From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 11 May 2018 11:29:53 +0000 (+0100)
Subject: JAL-2629 update spike branch to latest
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6d882bd2c72c5fe9e8d0a8eb9df4de7a86bbc773;p=jalview.git

JAL-2629 update spike branch to latest
---

diff --git a/.classpath b/.classpath
index f4b8cf8..0cdc4b9 100644
--- a/.classpath
+++ b/.classpath
@@ -48,6 +48,7 @@
 	<classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
 	<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
 	<classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
+	<classpathentry kind="lib" path="lib/VAqua4.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
 	<classpathentry kind="lib" path="lib/xml-apis.jar"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS
index e0be904..e2baa85 100644
--- a/THIRDPARTYLIBS
+++ b/THIRDPARTYLIBS
@@ -49,6 +49,8 @@ jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfre
 
 quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ 
 
+vaqua: v4 (latest stable) by Alan Snyder et al. GPLv2 with Classpathe xception, also includes contributions from Quaqua: ownloaded from http://violetlib.org/vaqua/overview.html
+
 lib/htsjdk-1.120-SNAPSHOT.jar: (currently not required for 2.10) built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
 
 lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE
diff --git a/help/help.jhm b/help/help.jhm
index 506b3f3..4ea119c 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -54,6 +54,7 @@
    <mapID target="pdbmcviewer" url="html/features/pdbviewer.html"/>
    <mapID target="pdbjmol" url="html/features/jmol.html"/>
    <mapID target="chimera" url="html/features/chimera.html"/>
+   <mapID target="chimera.annotxfer" url="html/features/chimera.html#annotxfer"/>
    <mapID target="varna" url="html/features/varna.html"/>
    <mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
    <mapID target="preferences" url="html/features/preferences.html"/>     
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 71b7ef9..ca86625 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -24,6 +24,8 @@
 	<tocitem text="Jalview Documentation" target="home" expand="true">
 			<tocitem text="What's new" target="new" expand="true">
 				<tocitem text="Latest Release Notes" target="release"/>
+				<tocitem text="Structure Chooser" target="pdbchooser"/>
+				<tocitem text="Chimera Annotation Exchange" target="chimera.annotxfer"/>
 		</tocitem>
 		
 		<tocitem text="Editing Alignments" target="edit" />
diff --git a/help/html/features/chimera.html b/help/html/features/chimera.html
index 68ac465..e1227de 100644
--- a/help/html/features/chimera.html
+++ b/help/html/features/chimera.html
@@ -211,41 +211,32 @@
             structure in the alignment. The regions used to calculate
             the superposition will be highlighted using the 'Cartoon'
             rendering style, and the remaining data shown as a chain
-            trace.<br/><br/>
+            trace.<br />
+          <br />
         </em></li>
-        <li><strong><a name="experimental">EXPERIMENTAL FEATURES</a></strong><br/>
-          <em>
-            These are only available if the <strong>Tools&#8594;Enable
-            Experimental Features</strong> option is enabled. (Since Jalview 2.10.2)</em>
-          <ul>
-            <li><strong>Write Jalview features</strong><br /> <em>Selecting
-                this option will create new residue attributes for any
-                features currently visible in the associated alignment
-                views, allowing those positions to be selected and
-                analysed with via Chimera's 'Render by Attribute' tool
-                (found in the Tools submenu called Structure Analysis).<br />
-                <br />If you use this option, please remember to select
-                the <em>Refresh Menus</em> option in Chimera's Render by
-                Attribute dialog box in order to see the attributes
-                derived from Jalview sequence features.
-            </em><br />
-            <a href="https://issues.jalview.org/browse/JAL-2295">View
-                this function's issue in Jalview's bug tracker</a></li>
-            <li><strong>Fetch Chimera Attributes</strong><br /> <em>This
-                submenu lists available Chimera residue attributes that
-                can be imported as Jalview features on associated
-                sequences.<br />This is particularly useful for
-                transferring quantitative positional annotation. For
-                example, structure similarity for an alignment can be
-                visualised by transferring the local RMSD attributes
-                generated by Chimera's Match->Align tool onto aligned
-                sequences and displayed with a <a
-                href="featureschemes.html">Graduated feature colour
-                  scheme</a>.
-            </em><a href="https://issues.jalview.org/browse/JAL-2296">View
-                this function's issue in Jalview's bug tracker</a></li>
-          </ul></li>
-        <li><strong>Help<br>
+        <li><a name="annotxfer"><strong>Write Jalview
+              features</strong></a><br /> <em>Selecting this option will create
+            new residue attributes for any features currently visible in
+            the associated alignment views, allowing those positions to
+            be selected and analysed with via Chimera's 'Render by
+            Attribute' tool (found in the Tools submenu called Structure
+            Analysis).<br /> <br />If you use this option, please
+            remember to select the <em>Refresh Menus</em> option in
+            Chimera's Render by Attribute dialog box in order to see the
+            attributes derived from Jalview sequence features.
+        </em></li>
+        <li><strong>Fetch Chimera Attributes</strong><br /> <em>This
+            submenu lists available Chimera residue attributes that can
+            be imported as Jalview features on associated sequences.<br />This
+            is particularly useful for transferring quantitative
+            positional annotation. For example, structure similarity for
+            an alignment can be visualised by transferring the local
+            RMSD attributes generated by Chimera's Match->Align tool
+            onto aligned sequences and displayed with a <a
+            href="featureschemes.html">Graduated feature colour
+              scheme</a>. </li>
+      </ul></li>
+    <li><strong>Help<br>
     </strong>
       <ul>
         <li><strong>Chimera Help<br>
diff --git a/help/html/features/jmol.html b/help/html/features/jmol.html
index 0cd6168..ac2489b 100644
--- a/help/html/features/jmol.html
+++ b/help/html/features/jmol.html
@@ -61,16 +61,10 @@
 </p> -->
   <p>
     <a name="align"><strong>Superposing structures based on
-        their aligned sequences</strong></a><br> If several structures are
-    available on the alignment, you may add additional structures to an
-    existing Jmol view by selecting their entry in the appropriate
-    pop-up menu. Jalview will ask you if you wish to add the structure
-    to the existing alignment, and if you do, it will import and
-    superimpose the new PDB file using the corresponding positions from
-    the alignment. If the alignment is subsequently edited, you can use
-    the <a href="#sAlign"><em>Jmol&#8594;Align</em></a> menu option from
-    the menu bar of the structure view window to superpose the
-    structures using the updated alignment.<br> <em>Sequence
+        their aligned sequences</strong></a><br> If several structures are shown
+    in a view, you can superimpose them using the corresponding
+    positions from the alignment via the <a href="#sAlign"><em>Jmol&#8594;Align</em></a>
+    menu option from the menu bar of the structure view window. <br> <em>Sequence
       based structure superposition was added in Jalview 2.6</em>
   </p>
   <p>
diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html
index 533af5c..5bca358 100755
--- a/help/html/features/preferences.html
+++ b/help/html/features/preferences.html
@@ -369,7 +369,7 @@
     and PDB file association (if available). The Jalview id/start-end
     option is ignored if Modeller output is selected.
   <p>
-    <a name="editing"><strong>e&quot;Editinge&quot; Preferences tab</strong></a>
+    <a name="editing"><strong>&quot;Editing&quot; Preferences tab</strong></a>
   </p>
   <p>There are currently three options available which can be
     selected / deselected.</p>
diff --git a/help/html/features/schooser_enter-id.png b/help/html/features/schooser_enter-id.png
index f551c50..4af0d53 100644
Binary files a/help/html/features/schooser_enter-id.png and b/help/html/features/schooser_enter-id.png differ
diff --git a/help/html/features/schooser_main.png b/help/html/features/schooser_main.png
index ab69427..ca793fd 100644
Binary files a/help/html/features/schooser_main.png and b/help/html/features/schooser_main.png differ
diff --git a/help/html/features/structurechooser.html b/help/html/features/structurechooser.html
index fc71826..785c429 100644
--- a/help/html/features/structurechooser.html
+++ b/help/html/features/structurechooser.html
@@ -25,14 +25,14 @@
 
 <body>
   <p>
-    <strong>Structure Chooser</strong>
+    <strong>Structure Chooser Dialog Box</strong>
   </p>
 
   <p>
-    The Structure Chooser interface allows you to interactively select
-    which PDB structures to view for the currently selected set of
+    The Structure Chooser allows you to select
+    3D structures to view for the currently selected set of
     sequences. It is opened by selecting the <strong>"3D
-      Structure Data.."</strong> option from the Sequence ID panel's <a
+      Structure Data..."</strong> option from the Sequence ID panel's <a
       href="../menus/popupMenu.html">pop-up menu</a>. The dialog
     provides:
   </p>
@@ -49,11 +49,16 @@
   <p>
     <strong>Selecting and Viewing Structures</strong>
   </p>
+  <p>The drop-down menu offers different options for structure
+    discovery; the 'Cached' view is shown automatically if existing
+    structure data has been imported for the selected sequences, and if
+    none is available, the import PDB/mmCIF file options are shown.</p>
   <p>
     Once one or more structures have been selected, pressing the <strong>View</strong>
-    button will import them into <a
+    or <strong>Add</strong> button will import them <a
       href="viewingpdbs.html#afterviewbutton">a new or existing
-      structure view</a>.
+      structure view</a>. When multiple views are available, use the
+    drop-down menu to pick the target viewer for the structures.
   </p>
   <p>
     <strong>Automated discovery of structure data</strong>
@@ -89,17 +94,16 @@
     criteria (e.g. worst quality rather than best).</p>
   <p>
 
