ff3322<br>
+ <!-- Not yet implemented in 2.5 release
hide=false<br>
- hidecols=false<br>
+ hidecols=false<br> -->
showunconserved=false</p>
-<ul><li>if the <strong>idColour</strong> property
+<ul><li><em>New Features in 2.4:</em><br>if the <strong>idColour</strong> property
is given without specifying a colour scheme with the <strong>colour</strong>
property, then the idColour will also be used to colour the sequence.</li>
<li>the <strong>colour</strong> property can take either a colour scheme name,
or a single colour specification (either a colour name like 'red' or an RGB
triplet like 'ff0066'). If a single colour is specified, then the group
will be coloured with that colour.</li>
- <li><em>New Features in 2.4.1</em></li>
- <li>hide and hidecols instruct jalview to hide the sequences or columns covered by the group.</li>
+ <!-- <li><em>New Features in 2.5</em></li>
+ <li>hide and hidecols instruct jalview to hide the sequences or columns covered by the group.</li> -->
<li>Sequence associated Groups<br>If a group is defined after a valid
<em>SEQUENCE_REF</em> sequence reference statement, the sequence representative
- for the group will be set to the referenced sequence.<br><strong>Note:</strong> if the <em>hide</em>
- property is set then only the representative sequence for the group will be shown in the alignment.</li>
+ for the group will be set to the referenced sequence.<!-- <br><strong>Note:</strong> if the <em>hide</em>
+ property is set then only the representative sequence for the group will be shown in the alignment.--></li>
</ul>
<p> </p>
<p>An example Annotation file is given below:
git://source.jalview.org / jalview.git / blobdiff