From 20bddfcf8ef1a53bce455b7599f8066b8ccba0d4 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Aug 2006 10:18:22 +0000
Subject: [PATCH] 2.1 updates

---
 help/help.jhm                           |    7 +--
 help/helpTOC.xml                        |   36 ++++++-------
 help/html/editing/index.html            |   14 ++++-
 help/html/features/featureSettings.gif  |  Bin 5855 -> 11374 bytes
 help/html/features/featuresettings.html |   88 ++++++++++++++++---------------
 help/html/io/export.html                |   12 +++--
 help/html/whatsNew.html                 |   66 +++++++----------------
 7 files changed, 107 insertions(+), 116 deletions(-)

diff --git a/help/help.jhm b/help/help.jhm
index 210933b..3790abe 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -12,11 +12,11 @@
    <mapID target="webservice" url="html/webServices/index.html"/>
    <mapID target="clustal" url="html/webServices/clustalw.html"/>
    <mapID target="muscle" url="html/webServices/muscle.html"/>
+   <mapID target="mafft" url="html/webServices/mafft.html"/>
    <mapID target="jnet" url="html/webServices/jnet.html"/>
    <mapID target="seqfetch" url="html/features/seqfetch.html"/>
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
    <mapID target="seqfeatures.settings" url="html/features/featuresettings.html"/>
-   <mapID target="pdbviewer" url="html/features/pdbviewer.html"/>
    <mapID target="viewingpdbs" url="html/features/viewingpdbs.html"/>
    <mapID target="preferences" url="html/features/preferences.html"/>     
    <mapID target="io" url="html/io/index.html"/>
@@ -24,15 +24,16 @@
    <mapID target="export" url="html/io/export.html"/>
    <mapID target="alformats" url="html/io/fileformats.html"/>
    <mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>
-   <mapID target="features.fileformat" url="html/features/featuresFormat.html"/>   
+   <mapID target="features.fileformat" url="html/features/featuresFormat.html"/>
+   <mapID target="das.settings" url="html/features/dassettings.html"/>
    <mapID target="edit" url="html/editing/index.html"/>
-   <mapID target="edit.selareas" url="html/editing/selectionAreas.html"/>
    <mapID target="jalarchive" url="html/features/jalarchive.html"/>
    <mapID target="trees" url="html/calculations/tree.html"/>
    <mapID target="sorting" url="html/calculations/sorting.html"/>
    <mapID target="pca" url="html/calculations/pca.html"/>
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>
    <mapID target="redundancy" url="html/calculations/redundancy.html"/>
+   <mapID target="hiddenRegions" url="html/features/hiddenRegions.html"/>
    
    <mapID target="colours" url="html/colourSchemes/index.html" />
    <mapID target="colours.clustal" url="html/colourSchemes/clustal.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 09c7125..9265599 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -3,34 +3,28 @@
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
 	<tocitem text="What's new" target="new" expand="false">
-          <tocitem text="Cursor Mode" target="cursor"/>
-          <tocitem text="Selection Area Based Editing" target="edit.selareas"/>
-          <tocitem text="User Defined Sequence Features" target="search"/>
-          <tocitem text="Sequence Feature Groups" target="seqfeatures"/>
-          <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
-          <tocitem text="Extended Sequence Feature Input File" target="features.fileformat"/>
-          <tocitem text="Annotations File" target="annotations.fileformat"/>
-          <tocitem text="Colour by Annotation Value" target="colours.annotation"/>
-          <tocitem text="Modeller PIR File IO" target="io.modellerpir"/>
+        	<tocitem text="MAFFT Alignment" target="mafft"/>
+        	<tocitem text="DAS Feature Fetching" target="das.settings"/>
+        	<tocitem text="Hide Regions" target="hiddenRegions"/> 	         
         </tocitem>
-	<tocitem text="Release History" target="release"/>
-      	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
-          <tocitem text="Conservation" target="calcs.alconserv"/>
-          <tocitem text="Quality" target="calcs.alquality"/>
-          <tocitem text="Consensus" target="calcs.consensus"/>
-          <tocitem text="Annotations File Format" target="annotations.fileformat"/>
-        </tocitem>
-	<tocitem text="Input / Output" target="io"/>
+        <tocitem text="Release History" target="release"/>
+        <tocitem text="Editing Alignments" target ="edit"/>	
+        <tocitem text="Cursor Mode" target="cursor"/>
 	<tocitem text="Key Strokes" target="keys"/>
+	<tocitem text="Input / Output" target="io"/>
   	<tocitem text="Making figures" target="export"/>
-	<tocitem text="Editing Alignments" target ="edit"/>
+	<tocitem text="Hidden Regions" target="hiddenRegions"/>
+	<tocitem text="Viewing PDB Files" target="viewingpdbs"/>
 	<tocitem text="Sequence Features" target="seqfeatures" expand="false">
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