-    <img src="schooser_main.png" style="width: 464px; height: 369px;">
+    <img src="schooser_main.png" style="width: 499px; height: 437px;">
     <!-- <p><img src="schooser_config.png" style="width: 463px; height: 369px; ">
 	<p><img src="schooser_drop-down.png" style="width: 464px; height: 368px; ">
 	<p><img src="schooser_enter-id.png" style="width: 467px; height: 373px; ">
 	<p><img src="schooser_from-file.png" style="width: 468px; height: 370px; ">
 	<p><img src="schooser_cached.png"> -->
-    <br>The screenshot above shows the Structure Chooser interface
-    along with the meta-data of auto-discovered structures for the
-    sample alignment. If no structures were
-    auto-discovered, options for manually associating PDB records will be shown (see below).
-  <p>
+    <br>The screenshot above shows the Structure Chooser displayed after
+    selecting all the sequences in the Jalview example project. If no
+    structures were auto-discovered, options for manually associating
+    PDB records will be shown (see below).<p>
     <strong>Exploration of meta-data for available structures</strong>
   </p>
   <p>Information on each structure available is displayed in columns
@@ -109,7 +113,7 @@
     Columns' tab and tick the columns which you want to see.</p>
   <p>
     <img src="schooser_enter-id.png"
-      style="width: 464px; height: 369px;">
+      style="width: 464px; height: 173px;">
       <br/>
     <strong>Manual selection/association of PDB files with
       Sequences</strong>
diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html
index 45d979f..b1ad4ba 100755
--- a/help/html/features/viewingpdbs.html
+++ b/help/html/features/viewingpdbs.html
@@ -82,6 +82,7 @@
     provided it is installed and can be launched by Jalview. The default
     viewer can be configured in the <a href="preferences.html#structure">Structure
       tab</a> in the <strong>Tools&rarr;Preferences</strong> dialog box.
+  
   <p>
     Structure data imported into Jalview can also be processed to
     display secondary structure and temperature factor annotation. See
@@ -89,44 +90,30 @@
     for more information.
   </p>
   <p>
-    <strong><a name="afterviewbutton">After pressing the
-        'View' button in the Structure Chooser</a></strong><br /> The behaviour of
-    the 'View' button depends on the number of structures selected, and
-    whether structure views already exist for the selected structures or
-    aligned sequences.
+    <img src="schooser_viewbutton.png"
+      style="width: 465px; height: 81px" /><br/> <strong><a
+      name="afterviewbutton">Controlling where the new structures
+        will be shown</a></strong>
+        <br />The Structure Chooser offers several options
+    for viewing a structure. <br/><strong>New View</strong> will open a new
+    structure viewer for the selected structures, but if there are views
+    already open, you can select which one to use, and press the <strong>Add</strong>
+    button. Jalview can automatically superimpose new structures based
+    on the linked alignments - but if this is not desirable, simple
+    un-tick the <strong>Superpose Structures</strong> checkbox.
+
   </p>
-  <p>If multiple structures are selected, then Jalview will always
-    create a new structure view. The selected structures will be
-    imported into this view, and superposed with the matched positions
-    from the aligned sequences. A message in the structure viewer's
-    status bar will be shown if not enough aligned columns were
-    available to perform a superposition.</p>
   <p>
-    If a <strong>single</strong> PDB structure is selected, one of the
-    following will happen:
+    <em>Superposing structures</em><br/>Jalview superposes structures using
+    the visible portions of any associated sequence alignments. A
+    message in the structure viewer's status bar will be shown if not
+    enough aligned columns were available to perform a superposition.
   </p>
-
-  <ul>
-    <li>If no structures are open, then an interactive display of
-      the structure will be opened in a new window.</li>
-
-    <li>If another structure is already shown for the current
-      alignment, then you will be asked if you want to add and <a
-      href="jmol.html#align"></a> to the structure in the existing view.
-      (<em>new feature in Jalview 2.6</em>).
-    </li>
-
-    <li>If the structure is already shown, then you will be
-      prompted to associate the sequence with an existing view of the
-      selected structure. This is useful when working with multi-domain
-      or multi-chain PDB files.</li>
-
-    <li style="list-style: none">See the <a href="jmol.html">Jmol
-    </a> and <a href="chimera.html">Chimera</a> PDB viewer help pages for
-      more information about the display.
-    </li>
-  </ul>
-
+  <p>
+  See the <a href="jmol.html">Jmol
+    </a> and <a href="chimera.html">Chimera</a> help pages for
+      more information about their capabilities.</p>
+  
 
   <p>
     <strong>Retrieving sequences from the PDB</strong><br>You can
diff --git a/help/html/menus/desktopMenu.html b/help/html/menus/desktopMenu.html
index a93ce4b..d716e33 100755
--- a/help/html/menus/desktopMenu.html
+++ b/help/html/menus/desktopMenu.html
@@ -86,7 +86,7 @@
             the <a href="../features/groovy.html">Groovy Console</a> for
             interactive scripting.
         </em><strong><br></strong></li>
-        <li><strong>Enable Experimental Features</strong> <em>Enable or disable <a href="../whatsNew.html#experimental">features still under development</a> in Jalview's user interface. This setting is remembered in your preferences.</em>
+        <!--         <li><strong>Enable Experimental Features</strong> <em>Enable or disable <a href="../whatsNew.html#experimental">features still under development</a> in Jalview's user interface. This setting is remembered in your preferences.</em> -->
 
