tooltip displays formatted annotation row description including sequence reference...

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

diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html
index b5a52f5..afee3b8 100755 (executable)
--- a/help/html/features/annotationsFormat.html
+++ b/help/html/features/annotationsFormat.html
@@ -47,19 +47,67 @@ 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>You can associate an annotation with a sequence by preceding its
-definition with the line: <strong><pre>SEQUENCE_REF&#9;<em>seq_name</em>&#9;<em>[startIndex]</em></pre></strong>
+definition with the line: 
+<pre>SEQUENCE_REF&#9;<em>seq_name</em>&#9;<em>[startIndex]</em></pre>
 All Annotations defined after a SEQUENCE_REF command will then be
 associated with that sequence, and the first field in the Value field
 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> 
 <p>Sequence associations are turned off for subsequent annotation
-definitions by: <strong><pre>SEQUENCE_REF&#9;ALIGNMENT</pre></strong></p>
+definitions by: 
+<pre>SEQUENCE_REF&#9;ALIGNMENT</pre>
+</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
 (horizontal lines at a particular vertical axis value) using the
-following commands (respectively): <strong><pre>COLOUR&#9;<em>graph_name</em>&#9;<em>colour</em>
+following commands (respectively): 
+<pre>COLOUR&#9;<em>graph_name</em>&#9;<em>colour</em>
 COMBINE&#9;<em>graph_1_name</em>&#9;<em>graph_2_name</em>
-GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colour</em></pre></strong>
+GRAPHLINE&#9;<em>graph_name</em>&#9;<em>value</em>&#9;<em>label</em>&#9;<em>colour</em><strong><em>
+</em></strong></pre>
+<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>
+<p>The sequences can be defined by alignment index and a range of sequences can 
+  be defined in a comma delimited field such as</p>
+<p>2-5,8-15,20,22</p>
+<p>Enter * to select all groups. </p>
+<p>If the alignment indices are not known, enter -1 then a tab delimited list 
+  of sequence ids. </p>
+<p>If the SEQUENCE_REF has been defined, the group_start and group_end will be 
+  relative to the sequence residue numbering, otherwise the group_start and group_end 
+  will be the alignment column indices. </p>
+<p>The group can (optionally) be assigned various visualisation properties via 
+  another tab delimited line thus:</p>
+<pre>PROPERTIES        Group_name      tab_delimited_key_value_pairs
+</pre>
+<p>The key_value_pairs allow you to define a description and to colour the group 
+  in various ways. All, none or some of the following values could be used for 
+  a group:</p>
+<p>description=Text <br>
+  colour=Helix Propensity<br>
+  pidThreshold=0<br>
+  consThreshold=0<br>
+  outlineColour=red <br>
+  displayBoxes=true<br>
+  displayText=false<br>
+  colourText=false<br>
+  textCol1=black<br>
+  textCol2=black<br>
+  textColThreshold=0<br>
+  idColour=ff3322</p>
+<em>New Features in 2.4:</em><ul><li>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>
+</ul>
+<p> </p>
 <p>An example Annotation file is given below:
 <pre>#Comment lines follow the hash symbol
 JALVIEW_ANNOTATION
@@ -76,6 +124,13 @@ COLOUR&#9;Green Values&#9;green
 COLOUR&#9;Purple Letters&#9;151,52,228
 COMBINE&#9;Green Values&#9;Red Values
 GRAPHLINE&#9;Red Values&#9;2.6&#9;threshold&#9;black
+
+SEQUENCE_GROUP Group_A 30 50 *
+SEQUENCE_GROUP Group_B 1 351 2-5
+SEQUENCE_GROUP Group_C 12 14 -1 seq1   seq2    seq3
+PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false    colourText=false textCol1=black textCol2=black textColThreshold=0
+PROPERTIES Group_B outlineColour=red
+PROPERTIES Group_C colour=Clustal
 </pre>
 </p>
 </body>