+          <tocitem text="User Defined Sequence Features" target="search"/>
+          <tocitem text="DAS Features Settings" target="das.settings"/>
         </tocitem>
 	<tocitem text="Web Services" target="webservice" expand="false">
 		<tocitem text="Clustal Alignment" target="clustal"/>
                 <tocitem text="Muscle Alignment" target="muscle"/>
+                <tocitem text="MAFFT Alignment" target="mafft"/>
           	<tocitem text="JNet Prediction" target="jnet"/>
 	</tocitem>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
@@ -57,6 +51,12 @@
 		<tocitem text="Pairwise Alignments" target="pairwise"/>
 		<tocitem text="Remove Redundancy" target="redundancy"/>
 	</tocitem>
+      	<tocitem text="Alignment Annotations" target ="alannotation" expand="false">
+          <tocitem text="Conservation" target="calcs.alconserv"/>
+          <tocitem text="Quality" target="calcs.alquality"/>
+          <tocitem text="Consensus" target="calcs.consensus"/>
+          <tocitem text="Annotations File Format" target="annotations.fileformat"/>
+        </tocitem>
 	<tocitem text="Window Menus" target="menus" expand="false">
 		<tocitem text="Desktop Window" target="desktopMenu"/>
 		<tocitem text="Alignment Window" target="alMenu">
diff --git a/help/html/editing/index.html b/help/html/editing/index.html
index a33dea7..b0e8103 100755
--- a/help/html/editing/index.html
+++ b/help/html/editing/index.html
@@ -38,9 +38,19 @@ href="../keys.html">keystrokes table</a>.</p>
   contain only space characters (&quot;-&quot; or &quot;.&quot; or &quot; &quot;)</p>
 <p><em>Removing gaps</em> - Removes all gaps from the alignment. Gaps are &quot;-&quot;
   or &quot;.&quot; or &quot; &quot;.</p>
-<p><em>Set gap character</em> - Switches the gap character between &quot;.&quot;
-  and &quot;-&quot;. If the &quot;Render Gaps&quot; option from the &quot;View&quot;
+<p><em>Set gap character</em> - Switches the gap character between &quot;.&quot; 
+  and &quot;-&quot;. If the &quot;Render Gaps&quot; option from the &quot;View&quot; 
   menu is unticked all gaps will appear as blank spaces.</p>
 <p>&nbsp;</p>
+<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><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>
+<p>&nbsp;</p>
 </body>
 </html>
diff --git a/help/html/features/featureSettings.gif b/help/html/features/featureSettings.gif
index 87de549ff5a2190a2dfd03c5d087baff8becbcc8..29b1db0137adf57845f0697e570f33af0690c726 100755
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diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html
index 31369d8..81af8d0 100755
--- a/help/html/features/featuresettings.html
+++ b/help/html/features/featuresettings.html
@@ -1,43 +1,45 @@
-<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>
+<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="featureSettings.gif" width="432" height="327"> <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>
diff --git a/help/html/io/export.html b/help/html/io/export.html
index f0f615b..943451b 100755
--- a/help/html/io/export.html
+++ b/help/html/io/export.html
@@ -17,9 +17,15 @@ diagrams and powerpoint presentations</em>
 diagrams and publications.</em>
 </li></ul>
   
-<p><em>Tips for working with EPS Files</em></p><li>The EPS file generated by jalview contains vector
-  graphics which are directly editable in graphics applications such as
-  Adobe Illustrator.</li>
+<p><em>Tips for working with EPS Files</em></p>
+<li>The EPS file generated by jalview contains vector graphics which are directly 
+  editable in graphics applications such as Adobe Illustrator.</li>
+<li>EPS files can be produced as &quot;Text&quot; or &quot;Lineart&quot;. Use 
+  &quot;Text&quot; if you want the final document to be MUCH smaller in diskspace 
+  and be able to search, edit and select text. Use &quot;Lineart&quot; if you 
+  want an exact image of the alignment as displayed in Jalview. This is useful 
+  if a 3rd Party EPS viewer does not have the same Font which the EPS file was 
+  created with.</li>
 <li>When importing an EPS into to a Microsoft office document, a snapshot image of the
   file will be displayed which often looks blurred. Right-click the
   image and choose &quot;Edit image.&quot; to convert it to word
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 7d88e7f..5bb50f9 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -2,54 +2,26 @@
 <head><title>What's new ?</title></head>
 <body>
 <p><strong>What's new ?</strong> </p>
-<p>Jalview Version 2.08</p>
-<p><a href="editing/index.html">Editing</a> can be <a href="editing/selectionAreas.html">locked to the
-  selection area</a> so that any edits made within the locked area do
-  not unexpectedly shift other parts of the alignment.</p>
-<p> Keyboard editing - press F2 to toggle <a href="features/cursorMode.html">cursor mode</a> On / Off. For a full list 
-  of keyboard controls, look <a href="keys.html">here</a>.</p>
-<p> <a href="features/search.html">Create sequence features from searches</a>. 