       </ul></li>
     <li><strong>Vamsas</strong> <em>For more details, read the
diff --git a/help/html/releases.html b/help/html/releases.html
index 006ee5c..dd2bb62 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,19 +70,33 @@ li:before {
     <tr>
       <td width="60" nowrap>
         <div align="center">
-          <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>27/02/2018</em></strong>
+          <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>8/05/2018</em></strong>
         </div>
       </td>
       <td><div align="left">
           <em></em>
           <ul>
             <li>
-              <!-- JAL-984 -->Mouse cursor changes to indicate Sequence ID and annotation area margins can be click-dragged to adjust them.</li> 
+              <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
+              for disabling automatic superposition of multiple
+              structures and open structures in existing views
+            </li>
+            <li>
+              <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
+              ID and annotation area margins can be click-dragged to
+              adjust them.
+            </li>
+            <li>
+              <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
+              Ensembl services
+            </li>
             <li>
-            <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and Ensembl services 
+              <!-- JAL-2759 -->Improved performance for large alignments
+              and lots of hidden columns
             </li>
             <li>
-            <!-- JAL-2759 -->Improved performance for large alignments and lots of hidden columns
+              <!-- JAL-2593 -->Improved performance when rendering lots
+              of features (particularly when transparency is disabled)
             </li>
           </ul>
           </div>
@@ -90,20 +104,111 @@ li:before {
       <td><div align="left">
           <ul>
             <li>
-              <!-- JAL-2778 -->Slow redraw when Overview panel shown overlapping alignment panel
+              <!-- JAL-2899 -->Structure and Overview aren't updated
+              when Colour By Annotation threshold slider is adjusted
+            </li>
+            <li>
+              <!-- JAL-2778 -->Slow redraw when Overview panel shown
+              overlapping alignment panel
+            </li>
+            <li>
+              <!--  JAL-2929 -->overview doesn't show end of unpadded
+              sequence as gaps
+            </li>
+            <li>
+              <!-- JAL-2789, JAL-2893 -->Cross-reference handling improved: CDS not handled correctly if transcript has no UTR
+            </li>
+            <li>
+            
+            </li>
+            <li>
+              <!-- JAL-2666 -->Linked scrolling via protein horizontal
+              scroll bar doesn't work for some CDS/Protein views
+            </li>
+            <li>
+              <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
+              Java 1.8u153 onwards and Java 1.9u4+.
+            </li>
+            <li>
+              <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
+              columns in annotation row
+            </li>
+            <li>
+              <!-- JAL-2913 -->Preferences panel's ID Width control is
+              honored in interactive and batch mode
+            </li>
+            <li>
+              <!-- JAL-2945 -->Linked sequence highlighting doesn't work
+              for structures added to existing Jmol view
+            </li>
+            <li>
+              <!-- JAL-2223 -->'View Mappings' includes duplicate
+              entries after importing project with multiple views
+            </li>
+            <li>
+              <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
+              protein sequences via SIFTS from associated PDB entries
+              with negative residue numbers or missing residues fails
+            </li>
+            <li>
+              <!-- JAL-2952 -->Exception when shading sequence with negative
+              Temperature Factor values from annotated PDB files (e.g.
+              as generated by CONSURF)
             </li>
             <li>
-              <!-- JAL-2666 -->Linked scrolling via protein horizontal scroll bar doesn't work for some CDS/Protein views 
+              <!-- JAL-2922 -->Invert displayed features very slow when
+              structure and/or overview windows are also shown
+            </li>
+            <li>
+              <!-- JAL-2954 -->Selecting columns from highlighted regions
+              very slow for alignments with large numbers of sequences
+            </li>
+            <li>
+              <!-- JAL-2925 -->Copy Consensus fails for group consensus
+              with 'StringIndexOutOfBounds'
+            </li>
+            <li>
+              <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
+              platforms running Java 10
+            </li>
+            <li>
+              <!-- JAL-2960 -->Adding a structure to existing structure
+              view appears to do nothing because the view is hidden behind the alignment view
             </li>
-            <li><!-- JAL-2930 -->Trackpad scrolling is broken on OSX on Java 1.8u153 onwards and Java 1.9u4+.</li>
-            <li><!-- JAL-2924 -->Tooltip shouldn't be displayed for empty columns in annotation row</li>
-            <li><!-- JAL-2913 -->Preferences panel's ID Width control is honored in interactive and batch mode</li>
-            </ul><em>Applet</em><ul>
-            <li><!-- JAL-2926 -->Copy consensus sequence option in applet should copy the group consensus when popup is opened on it</li>
-             
           </ul>
-      </div>
-      </td>
+          <em>Applet</em>
+          <ul>
+            <li>
+              <!-- JAL-2926 -->Copy consensus sequence option in applet
+              should copy the group consensus when popup is opened on it
+            </li>
+          </ul>
+          <em>Batch Mode</em>
+          <ul>
+          <li>
+            <!-- JAL-2913 -->Fixed ID width preference is not respected
+          </li>
+          </ul>
+          <em>New Known Defects</em>
+          <ul>
+            <li>
+              <!-- JAL-2973 --> Exceptions occasionally raised when
+              editing a large alignment and overview is displayed
+            </li>
+            <li>
+              <!-- JAL-2974 -->'Overview updating' progress bar is shown
+              repeatedly after a series of edits even when the overview
+              is no longer reflecting updates
+            </li>
+            <li>
+              <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
+              structures for protein subsequence (if 'Trim Retrieved
+              Sequences' enabled) or Ensembl isoforms (Workaround in
+              2.10.4 is to fail back to N&amp;W mapping)
+            </li>
+          </ul>
+        </div>
+          </td>
     </tr>
     <tr>
       <td width="60" nowrap>
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index d3972f5..0abd2a7 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -27,27 +27,24 @@
     <strong>What's new in Jalview 2.10.4 ?</strong>
   </p>
   <p>
-    This is the February 2018 release of Jalview, with several minor bug fixes and enhanvements. 
-    The full list bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
-      Release Notes</a>. In addition, Jalview 2.10.4 provides:
+    This is the May 2018 release of Jalview, and the last in the 2.10.x series. Jalview 2.10.4 includes:
   </p>
   <ul>
-    <li></li>
+    <li>Numerous efficiency improvements in the renderer and overview when working with large alignments with lots of hidden columns</li>
+    <li>Use of HTTPS when connecting to Uniprot, Ensembl and other EBI web services</li>
+    <li>Critical patches for running Jalview on OSX with Java 10</li>
+    <li>Easier adjustment of the Alignment ID panel and Annotation panel</li>
+    <li>Improved support for mapping between 3D Structures and Uniprot Protein Sequences</li>
+    <li>Improved support for discovering CDS and transcripts for Proteins and Ensembl gene IDs</li>
+    <li>New buttons on the Structure Chooser for adding structures
+      to an existing view, and disabling automatic superposition
+      according to linked alignments</li>
+    <li>Annotation transfer between Chimera and Jalview <em>(formerly only
+        available in 'Experimental' mode)</em></li>
   </ul>
   <p>
-    <strong><a name="experimental">Experimental Features</a></strong>
+    The full list of bugs fixed in this release can be found in the <a href="releases.html#Jalview.2.10.4">2.10.4
+      Release Notes</a>. 
   </p>
-  <p>
-    Remember, please enable the <em>Experimental Features</em> option in
-    the Jalview Desktop's <em>Tools</em> menu, and then restart Jalview
-    if you want to try out features below:
-  </p>
-  <ul>
-    <li><em>Annotation transfer between Chimera and Jalview</em><br />Two
-      <a href="features/chimera.html#experimental">new entries in
-        the Chimera viewer's Chimera menu</a> allow positional annotation to
-      be exchanged between Chimera and Jalview.</li>
-  </ul>
-  
 </body>
 </html>
diff --git a/lib/VAqua4.jar b/lib/VAqua4.jar
new file mode 100644
index 0000000..c1e7cfc
Binary files /dev/null and b/lib/VAqua4.jar differ
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 609c6a8..db3dbf8 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -405,10 +405,6 @@ label.view_name_original = Original
 label.enter_view_name = Enter View Name
 label.enter_label = Enter label
 label.enter_label_for_the_structure = Enter a label for the structure
-label.pdb_entry_is_already_displayed = {0} is already displayed.\nDo you want to re-use this viewer ?
-label.map_sequences_to_visible_window = Map Sequences to Visible Window: {0}
-label.add_pdbentry_to_view = Do you want to add {0} to the view called\n{1}\n
-label.align_to_existing_structure_view = Align to existing structure view
 label.pdb_entries_couldnt_be_retrieved = The following pdb entries could not be retrieved from the PDB\:\n{0}\nPlease retry, or try downloading them manually.
 label.couldnt_load_file = Couldn't load file
 label.couldnt_find_pdb_id_in_file = Couldn't find a PDB id in the file supplied. Please enter an Id to identify this structure.
@@ -1222,7 +1218,6 @@ label.pdb_sequence_fetcher = PDB Sequence Fetcher
 label.result = result
 label.results = results
 label.structure_chooser = Structure Chooser
-label.select = Select : 
 label.invert = Invert 
 label.select_pdb_file = Select PDB File
 info.select_filter_option = Select Filter Option/Manual Entry
@@ -1387,6 +1382,7 @@ label.hmmer = HMMER
 label.trim_termini = Trim Non-Matching Termini
 label.trim_termini_desc = If true, non-matching regions on either end of the resulting alignment are removed.
 label.no_of_sequences = Number of sequences returned
+label.reporting_cutoff = Reporting Cut-off
 label.freq_alignment = Use alignment background frequencies
 label.freq_uniprot = Use Uniprot background frequencies
 label.hmmalign_options = hmmalign options
@@ -1397,17 +1393,17 @@ label.invalid_folder = Invalid Folder
 label.number_of_results = Number of Results to Return
 label.auto_align_seqs = Automatically Align Fetched Sequences
 label.use_accessions = Return Accessions
-label.seq_e_value = Sequence E-value Cutoff
+label.seq_evalue = Sequence E-value Cut-off
 label.seq_score = Sequence Score Threshold
-label.dom_e_value = Domain E-value Cutoff
+label.dom_evalue = Domain E-value Cut-off
 label.dom_score = Domain Score Threshold
 label.number_of_results_desc = The maximum number of hmmsearch results to display
 label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed
 label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequence's name
 label.seq_e_value_desc = The E-value cutoff for returned sequences (hmmsearch -E)
-label.seq_score_desc = The score threshold for returned sequences
-label.dom_e_value_desc = The E-value cutoff for returned domains (hmmsearch -domE)
-label.dom_score_desc = The score threshold for returned domains
+label.seq_score_desc = The score threshold for returned sequences (hmmsearch -T)
+label.dom_e_value_desc = The E-value cutoff for returned domains (hmmsearch --domE)
+label.dom_score_desc = The score threshold for returned domains (hmmsearch --domT)
 label.add_database = Add Database
 label.this_alignment = This alignment
 warn.invalid_format = This is not a valid database file format. The current supported formats are Fasta, Stockholm and Pfam.
diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 6dfefa3..0144522 100644
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -370,10 +370,6 @@ label.ignore_unmatched_dropped_files = Ignorar los ficheros sin coincidencias?
 label.enter_view_name = Introduzca un nombre para la vista
 label.enter_label = Introducir etiqueta
 label.enter_label_for_the_structure = Introducir una etiqueta para la estructura
-label.pdb_entry_is_already_displayed = {0} Ya est\u00E1 mostrado.\nQuieres volver a usar este visor?
-label.map_sequences_to_visible_window = Mapa de secuencias en ventana visible: {0}
-label.add_pdbentry_to_view = Quieres a\u00F1adir {0} a la vista llamada\n{1}\n
-label.align_to_existing_structure_view = Alinear a una estructura ya existente
 label.pdb_entries_couldnt_be_retrieved = Las siguientes entradas pdb no pueden ser extra\u00EDdas del PDB\:\n{0}\nPor favor, prueba descarg\u00E1ndolas manualmente.
 label.couldnt_load_file = No se pudo cargar el fichero
 label.couldnt_find_pdb_id_in_file = No se pudo encontrar un Id PDB en el fichero suministrado. Por favor, introduzca un Id para identificar esta estructura.
@@ -1176,7 +1172,6 @@ label.structures_filter=Filtro de Estructuras
 label.scale_protein_to_cdna=Adaptar proteína a cDNA
 label.scale_protein_to_cdna_tip=Hacer a los residuos de proteínas de la misma anchura que los codones en ventanas divididas
 status.loading_cached_pdb_entries=Cargando Entradas PDB en Caché
-label.select=Seleccionar :
 label.select_by_annotation=Seleccionar/Ocultar Columnas por Anotación
 action.select_by_annotation=Seleccionar/Ocultar Columnas por Anotación...
 action.export_features=Exportar Características
diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 48824e7..d5cd5bc 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -287,6 +287,11 @@
 									</xs:attribute>
 								</xs:complexType>
 							</xs:element>
+							<xs:element name="hmmerProfile" minOccurs="0" type="xs:string">
+								<xs:annotation>
+									<xs:documentation>name of the project jar entry that holds the HMM file with the profile for the sequence</xs:documentation>
+								</xs:annotation>
+							</xs:element>
 						</xs:sequence>
 						<xs:attribute name="colour" type="xs:int" use="optional" />
 						<xs:attribute name="start" type="xs:int" use="required" />
diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 29b994e..904a860 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -45,11 +45,11 @@ public class PDBChain
 
   public String id;
 
-  public Vector<Bond> bonds = new Vector<Bond>();
+  public Vector<Bond> bonds = new Vector<>();
 
-  public Vector<Atom> atoms = new Vector<Atom>();
+  public Vector<Atom> atoms = new Vector<>();
 
-  public Vector<Residue> residues = new Vector<Residue>();
+  public Vector<Residue> residues = new Vector<>();
 
   public int offset;
 
@@ -343,12 +343,13 @@ public class PDBChain
     boolean deoxyn = false;
     boolean nucleotide = false;
     StringBuilder seq = new StringBuilder(256);
-    Vector<SequenceFeature> resFeatures = new Vector<SequenceFeature>();
-    Vector<Annotation> resAnnotation = new Vector<Annotation>();
-    int i, iSize = atoms.size() - 1;
+    Vector<SequenceFeature> resFeatures = new Vector<>();
+    Vector<Annotation> resAnnotation = new Vector<>();
+    int iSize = atoms.size() - 1;
     int resNumber = -1;
     char insCode = ' ';
-    for (i = 0; i <= iSize; i++)
+
+    for (int i = 0; i <= iSize; i++)
     {
       Atom tmp = atoms.elementAt(i);
       resNumber = tmp.resNumber;
@@ -362,7 +363,7 @@ public class PDBChain
         offset = resNumber;
       }
 
