doco

diff --git a/help/help.jhm b/help/help.jhm
index f3d96c4..fcfc0a8 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -25,7 +25,7 @@
    <mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>\r
    <mapID target="features.fileformat" url="html/features/featuresFormat.html"/>   \r
    <mapID target="edit" url="html/editing/index.html"/>\r
    <mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>\r
    <mapID target="features.fileformat" url="html/features/featuresFormat.html"/>   \r
    <mapID target="edit" url="html/editing/index.html"/>\r

-   <mapID target="editInSelArea" url="html/editing/selectionAreas.html"/>\r
+   <mapID target="edit.selareas" url="html/editing/selectionAreas.html"/>\r

    <mapID target="jalarchive" url="html/features/jalarchive.html"/>\r
    <mapID target="trees" url="html/calculations/tree.html"/>\r
    <mapID target="sorting" url="html/calculations/sorting.html"/>\r
    <mapID target="jalarchive" url="html/features/jalarchive.html"/>\r
    <mapID target="trees" url="html/calculations/tree.html"/>\r
    <mapID target="sorting" url="html/calculations/sorting.html"/>\r

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index cc3555e..62cba6b 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -5,7 +5,7 @@
        <tocitem text="What's new" target="new" expand="false">\r
           <tocitem text="Cursor Mode" target="cursor"/>\r
           <tocitem text="Selection Area Based Editing"\r
        <tocitem text="What's new" target="new" expand="false">\r
           <tocitem text="Cursor Mode" target="cursor"/>\r
           <tocitem text="Selection Area Based Editing"\r

-          target="editInSelArea"/>\r
+          target="edit.selareas"/>\r

           <tocitem text="User Defined Sequence Features" target="search"/>\r
           <tocitem text="Sequence Feature Groups" target="seqfeatures"/>\r
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r
           <tocitem text="User Defined Sequence Features" target="search"/>\r
           <tocitem text="Sequence Feature Groups" target="seqfeatures"/>\r
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>\r

diff --git a/help/html/editing/index.html b/help/html/editing/index.html
index bcb4e94..a33dea7 100755 (executable)
--- a/help/html/editing/index.html
+++ b/help/html/editing/index.html
@@ -14,12 +14,14 @@ href="../keys.html">keystrokes table</a>.</p>
 <p><strong>Tip:</strong> For large alignments, deselect &quot;Calculate -&gt; \r
   Autocalculate Consensus&quot; to prevent the alignment performing lengthy calculations \r
   after every edit. </p>\r
 <p><strong>Tip:</strong> For large alignments, deselect &quot;Calculate -&gt; \r
   Autocalculate Consensus&quot; to prevent the alignment performing lengthy calculations \r
   after every edit. </p>\r

-<p><em>Inserting / removing gaps</em> - hold down the &quot;Shift&quot; key. Click\r
-  a residue with the mouse and drag the residue to the right to insert gaps or\r
-  to the left to remove gaps.<br>\r
-  If the residue selected is within a defined group, hold down either &quot;Control&quot; \r
+<p><em>Inserting / removing gaps</em> - hold down the\r
+  &quot;Shift&quot; key. Click on a residue with the mouse and drag it\r
+  to the left or right to insert gaps and remove gaps.<br>\r
+  If the current selection is a group over all sequences in the\r
+  alignment, or a group over some sequences or all columns in the\r
+  alignment, then hold down either &quot;Control&quot; \r

   key and drag the residue left or right to edit all sequences in the defined \r
   key and drag the residue left or right to edit all sequences in the defined \r

-  group at once. </p>\r
+  group at once.</p>\r

 <p><em>Copy/paste/cut/delete</em> - any sequences which are in the current selection\r
   box (indicated in red) may be cut and / or copied to a new alignment or deleted.\r
 </p>\r
 <p><em>Copy/paste/cut/delete</em> - any sequences which are in the current selection\r
   box (indicated in red) may be cut and / or copied to a new alignment or deleted.\r
 </p>\r

diff --git a/help/html/editing/selectionAreas.html b/help/html/editing/selectionAreas.html
new file mode 100755 (executable)
index 0000000..384d6fa
--- /dev/null
+++ b/help/html/editing/selectionAreas.html
@@ -0,0 +1,18 @@
+<html>
+<head>
+<title>Editing In Selection Areas</title>
+</head>
+<body>
+<p><strong>Editing In Selection Areas</strong></p>
+ <a href="index.html">Editing</a> can be restricted to the current 
+  selection area. This allows the user to &quot;Lock&quot; the alignment either 
+  side of the selection area. Any gap insertions or deletions will only affect 
+  the current selection area. </p>
+<p><img src="editing.jpg" width="428" height="186" align="top"></p>
+<p>In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104, 
+  the same number of gaps will be inserted at position 116, (between M and L). 
+</p>
+
+<p><em>Locked selection area based editing was introduced in Jalview 2.08</em></p>
+</body>
+</html>

diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html
new file mode 100755 (executable)
index 0000000..31369d8
--- /dev/null
+++ b/help/html/features/featuresettings.html
@@ -0,0 +1,43 @@
+<html>
+<head>
+<title>Sequence Feature Settings Dialog Box</title>
+</head>
+<body>
+<p><strong>Sequence Feature Settings Dialog Box</strong></p>
+<p>Select <strong>View&#8594;Feature Settings...</strong> menu entry in
+an alignment window to open the feature settings dialog box, which
+allows you to precisely control the presence and appearance of
+sequence features for the current alignment.</p>
+<center><img src="appFeatureSettings.gif" align="center"><br>Sequence Feature
+  Settings for the Jalview Application</img></center>
+<p>The top section of the dialog box lists all the sequence feature
+  groups, along with a tickbox for each that controls whether its
+  features are displayed. The table in the middle lists all the
+  features in the currently selected groups, along with their display
+  colour and whether they are currently being displayed (only the
+  ticked features and groups are displayed). <strong><em>You can change the
+  colour used for a feature in the associated alignment by clicking on
+  its colour box.</em></strong></p>
+<p><strong>Transparency and Feature Ordering</strong></p><p>
+  It is important to realise that sequence features are often not
+  distinct and often overlap (for example, a metal binding site
+  feature may be attached to one position along a stretch of sequence
+  marked with a secondary structure feature).</p>
+<p>The ordering of the sequence features in the dialog box list is the
+  order used by jalview for rendering sequence features. A feature at
+  the bottom of the list is rendered <em>below</em> a feature higher
+  up in the list.<br><em><strong>You can change the order of a feature
+  by dragging it up and down the list with the
+  mouse</strong></em>.</p>
+<p>
+  The <strong><em>transparency slider setting</em></strong> (currently only available
+  in the application version) controls the visibility of features
+  rendered below other features. Reducing the transparency will mean
+  that features at the top of the list can obscure features lower
+  down, and increasing it allows the user to 'see through' the upper
+  layers of a set of features.</p>
+<p><strong><em>You can save all features, with their current colours and visibility 
+  in a Jalview format file. </em></strong>
+</p>
+</body>
+</html>