-  Previously, the regions of sequences highlighted as the result of
-  searches were added as new regions in the alignment. Now, the sequence region
-  selected by a search can be used to define named sequences features
-  attached to the sequence, rather than the alignment.
-  </p>
-<p>Sequence feature display and rendering has also been enhanced, with
-  the addition of sequence feature groups (which can be used to show
-  or hide a set of features <em>en masse</em>) and user defined
-  feature colours as well as transparency controls, using the <a
-  href="features/featuresettings.html">Sequence Feature Settings</a>
-  window. The <a href="features/featuresFormat.html">Features file</a>
-  has also been extended to accomodate these enhancements.</p>
-<p>Alignment annotation and colouring is also considerably
-  enhanced. Precalculated symbolic and quantitative annotations (text labels,
-  secondary structure symbols and multiple scalar graphs) can now be
-  loaded onto alignments via the <a
-  href="features/annotationsFormat.html">Annotation
-  File</a>. Additionally, the <a
-  href="colourSchemes/annotationColouring.html">Annotation
-  Colouring</a> dialog box allows an alignment to be coloured based on
-  any of the graphed quantities with which it is annotated.</p>
-<p>Rendering speed has been improved by disabling anti-aliasing via
-  the <strong>Smooth Fonts</strong>
-  option in the <strong>View 
-  menu</strong> (its default set in <strong>Preferences</strong>). In addition, response
-  times when editing alignments can be reduced by turning off the automatic
-  calculation of amino acid property Consensus (which has been
-  reintroduced to the <strong>Calculate</strong> menu as <strong>Autocalculate Consensus</strong>).<br>
-</p>
+<p>Jalview Version 2.1</p>
+<p>The multiple sequence alignment program <a href="webServices/mafft.html">MAFFT</a> 
+  is available from the default Web Service list.</p>
+<p>The sequence feature retrieval system using DBFetch from EBI has been replaced 
+  with <a href="features/dassettings.html">DAS Feature fetching</a> capabilities.</p>
+<p><a href="features/hiddenRegions.html">Hide sequences and columns</a></p>
+<p>Export Annotations and Features</p>
+<p>GFF file reading / writing</p>
+<p>Associate structures with sequences from local PDB files</p>
+<p>Add sequences to exisiting alignment</p>
+<p>Recently opened files / URL lists</p>
+<p>Applet can launch the full application</p>
+<p>Applet has transparency for features (Java 1.2 required)</p>
+<p>Applet has user defined colours parameter</p>
+<p>&nbsp; </p>
 <p><strong>Issues Resolved</strong></p>
-<ul>
-<li>Drag &amp; Drop now works on common Linux desktops (at least KDE
-and Gnome)</li>
-<li>Jalview XML Archive Input/Output is now faster (using an
-internal Jalview schema), and sequence description strings are now
-preserved in the archive.</li>
-<li>Jalview can now correctly read and write <a
-href="io/modellerpir.html">MODELLER style
-PIR</a> files.
-</li>
-</ul>
+<p>Redundancy Panel reinstalled in the Applet</p>
+<p>Monospaced font - EPS / rescaling bug fixed</p>
+<p>Annotation files with sequence references bug fixed</p>
+<p>&nbsp;</p>
 <p>See the <a href="releases.html">Release History</a> page for details of all
   new features and resolved issues. </p>
 </body>
-- 
1.7.10.2