-      Vector<Atom> resAtoms = new Vector<Atom>();
+      Vector<Atom> resAtoms = new Vector<>();
       // Add atoms to a vector while the residue number
       // remains the same as the first atom's resNumber (res)
       while ((resNumber == res) && (ins == insCode) && (i < atoms.size()))
@@ -469,7 +470,8 @@ public class PDBChain
 
     if (StructureImportSettings.isShowSeqFeatures())
     {
-      for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
+      iSize = resFeatures.size();
+      for (int i = 0; i < iSize; i++)
       {
         sequence.addSequenceFeature(resFeatures.elementAt(i));
         resFeatures.setElementAt(null, i);
@@ -478,20 +480,20 @@ public class PDBChain
     if (visibleChainAnnotation)
     {
       Annotation[] annots = new Annotation[resAnnotation.size()];
-      float max = 0;
-      for (i = 0, iSize = annots.length; i < iSize; i++)
+      float max = 0f;
+      float min = 0f;
+      iSize = annots.length;
+      for (int i = 0; i < iSize; i++)
       {
         annots[i] = resAnnotation.elementAt(i);
-        if (annots[i].value > max)
-        {
-          max = annots[i].value;
-        }
+        max = Math.max(max, annots[i].value);
+        min = Math.min(min, annots[i].value);
         resAnnotation.setElementAt(null, i);
       }
 
       AlignmentAnnotation tfactorann = new AlignmentAnnotation(
               "Temperature Factor", "Temperature Factor for " + pdbid + id,
-              annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
+              annots, min, max, AlignmentAnnotation.LINE_GRAPH);
       tfactorann.setSequenceRef(sequence);
       sequence.addAlignmentAnnotation(tfactorann);
     }
diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java
index b4612cf..8f778f7 100644
--- a/src/jalview/api/structures/JalviewStructureDisplayI.java
+++ b/src/jalview/api/structures/JalviewStructureDisplayI.java
@@ -20,6 +20,9 @@
  */
 package jalview.api.structures;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.structures.models.AAStructureBindingModel;
 
@@ -69,4 +72,57 @@ public interface JalviewStructureDisplayI
    */
   boolean hasMapping();
 
+  /**
+   * Checks if the PDB file is already loaded in this viewer, if so just adds
+   * mappings as necessary and answers true, else answers false. This supports
+   * the use case of adding additional chains of the same structure to a viewer.
+   * 
+   * @param seq
+   * @param chains
+   * @param apanel
+   * @param pdbId
+   * @return
+   */
+  boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+          AlignmentViewPanel apanel, String pdbId);
+
+  /**
+   * Adds one or more chains (sequences) of a PDB structure to this structure
+   * viewer
+   * 
+   * @param pdbentry
+   * @param seq
+   * @param chains
+   * @param apanel
+   * @param pdbId
+   * @return
+   */
+  void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+          String[] chains, AlignmentViewPanel apanel, String pdbId);
+
+  /**
+   * refresh GUI after reconfiguring structure(s) and alignment panels
+   */
+  void updateTitleAndMenus();
+
+  /**
+   * Answers true if the viewer should attempt to align any added structures,
+   * else false
+   * 
+   * @return
+   */
+  boolean isAlignAddedStructures();
+
+  /**
+   * Sets the flag for whether added structures should be aligned
+   * 
+   * @param alignAdded
+   */
+  void setAlignAddedStructures(boolean alignAdded);
+
+  /**
+   * Raise the panel to the top of the stack...
+   */
+  void raiseViewer();
+
 }
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index bc93c37..e66b7ae 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -279,6 +279,8 @@ public class Jalview
       UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
     } catch (Exception ex)
     {
+      System.err.println("Unexpected Look and Feel Exception");
+      ex.printStackTrace();
     }
     if (Platform.isAMac())
     {
@@ -294,6 +296,20 @@ public class Jalview
         System.err.println(
                 "Failed to set QuaQua look and feel: " + e.toString());
       }
+      if (!ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel()
+              .equals(UIManager.getLookAndFeel()))
+      {
+        try
+        {
+          System.err.println(
+                  "Quaqua LaF not available. Using VAqua(4).");
+          // UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
+        } catch (Throwable e)
+        {
+          System.err.println(
+                  "Failed to reset look and feel: " + e.toString());
+        }
+      }
     }
 
     /*
diff --git a/src/jalview/datamodel/HiddenMarkovModel.java b/src/jalview/datamodel/HiddenMarkovModel.java
index 3c2c437..e3eb160 100644
--- a/src/jalview/datamodel/HiddenMarkovModel.java
+++ b/src/jalview/datamodel/HiddenMarkovModel.java
@@ -1,6 +1,5 @@
 package jalview.datamodel;
 
-import jalview.bin.Cache;
 import jalview.io.HMMFile;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Comparison;
@@ -100,11 +99,14 @@ public class HiddenMarkovModel
     this.hmmSeq = sq;
     if (sq.getDatasetSequence() == hmm.mapToHmmConsensus.getTo())
     {
+      // same dataset sequence e.g. after realigning search results
       this.mapToHmmConsensus = hmm.mapToHmmConsensus;
     }
     else
     {
-      Cache.log.error("Error: HMM copied with change of mapped sequence");
+      // different dataset sequence e.g. after loading HMM from project
+      this.mapToHmmConsensus = new Mapping(sq.getDatasetSequence(),
+              hmm.mapToHmmConsensus.getMap());
     }
   }
 
diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index cde50e5..d1e3fcc 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -267,9 +267,12 @@ public class SearchResults implements SearchResultsI
   {
     int count = 0;
     BitSet mask = new BitSet();
+    int startRes = sqcol.getStartRes();
+    int endRes = sqcol.getEndRes();
+
     for (SequenceI s : sqcol.getSequences())
     {
-      int[] cols = getResults(s, sqcol.getStartRes(), sqcol.getEndRes());
+      int[] cols = getResults(s, startRes, endRes);
       if (cols != null)
       {
         for (int pair = 0; pair < cols.length; pair += 2)
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 9464c74..7972626 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -825,7 +825,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param curs
    * @return
    */
-  protected int findIndex(int pos, SequenceCursor curs)
+  protected int findIndex(final int pos, SequenceCursor curs)
   {
     if (!isValidCursor(curs))
     {
@@ -851,10 +851,15 @@ public class Sequence extends ASequence implements SequenceI
     while (newPos != pos)
     {
       col += delta; // shift one column left or right
-      if (col < 0 || col == sequence.length)
+      if (col < 0)
       {
         break;
       }
+      if (col == sequence.length)
+      {
+        col--; // return last column if we failed to reach pos
+        break;
+      }
       if (!Comparison.isGap(sequence[col]))
       {
         newPos += delta;
@@ -862,7 +867,14 @@ public class Sequence extends ASequence implements SequenceI
     }
 
     col++; // convert back to base 1
-    updateCursor(pos, col, curs.firstColumnPosition);
+
+    /*
+     * only update cursor if we found the target position
+     */
+    if (newPos == pos)
+    {
+      updateCursor(pos, col, curs.firstColumnPosition);
+    }
 
     return col;
   }
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 41bc116..8832278 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -478,6 +478,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
     lastCommand = command;
   }
 
+  Thread colourby = null;
   /**
    * Sends a set of colour commands to the structure viewer
    * 
@@ -485,15 +486,28 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
    */
   @Override
   protected void colourBySequence(
-          StructureMappingcommandSet[] colourBySequenceCommands)
+          final StructureMappingcommandSet[] colourBySequenceCommands)
   {
-    for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+    if (colourby != null)
     {
-      for (String cbyseq : cpdbbyseq.commands)
+      colourby.interrupt();
+      colourby = null;
+    }
+    colourby = new Thread(new Runnable()
+    {
+      @Override
+      public void run()
       {
-        executeWhenReady(cbyseq);
+        for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+        {
+          for (String cbyseq : cpdbbyseq.commands)
+          {
+            executeWhenReady(cbyseq);
+          }
+        }
       }
-    }
+    });
+    colourby.start();
   }
 
   /**
@@ -862,19 +876,30 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       try
       {
         // recover PDB filename for the model hovered over.
-        int _mp = _modelFileNameMap.length - 1,
-                mnumber = new Integer(mdlId).intValue() - 1;
-        while (mnumber < _modelFileNameMap[_mp])
+        int mnumber = new Integer(mdlId).intValue() - 1;
+        if (_modelFileNameMap != null)
         {
-          _mp--;
+          int _mp = _modelFileNameMap.length - 1;
+
+          while (mnumber < _modelFileNameMap[_mp])
+          {
+            _mp--;
+          }
+          pdbfilename = modelFileNames[_mp];
         }
-        pdbfilename = modelFileNames[_mp];
-        if (pdbfilename == null)
+        else
         {
-          pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
-                  .getAbsolutePath();
-        }
+          if (mnumber >= 0 && mnumber < modelFileNames.length)
+          {
+            pdbfilename = modelFileNames[mnumber];
+          }
 
+          if (pdbfilename == null)
+          {
+            pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
+                    .getAbsolutePath();
+          }
+        }
       } catch (Exception e)
       {
       }
diff --git a/src/jalview/fts/core/FTSRestClient.java b/src/jalview/fts/core/FTSRestClient.java
index 076e212..f94d455 100644
--- a/src/jalview/fts/core/FTSRestClient.java
+++ b/src/jalview/fts/core/FTSRestClient.java
@@ -284,7 +284,8 @@ public abstract class FTSRestClient implements FTSRestClientI
               public boolean equals(Object otherObject)
               {
                 FTSDataColumnI that = (FTSDataColumnI) otherObject;
-                return this.getCode().equals(that.getCode())
+                return otherObject == null ? false
+                        : this.getCode().equals(that.getCode())
                         && this.getName().equals(that.getName())
                         && this.getGroup().equals(that.getGroup());
               }
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index bcb8423..d52aa97 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -141,10 +141,8 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Deque;
 import java.util.Enumeration;
-import java.util.HashMap;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Map;
 import java.util.Scanner;
 import java.util.Vector;
 
@@ -168,9 +166,6 @@ import javax.swing.SwingUtilities;
 public class AlignFrame extends GAlignFrame implements DropTargetListener,
         IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
 {
-
-  Map<String, Float> distribution = new HashMap<>(); // temporary
-
   public static final int DEFAULT_WIDTH = 700;
 
   public static final int DEFAULT_HEIGHT = 500;
@@ -1155,7 +1150,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     String path = openFileChooser(false);
-    if (new File(path).exists())
+    if (path != null && new File(path).exists())
     {
       IdentifyFile identifier = new IdentifyFile();
       FileFormatI format = identifier.identify(path, DataSourceType.FILE);
@@ -1183,21 +1178,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 MessageManager.getString("warn.invalid_format"));
       }
     }
-    else
-    {
-      JOptionPane.showMessageDialog(this,
-              MessageManager.getString("label.not_enough_sequences"));
-    }
   }
 
   /**
-   * Opens a file chooser
+   * Opens a file chooser, optionally restricted to selecting folders
+   * (directories) only. Answers the path to the selected file or folder, or
+   * null if none is chosen.
    * 
-   * @param forFolder
+   * @param
    * @return
    */
   protected String openFileChooser(boolean forFolder)
   {
+    // TODO duplicates GPreferences method - relocate to JalviewFileChooser?
     String choice = null;
     JFileChooser chooser = new JFileChooser();
     if (forFolder)
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 153f70c..384635b 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -459,4 +459,11 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     }
   }
 
+  @Override
+  protected void sliderDragReleased()
+  {
+    super.sliderDragReleased();
+    ap.paintAlignment(true, true);
+  }
+
 }
diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 71ad6a5..f13cb10 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -172,11 +172,7 @@ public abstract class AnnotationRowFilter extends JPanel
       @Override
       public void mouseReleased(MouseEvent evt)
       {
-        if (sliderDragging)
-        {
-          sliderDragging = false;
-          valueChanged(true);
-        }
+        sliderDragReleased();
       }
     });
   }
@@ -523,4 +519,13 @@ public abstract class AnnotationRowFilter extends JPanel
   {
     this.annotations = anns;
   }
+
+  protected void sliderDragReleased()
+  {
+    if (sliderDragging)
+    {
+      sliderDragging = false;
+      valueChanged(true);
+    }
+  }
 }
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index fef7451..6c934c8 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -44,7 +44,6 @@ import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
 import javax.swing.JPanel;
 import javax.swing.JSplitPane;
 import javax.swing.SwingUtilities;
@@ -58,7 +57,7 @@ public class AppJmol extends StructureViewerBase
 
   private static final String SPACE = " ";
 
-  private static final String BACKSLASH = "\"";
+  private static final String QUOTE = "\"";
 
   AppJmolBinding jmb;
 
@@ -162,8 +161,9 @@ public class AppJmol extends StructureViewerBase
   {
     return progressBar;
   }
+  
   /**
-   * add a single PDB structure to a new or existing Jmol view
+   * display a single PDB structure in a new Jmol view
    * 
    * @param pdbentry
    * @param seq
@@ -174,33 +174,14 @@ public class AppJmol extends StructureViewerBase
           final AlignmentPanel ap)
   {
     progressBar = ap.alignFrame;
-    String pdbId = pdbentry.getId();
 
-    /*
-     * If the PDB file is already loaded, the user may just choose to add to an
-     * existing viewer (or cancel)
-     */
-    if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * Check if there are other Jmol views involving this alignment and prompt
-     * user about adding this molecule to one of them
-     */
-    if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * If the options above are declined or do not apply, open a new viewer
-     */
-    openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+    openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
+            new SequenceI[][]
+            { seq });
   }
 
-  private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+  private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
+          PDBEntry[] pdbentrys,
           SequenceI[][] seqs)
   {
     progressBar = ap.alignFrame;
@@ -209,11 +190,9 @@ public class AppJmol extends StructureViewerBase
     addAlignmentPanel(ap);
     useAlignmentPanelForColourbyseq(ap);
 
-    if (pdbentrys.length > 1)
-    {
-      alignAddedStructures = true;
-      useAlignmentPanelForSuperposition(ap);
-    }
+    alignAddedStructures = alignAdded;
+    useAlignmentPanelForSuperposition(ap);
+
     jmb.setColourBySequence(true);
     setSize(400, 400); // probably should be a configurable/dynamic default here
     initMenus();
@@ -234,41 +213,21 @@ public class AppJmol extends StructureViewerBase
   }
 
   /**
-   * create a new Jmol containing several structures superimposed using the
-   * given alignPanel.
+   * create a new Jmol containing several structures optionally superimposed
+   * using the given alignPanel.
    * 
    * @param ap
+   * @param alignAdded
+   *          - true to superimpose
    * @param pe
    * @param seqs
    */
-  public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+  public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
+          SequenceI[][] seqs)
   {
-    openNewJmol(ap, pe, seqs);
+    openNewJmol(ap, alignAdded, pe, seqs);
   }
 
-  /**
-   * Returns a list of any Jmol viewers. The list is restricted to those linked
-   * to the given alignment panel if it is not null.
-   */
-  @Override
-  protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
-  {
-    List<StructureViewerBase> result = new ArrayList<>();
-    JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
-    for (JInternalFrame frame : frames)
-    {
-      if (frame instanceof AppJmol)
-      {
-        if (apanel == null
-                || ((StructureViewerBase) frame).isLinkedWith(apanel))
-        {
-          result.add((StructureViewerBase) frame);
-        }
-      }
-    }
-    return result;
-  }
 
   void initJmol(String command)
   {
@@ -300,8 +259,6 @@ public class AppJmol extends StructureViewerBase
     jmb.setFinishedInit(true);
   }
 
-  boolean allChainsSelected = false;
-
   @Override
   void showSelectedChains()
   {
@@ -368,8 +325,8 @@ public class AppJmol extends StructureViewerBase
     StringBuilder fileList = new StringBuilder();
     for (String s : files)
     {
-      fileList.append(SPACE).append(BACKSLASH)
-              .append(Platform.escapeString(s)).append(BACKSLASH);
+      fileList.append(SPACE).append(QUOTE)
+              .append(Platform.escapeString(s)).append(QUOTE);
     }
     String filesString = fileList.toString();
 
@@ -444,7 +401,7 @@ public class AppJmol extends StructureViewerBase
       jmb.updateColours(ap);
     }
     // do superposition if asked to
-    if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+    if (alignAddedStructures)
     {
       alignAddedStructures();
     }
@@ -478,7 +435,7 @@ public class AppJmol extends StructureViewerBase
         }
       }
     });
-    alignAddedStructures = false;
+
   }
 
   /**
@@ -507,6 +464,7 @@ public class AppJmol extends StructureViewerBase
         String file = jmb.getPdbEntry(pi).getFile();
         if (file == null)
         {
+          // todo: extract block as method and pull up (also ChimeraViewFrame)
           // retrieve the pdb and store it locally
           AlignmentI pdbseq = null;
           pdbid = jmb.getPdbEntry(pi).getId();
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 89de2e8..d07a7c2 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -100,41 +100,34 @@ public class ChimeraViewFrame extends StructureViewerBase
     savemenu.setVisible(false); // not yet implemented
     viewMenu.add(fitToWindow);
 
-    /*
-     * exchange of Jalview features and Chimera attributes is for now
-     * an optionally enabled experimental feature
-     */
-    if (Desktop.instance.showExperimental())
+    JMenuItem writeFeatures = new JMenuItem(
+            MessageManager.getString("label.create_chimera_attributes"));
+    writeFeatures.setToolTipText(MessageManager
+            .getString("label.create_chimera_attributes_tip"));
+    writeFeatures.addActionListener(new ActionListener()
     {
-      JMenuItem writeFeatures = new JMenuItem(
-              MessageManager.getString("label.create_chimera_attributes"));
-      writeFeatures.setToolTipText(MessageManager
-              .getString("label.create_chimera_attributes_tip"));
-      writeFeatures.addActionListener(new ActionListener()
-      {
-        @Override
-        public void actionPerformed(ActionEvent e)
-        {
-          sendFeaturesToChimera();
-        }
-      });
-      viewerActionMenu.add(writeFeatures);
-
-      final JMenu fetchAttributes = new JMenu(
-              MessageManager.getString("label.fetch_chimera_attributes"));
-      fetchAttributes.setToolTipText(MessageManager
-              .getString("label.fetch_chimera_attributes_tip"));
-      fetchAttributes.addMouseListener(new MouseAdapter()
+      @Override
+      public void actionPerformed(ActionEvent e)
       {
+        sendFeaturesToChimera();
+      }
+    });
+    viewerActionMenu.add(writeFeatures);
 
-        @Override
-        public void mouseEntered(MouseEvent e)
-        {
-          buildAttributesMenu(fetchAttributes);
-        }
-      });
-      viewerActionMenu.add(fetchAttributes);
-    }
+    final JMenu fetchAttributes = new JMenu(
+            MessageManager.getString("label.fetch_chimera_attributes"));
+    fetchAttributes.setToolTipText(
+            MessageManager.getString("label.fetch_chimera_attributes_tip"));
+    fetchAttributes.addMouseListener(new MouseAdapter()
+    {
+
+      @Override
+      public void mouseEntered(MouseEvent e)
+      {
+        buildAttributesMenu(fetchAttributes);
+      }
+    });
+    viewerActionMenu.add(fetchAttributes);
   }
 
   /**
@@ -202,7 +195,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * add a single PDB structure to a new or existing Chimera view
+   * open a single PDB structure in a new Chimera view
    * 
    * @param pdbentry
    * @param seq
@@ -213,30 +206,7 @@ public class ChimeraViewFrame extends StructureViewerBase
           String[] chains, final AlignmentPanel ap)
   {
     this();
-    String pdbId = pdbentry.getId();
-
-    /*
-     * If the PDB file is already loaded, the user may just choose to add to an
-     * existing viewer (or cancel)
-     */
-    if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
-    {
-      return;
-    }
 
-    /*
-     * Check if there are other Chimera views involving this alignment and give
-     * user the option to add and align this molecule to one of them (or cancel)
-     */
-    if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
-    {
-      return;
-    }
-
-    /*
-     * If the options above are declined or do not apply, show the structure in
-     * a new viewer
-     */
     openNewChimera(ap, new PDBEntry[] { pdbentry },
             new SequenceI[][]
             { seq });
@@ -264,7 +234,6 @@ public class ChimeraViewFrame extends StructureViewerBase
 
     if (pdbentrys.length > 1)
     {
-      alignAddedStructures = true;
       useAlignmentPanelForSuperposition(ap);
     }
     jmb.setColourBySequence(true);
@@ -323,17 +292,19 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * create a new viewer containing several structures superimposed using the
-   * given alignPanel.
+   * create a new viewer containing several structures, optionally superimposed
+   * using the given alignPanel.
    * 
    * @param pe
    * @param seqs
    * @param ap
    */
-  public ChimeraViewFrame(PDBEntry[] pe, SequenceI[][] seqs,
+  public ChimeraViewFrame(PDBEntry[] pe, boolean alignAdded,
+          SequenceI[][] seqs,
           AlignmentPanel ap)
   {
     this();
+    setAlignAddedStructures(alignAdded);
     openNewChimera(ap, pe, seqs);
   }
 
@@ -352,29 +323,6 @@ public class ChimeraViewFrame extends StructureViewerBase
   }
 
   /**
-   * Returns a list of any Chimera viewers in the desktop. The list is
-   * restricted to those linked to the given alignment panel if it is not null.
-   */
-  @Override
-  protected List<StructureViewerBase> getViewersFor(AlignmentPanel ap)
-  {
-    List<StructureViewerBase> result = new ArrayList<>();
-    JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
-    for (JInternalFrame frame : frames)
-    {
-      if (frame instanceof ChimeraViewFrame)
-      {
-        if (ap == null || ((StructureViewerBase) frame).isLinkedWith(ap))
-        {
-          result.add((StructureViewerBase) frame);
-        }
-      }
-    }
-    return result;
-  }
-
-  /**
    * Launch Chimera. If we have a chimera session file name, send Chimera the
    * command to open its saved session file.
    */
@@ -641,7 +589,7 @@ public class ChimeraViewFrame extends StructureViewerBase
         jmb.updateColours(ap);
       }
       // do superposition if asked to
-      if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+      if (alignAddedStructures)
       {
         new Thread(new Runnable()
         {
@@ -651,7 +599,6 @@ public class ChimeraViewFrame extends StructureViewerBase
             alignStructs_withAllAlignPanels();
           }
         }).start();
-        alignAddedStructures = false;
       }
       addingStructures = false;
     }
@@ -681,7 +628,6 @@ public class ChimeraViewFrame extends StructureViewerBase
 
   private String fetchPdbFile(PDBEntry processingEntry) throws Exception
   {
-    // FIXME: this is duplicated code with Jmol frame ?
     String filePath = null;
     Pdb pdbclient = new Pdb();
     AlignmentI pdbseq = null;
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index b26a8af..be64c85 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -3397,4 +3397,41 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
   }
+
+  /**
+   * Answers a (possibly empty) list of any structure viewer frames (currently
+   * for either Jmol or Chimera) which are currently open. This may optionally
+   * be restricted to viewers of a specified class, or viewers linked to a
+   * specified alignment panel.
+   * 
+   * @param apanel
+   *          if not null, only return viewers linked to this panel
+   * @param structureViewerClass
+   *          if not null, only return viewers of this class
+   * @return
+   */
+  public List<StructureViewerBase> getStructureViewers(
+          AlignmentPanel apanel,
+          Class<? extends StructureViewerBase> structureViewerClass)
+  {
+    List<StructureViewerBase> result = new ArrayList<>();
+    JInternalFrame[] frames = Desktop.instance.getAllFrames();
+
+    for (JInternalFrame frame : frames)
+    {
+      if (frame instanceof StructureViewerBase)
+      {
+        if (structureViewerClass == null
+                || structureViewerClass.isInstance(frame))
+        {
+          if (apanel == null
+                  || ((StructureViewerBase) frame).isLinkedWith(apanel))
+          {
+            result.add((StructureViewerBase) frame);
+          }
+        }
+      }
+    }
+    return result;
+  }
 }
diff --git a/src/jalview/gui/JDatabaseTree.java b/src/jalview/gui/JDatabaseTree.java
index 0a6b9d6..1018d6e 100644
--- a/src/jalview/gui/JDatabaseTree.java
+++ b/src/jalview/gui/JDatabaseTree.java
@@ -101,10 +101,10 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
      * identical DB sources, and should be collapsed.
      */
     DefaultMutableTreeNode tn = null, root = new DefaultMutableTreeNode();
-    Hashtable<String, DefaultMutableTreeNode> source = new Hashtable<String, DefaultMutableTreeNode>();
+    Hashtable<String, DefaultMutableTreeNode> source = new Hashtable<>();
     sfetcher = sfetch;
     String dbs[] = sfetch.getSupportedDb();
-    Hashtable<String, String> ht = new Hashtable<String, String>();
+    Hashtable<String, String> ht = new Hashtable<>();
     for (int i = 0; i < dbs.length; i++)
     {
       tn = source.get(dbs[i]);
@@ -370,7 +370,7 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
 
     tsel = dbviews.getSelectionPaths();
     boolean forcedFirstChild = false;
-    List<DbSourceProxy> srcs = new ArrayList<DbSourceProxy>();
+    List<DbSourceProxy> srcs = new ArrayList<>();
     if (tsel != null)
     {
       for (TreePath tp : tsel)
@@ -489,7 +489,7 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
       return null;
     }
     StringBuffer sb = new StringBuffer();
-    HashSet<String> hs = new HashSet<String>();
+    HashSet<String> hs = new HashSet<>();
     for (DbSourceProxy dbs : getSelectedSources())
     {
       String tq = dbs.getTestQuery();
@@ -506,7 +506,7 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
     return sb.toString();
   }
 
-  List<ActionListener> lstners = new Vector<ActionListener>();
+  List<ActionListener> lstners = new Vector<>();
 
   public void addActionListener(ActionListener actionListener)
   {
@@ -596,4 +596,11 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
     // TODO Auto-generated method stub
 
   }
+
+  @Override
+  public void setVisible(boolean arg0)
+  {
+    System.out.println("setVisible: " + arg0);
+    super.setVisible(arg0);
+  }
 }
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 3840597..aed73d6 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -30,6 +30,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.RnaViewerModel;
 import jalview.datamodel.SequenceFeature;
@@ -45,6 +46,7 @@ import jalview.ext.varna.RnaModel;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
+import jalview.io.HMMFile;
 import jalview.renderer.ResidueShaderI;
 import jalview.schemabinding.version2.AlcodMap;
 import jalview.schemabinding.version2.AlcodonFrame;
@@ -52,7 +54,6 @@ import jalview.schemabinding.version2.Annotation;
 import jalview.schemabinding.version2.AnnotationColours;
 import jalview.schemabinding.version2.AnnotationElement;
 import jalview.schemabinding.version2.CalcIdParam;
-import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.CompoundMatcher;
 import jalview.schemabinding.version2.DBRef;
 import jalview.schemabinding.version2.Features;
@@ -167,6 +168,8 @@ public class Jalview2XML
 
   private static final String RNA_PREFIX = "rna_";
 
+  private static final String HMMER_PREFIX = "hmmer_";
+
   private static final String UTF_8 = "UTF-8";
 
   // use this with nextCounter() to make unique names for entities
@@ -867,73 +870,28 @@ public class Jalview2XML
         }
       }
 
-      // TODO: omit sequence features from each alignment view's XML dump if we
-      // are storing dataset
-      List<jalview.datamodel.SequenceFeature> sfs = jds
-              .getSequenceFeatures();
+      /*
+       * save sequence features
+       * TODO: omit sequence features from each alignment view's 
+       * XML dump if we are storing dataset
+       */
+      List<SequenceFeature> sfs = jds.getSequenceFeatures();
       for (SequenceFeature sf : sfs)
       {
-        Features features = new Features();
-
-        features.setBegin(sf.getBegin());
-        features.setEnd(sf.getEnd());
-        features.setDescription(sf.getDescription());
-        features.setType(sf.getType());
-        features.setFeatureGroup(sf.getFeatureGroup());
-        features.setScore(sf.getScore());
-        if (sf.links != null)
-        {
-          for (int l = 0; l < sf.links.size(); l++)
-          {
-            OtherData keyValue = new OtherData();
-            keyValue.setKey("LINK_" + l);
-            keyValue.setValue(sf.links.elementAt(l).toString());
-            features.addOtherData(keyValue);
-          }
-        }
-        if (sf.otherDetails != null)
-        {
-          /*
-           * save feature attributes, which may be simple strings or
-           * map valued (have sub-attributes)
-           */
-          for (Entry<String, Object> entry : sf.otherDetails.entrySet())
-          {
-            String key = entry.getKey();
-            Object value = entry.getValue();
-            if (value instanceof Map<?, ?>)
-            {
-              for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
-                      .entrySet())
-              {
-                OtherData otherData = new OtherData();
-                otherData.setKey(key);
-                otherData.setKey2(subAttribute.getKey());
-                otherData.setValue(subAttribute.getValue().toString());
-                features.addOtherData(otherData);
-              }
-            }
-            else
-            {
-              OtherData otherData = new OtherData();
-              otherData.setKey(key);
-              otherData.setValue(value.toString());
-              features.addOtherData(otherData);
-            }
-          }
-        }
-
+        Features features = saveFeature(sf);
         jseq.addFeatures(features);
       }
 
+      /*
+       * save PDB entries for sequence
+       */
       if (jdatasq.getAllPDBEntries() != null)
       {
-        Enumeration en = jdatasq.getAllPDBEntries().elements();
+        Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
         while (en.hasMoreElements())
         {
           Pdbids pdb = new Pdbids();
-          jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en
-                  .nextElement();
+          PDBEntry entry = en.nextElement();
 
           String pdbId = entry.getId();
           pdb.setId(pdbId);
@@ -1017,6 +975,11 @@ public class Jalview2XML
 
       saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
 
+      if (jds.hasHMMProfile())
+      {
+        saveHmmerProfile(jout, jseq, jds);
+      }
+
       jms.addJSeq(jseq);
     }
 
@@ -1508,6 +1471,98 @@ public class Jalview2XML
   }
 
   /**
+   * Saves the HMMER profile associated with the sequence as a file in the jar,
+   * in HMMER format, and saves the name of the file as a child element of the
+   * XML sequence element
+   * 
+   * @param jout
+   * @param xmlSeq
+   * @param seq
+   */
+  protected void saveHmmerProfile(JarOutputStream jout, JSeq xmlSeq,
+          SequenceI seq)
+  {
+    HiddenMarkovModel profile = seq.getHMM();
+    if (profile == null)
+    {
+      warn("Want to save HMM profile for " + seq.getName()
+              + " but none found");
+      return;
+    }
+    HMMFile hmmFile = new HMMFile(profile);
+    String hmmAsString = hmmFile.print();
+    String jarEntryName = HMMER_PREFIX + nextCounter();
+    try
+    {
+      writeJarEntry(jout, jarEntryName, hmmAsString.getBytes());
+      xmlSeq.setHmmerProfile(jarEntryName);
+    } catch (IOException e)
+    {
+      warn("Error saving HMM profile: " + e.getMessage());
+    }
+  }
+
+  /**
+   * Converts a Jalview SequenceFeature into the XML model of it to save
+   * 
+   * @param sf
+   * @return
+   */
+  protected Features saveFeature(SequenceFeature sf)
+  {
+    Features features = new Features();
+
+    features.setBegin(sf.getBegin());
+    features.setEnd(sf.getEnd());
+    features.setDescription(sf.getDescription());
+    features.setType(sf.getType());
+    features.setFeatureGroup(sf.getFeatureGroup());
+    features.setScore(sf.getScore());
+    if (sf.links != null)
+    {
+      for (int l = 0; l < sf.links.size(); l++)
+      {
+        OtherData keyValue = new OtherData();
+        keyValue.setKey("LINK_" + l);
+        keyValue.setValue(sf.links.elementAt(l).toString());
+        features.addOtherData(keyValue);
+      }
+    }
+    if (sf.otherDetails != null)
+    {
+      /*
+       * save feature attributes, which may be simple strings or
+       * map valued (have sub-attributes)
+       */
+      for (Entry<String, Object> entry : sf.otherDetails.entrySet())
+      {
+        String key = entry.getKey();
+        Object value = entry.getValue();
+        if (value instanceof Map<?, ?>)
+        {
+          for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
+                  .entrySet())
+          {
+            OtherData otherData = new OtherData();
+            otherData.setKey(key);
+            otherData.setKey2(subAttribute.getKey());
+            otherData.setValue(subAttribute.getValue().toString());
+            features.addOtherData(otherData);
+          }
+        }
+        else
+        {
+          OtherData otherData = new OtherData();
+          otherData.setKey(key);
+          otherData.setValue(value.toString());
+          features.addOtherData(otherData);
+        }
+      }
+    }
+    return features;
+  }
+
+  /**
    * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
    * for each viewer, with
    * <ul>
@@ -1708,9 +1763,8 @@ public class Jalview2XML
       }
       else if (!matchedFile.equals(pdbentry.getFile()))
       {
-        Cache.log.warn(
-                "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
-                        + pdbentry.getFile());
+        warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+                + pdbentry.getFile());
       }
       // record the
       // file so we
@@ -2194,12 +2248,12 @@ public class Jalview2XML
         mpc.setDseqFor(jmpid);
         if (!seqRefIds.containsKey(mpc.getDseqFor()))
         {
-          jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+          debug("creating new DseqFor ID");
           seqRefIds.put(mpc.getDseqFor(), ps);
         }
         else
         {
-          jalview.bin.Cache.log.debug("reusing DseqFor ID");
+          debug("reusing DseqFor ID");
         }
 
         mp.setMappingChoice(mpc);
@@ -3014,24 +3068,26 @@ public class Jalview2XML
       //
       for (int i = 0; i < vamsasSeq.length; i++)
       {
+        SequenceI alignmentSeq = al.getSequenceAt(i);
         if (jseqs[i].getFeaturesCount() > 0)
         {
           Features[] features = jseqs[i].getFeatures();
           for (int f = 0; f < features.length; f++)
           {
-            SequenceFeature sf = new SequenceFeature(features[f].getType(),
-                    features[f].getDescription(), features[f].getBegin(),
-                    features[f].getEnd(), features[f].getScore(),
-                    features[f].getFeatureGroup());
-            sf.setStatus(features[f].getStatus());
+            Features feature = features[f];
+            SequenceFeature sf = new SequenceFeature(feature.getType(),
+                    feature.getDescription(), feature.getBegin(),
+                    feature.getEnd(), feature.getScore(),
+                    feature.getFeatureGroup());
+            sf.setStatus(feature.getStatus());
 
             /*
              * load any feature attributes - include map-valued attributes
              */
             Map<String, Map<String, String>> mapAttributes = new HashMap<>();
-            for (int od = 0; od < features[f].getOtherDataCount(); od++)
+            for (int od = 0; od < feature.getOtherDataCount(); od++)
             {
-              OtherData keyValue = features[f].getOtherData(od);
+              OtherData keyValue = feature.getOtherData(od);
               String attributeName = keyValue.getKey();
               String attributeValue = keyValue.getValue();
               if (attributeName.startsWith("LINK"))
@@ -3065,16 +3121,15 @@ public class Jalview2XML
             }
 
             // adds feature to datasequence's feature set (since Jalview 2.10)
-            al.getSequenceAt(i).addSequenceFeature(sf);
+            alignmentSeq.addSequenceFeature(sf);
           }
         }
         if (vamsasSeq[i].getDBRefCount() > 0)
         {
           // adds dbrefs to datasequence's set (since Jalview 2.10)
           addDBRefs(
-                  al.getSequenceAt(i).getDatasetSequence() == null
-                          ? al.getSequenceAt(i)
-                          : al.getSequenceAt(i).getDatasetSequence(),
+                  alignmentSeq.getDatasetSequence() == null ? alignmentSeq
+                          : alignmentSeq.getDatasetSequence(),
                   vamsasSeq[i]);
         }
         if (jseqs[i].getPdbidsCount() > 0)
@@ -3122,16 +3177,25 @@ public class Jalview2XML
                     .getStructureSelectionManager(Desktop.instance)
                     .registerPDBEntry(entry);
             // adds PDBEntry to datasequence's set (since Jalview 2.10)
-            if (al.getSequenceAt(i).getDatasetSequence() != null)
+            if (alignmentSeq.getDatasetSequence() != null)
             {
-              al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+              alignmentSeq.getDatasetSequence().addPDBId(entry);
             }
             else
             {
-              al.getSequenceAt(i).addPDBId(entry);
+              alignmentSeq.addPDBId(entry);
             }
           }
         }
+
+        /*
+         * load any HMMER profile
+         */
+        String hmmJarFile = jseqs[i].getHmmerProfile();
+        if (hmmJarFile != null)
+        {
+          loadHmmerProfile(jprovider, hmmJarFile, alignmentSeq);
+        }
       }
     } // end !multipleview
 
@@ -3629,6 +3693,31 @@ public class Jalview2XML
   }
 
   /**
+   * Loads a HMMER profile from a file stored in the project, and associates it
+   * with the specified sequence
+   * 
+   * @param jprovider
+   * @param hmmJarFile
+   * @param seq
+   */
+  protected void loadHmmerProfile(jarInputStreamProvider jprovider,
+          String hmmJarFile, SequenceI seq)
+  {
+    try
+    {
+      String hmmFile = copyJarEntry(jprovider, hmmJarFile, "hmm", null);
+      HMMFile parser = new HMMFile(hmmFile, DataSourceType.FILE);
+      HiddenMarkovModel hmmModel = parser.getHMM();
+      hmmModel = new HiddenMarkovModel(hmmModel, seq);
+      seq.setHMM(hmmModel);
+    } catch (IOException e)
+    {
+      warn("Error loading HMM profile for " + seq.getName() + ": "
+              + e.getMessage());
+    }
+  }
+
+  /**
    * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
    * panel is restored from separate jar entries, two (gapped and trimmed) per
    * sequence and secondary structure.
@@ -5055,10 +5144,7 @@ public class Jalview2XML
             id = object.getJalviewModelSequence().getViewport()[0]
                     .getSequenceSetId()))
     {
-      if (Cache.log != null && Cache.log.isDebugEnabled())
-      {
-        Cache.log.debug("Skipping seuqence set id " + id);
-      }
+      debug("Skipping sequence set id " + id);
       return true;
     }
     return false;
@@ -5432,7 +5518,7 @@ public class Jalview2XML
           seqRefIds.put(sqid, djs);
 
         }
-        jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+        debug("about to recurse on addDBRefs.");
         addDBRefs(djs, ms);
 
       }
@@ -5610,7 +5696,7 @@ public class Jalview2XML
       }
       else
       {
-        Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+        debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
       }
     }
   }
@@ -5942,7 +6028,10 @@ public class Jalview2XML
         maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
       } catch (Exception e)
       {
-        Cache.log.warn("Couldn't parse out graduated feature color.", e);
+        if (Cache.log != null)
+        {
+          Cache.log.warn("Couldn't parse out graduated feature color.", e);
+        }
       }
   
       NoValueColour noCol = colourModel.getNoValueColour();
diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index 34af13d..dcd07ef 100644
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -101,7 +101,7 @@ public class OptsAndParamsPage
   public class OptionBox extends JPanel
           implements MouseListener, ActionListener
   {
-    JCheckBox enabled = new JCheckBox();
+    JCheckBox enabled;
 
     final URL finfo;
 
@@ -113,14 +113,13 @@ public class OptsAndParamsPage
 
     OptionI option;
 
-    JLabel optlabel = new JLabel();
-
-    JComboBox<String> val = new JComboBox<>();
+    JComboBox<String> val;
 
     public OptionBox(OptionI opt)
     {
       option = opt;
       setLayout(new FlowLayout(FlowLayout.LEFT));
+      enabled = new JCheckBox();
       enabled.setSelected(opt.isRequired()); // TODO: lock required options
       enabled.setFont(new Font("Verdana", Font.PLAIN, 11));
       enabled.setText("");
@@ -149,6 +148,9 @@ public class OptsAndParamsPage
         }
       }
       add(enabled);
+
+      // todo combo or radio buttons?
+      val = new JComboBox<>();
       for (String str : opt.getPossibleValues())
       {
         val.addItem(str);
@@ -366,7 +368,8 @@ public class OptsAndParamsPage
          * ensure slider has an integer range corresponding to
          * the min-max range of the parameter
          */
-        if (validator.getMin() != null && !isIntegerParameter
+        if (validator.getMin() != null && validator.getMax() != null
+        // && !isIntegerParameter
                 && !isStringParameter)
         {
           double min = validator.getMin().doubleValue();
@@ -380,10 +383,10 @@ public class OptsAndParamsPage
           // todo scaleMin, scaleMax could also be final fields
         }
       }
-      else
-      {
-        isChoiceParameter = parameter.getPossibleValues() != null;
-      }
+
+      List<String> possibleValues = parameter.getPossibleValues();
+      isChoiceParameter = possibleValues != null
+              && !possibleValues.isEmpty();
 
       if (compact)
       {
@@ -549,13 +552,23 @@ public class OptsAndParamsPage
      */
     private void checkIfModified()
     {
-      Object newValue = updateSliderFromValueField();
-      boolean modified = true;
-      if (newValue.getClass() == lastVal.getClass())
+      if (!adjusting)
       {
-        modified = !newValue.equals(lastVal);
+        try
+        {
+          adjusting = true;
+          Object newValue = updateSliderFromValueField();
+          boolean modified = true;
+          if (newValue.getClass() == lastVal.getClass())
+          {
+            modified = !newValue.equals(lastVal);
+          }
+          pmdialogbox.argSetModified(this, modified);
+        } finally
+        {
+          adjusting = false;
+        }
       }
-      pmdialogbox.argSetModified(this, modified);
     }
 
     @Override
@@ -629,8 +642,13 @@ public class OptsAndParamsPage
     @Override
     public void stateChanged(ChangeEvent e)
     {
-      if (!adjusting)
+      if (adjusting)
       {
+        return;
+      }
+      try
+      {
+        adjusting = true;
         if (!isLogarithmicParameter)
         {
           /*
@@ -648,6 +666,9 @@ public class OptsAndParamsPage
           valueField.setText(formatDouble(value));
         }
         checkIfModified();
+      } finally
+      {
+        adjusting = false;
       }
     }
 
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index 9f52d26..7ceceee 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -464,7 +464,16 @@ public class PCAPanel extends GPCAPanel
     public void run()
     {
       PrinterJob printJob = PrinterJob.getPrinterJob();
-      PageFormat pf = printJob.pageDialog(printJob.defaultPage());
+      PageFormat defaultPage = printJob.defaultPage();
+      PageFormat pf = printJob.pageDialog(defaultPage);
+
+      if (defaultPage == pf)
+      {
+        /*
+         * user cancelled
+         */
+        return;
+      }
 
       printJob.setPrintable(this, pf);
 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 193d0ee..ce6bcbd 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -2292,4 +2292,13 @@ public class SeqPanel extends JPanel
 
     return true;
   }
+
+  /**
+   * 
+   * @return null or last search results handled by this panel
+   */
+  public SearchResultsI getLastSearchResults()
+  {
+    return lastSearchResults;
+  }
 }
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 8d46792..f545e70 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -273,7 +273,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         return Collections.emptyList();
       }
     }
-    sf.newAlframes = new ArrayList<AlignFrame>();
+    sf.newAlframes = new ArrayList<>();
     sf.run();
     return sf.newAlframes;
   }
@@ -674,10 +674,10 @@ public class SequenceFetcher extends JPanel implements Runnable
     // TODO: Refactor to GUI independent code and write tests.
     // indicate if successive sources should be merged into one alignment.
     boolean addToLast = false;
-    List<String> aresultq = new ArrayList<String>();
-    List<String> presultTitle = new ArrayList<String>();
-    List<AlignmentI> presult = new ArrayList<AlignmentI>();
-    List<AlignmentI> aresult = new ArrayList<AlignmentI>();
+    List<String> aresultq = new ArrayList<>();
+    List<String> presultTitle = new ArrayList<>();
+    List<AlignmentI> presult = new ArrayList<>();
+    List<AlignmentI> aresult = new ArrayList<>();
     Iterator<DbSourceProxy> proxies = database.getSelectedSources()
             .iterator();
     String[] qries;
@@ -695,7 +695,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         nqueries = nextFetch.size();
         // save the remaining queries in the original array
         qries = nextFetch.toArray(new String[nqueries]);
-        nextFetch = new ArrayList<String>();
+        nextFetch = new ArrayList<>();
       }
 
       DbSourceProxy proxy = proxies.next();
@@ -861,7 +861,7 @@ public class SequenceFetcher extends JPanel implements Runnable
           List<AlignmentI> aresult, List<String> nextFetch) throws Exception
   {
     StringBuilder multiacc = new StringBuilder();
-    List<String> tosend = new ArrayList<String>();
+    List<String> tosend = new ArrayList<>();
     while (accessions.hasNext())
     {
       String nel = accessions.next();
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 198aa62..e18d6af 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -22,6 +22,7 @@
 package jalview.gui;
 
 import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -68,6 +69,8 @@ import javax.swing.table.AbstractTableModel;
 public class StructureChooser extends GStructureChooser
         implements IProgressIndicator
 {
+  private static final String AUTOSUPERIMPOSE = "AUTOSUPERIMPOSE";
+
   private static int MAX_QLENGTH = 7820;
 
   private SequenceI selectedSequence;
@@ -88,6 +91,8 @@ public class StructureChooser extends GStructureChooser
 
   private boolean cachedPDBExists;
 
+  private static StructureViewer lastTargetedView = null;
+
   public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
           AlignmentPanel ap)
   {
@@ -101,13 +106,15 @@ public class StructureChooser extends GStructureChooser
   /**
    * Initializes parameters used by the Structure Chooser Panel
    */
-  public void init()
+  protected void init()
   {
     if (!Jalview.isHeadlessMode())
     {
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
     }
 
+    chk_superpose.setSelected(Cache.getDefault(AUTOSUPERIMPOSE, true));
+
     // ensure a filter option is in force for search
     populateFilterComboBox(true, cachedPDBExists);
     Thread discoverPDBStructuresThread = new Thread(new Runnable()
@@ -125,6 +132,7 @@ public class StructureChooser extends GStructureChooser
         fetchStructuresMetaData();
         // revise filter options if no results were found
         populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
+        discoverStructureViews();
         updateProgressIndicator(null, startTime);
         mainFrame.setVisible(true);
         updateCurrentView();
@@ -134,6 +142,59 @@ public class StructureChooser extends GStructureChooser
   }
 
   /**
+   * Builds a drop-down choice list of existing structure viewers to which new
+   * structures may be added. If this list is empty then it, and the 'Add'
+   * button, are hidden.
+   */
+  private void discoverStructureViews()
+  {
+    if (Desktop.instance != null)
+    {
+      targetView.removeAllItems();
+      if (lastTargetedView != null && !lastTargetedView.isVisible())
+      {
+        lastTargetedView = null;
+      }
+      int linkedViewsAt = 0;
+      for (StructureViewerBase view : Desktop.instance
+              .getStructureViewers(null, null))
+      {
+        StructureViewer viewHandler = (lastTargetedView != null
+                && lastTargetedView.sview == view) ? lastTargetedView
+                        : StructureViewer.reconfigure(view);
+
+        if (view.isLinkedWith(ap))
+        {
+          targetView.insertItemAt(viewHandler,
+                  linkedViewsAt++);
+        }
+        else
+        {
+          targetView.addItem(viewHandler);
+        }
+      }
+
+      /*
+       * show option to Add to viewer if at least 1 viewer found
+       */
+      targetView.setVisible(false);
+      if (targetView.getItemCount() > 0)
+      {
+        targetView.setVisible(true);
+        if (lastTargetedView != null)
+        {
+          targetView.setSelectedItem(lastTargetedView);
+        }
+        else
+        {
+          targetView.setSelectedIndex(0);
+        }
+      }
+      btn_add.setVisible(targetView.isVisible());
+    }
+  }
+
+  /**
    * Updates the progress indicator with the specified message
    * 
    * @param message
@@ -141,7 +202,7 @@ public class StructureChooser extends GStructureChooser
    * @param id
    *          unique handle for this indicator
    */
-  public void updateProgressIndicator(String message, long id)
+  protected void updateProgressIndicator(String message, long id)
   {
     if (progressIndicator != null)
     {
@@ -153,7 +214,7 @@ public class StructureChooser extends GStructureChooser
    * Retrieve meta-data for all the structure(s) for a given sequence(s) in a
    * selection group
    */
-  public void fetchStructuresMetaData()
+  void fetchStructuresMetaData()
   {
     long startTime = System.currentTimeMillis();
     pdbRestCleint = PDBFTSRestClient.getInstance();
@@ -224,7 +285,7 @@ public class StructureChooser extends GStructureChooser
     }
   }
 
-  public void loadLocalCachedPDBEntries()
+  protected void loadLocalCachedPDBEntries()
   {
     ArrayList<CachedPDB> entries = new ArrayList<>();
     for (SequenceI seq : selectedSequences)
@@ -255,7 +316,7 @@ public class StructureChooser extends GStructureChooser
    * @return the built query string
    */
 
-  public static String buildQuery(SequenceI seq)
+  static String buildQuery(SequenceI seq)
   {
     boolean isPDBRefsFound = false;
     boolean isUniProtRefsFound = false;
@@ -357,7 +418,7 @@ public class StructureChooser extends GStructureChooser
    * @param seqName
    * @return
    */
-  public static boolean isValidSeqName(String seqName)
+  static boolean isValidSeqName(String seqName)
   {
     // System.out.println("seqName : " + seqName);
     String ignoreList = "pdb,uniprot,swiss-prot";
@@ -380,7 +441,7 @@ public class StructureChooser extends GStructureChooser
     return true;
   }
 
-  public static String getDBRefId(DBRefEntry dbRef)
+  static String getDBRefId(DBRefEntry dbRef)
   {
     String ref = dbRef.getAccessionId().replaceAll("GO:", "");
     return ref;
@@ -392,7 +453,7 @@ public class StructureChooser extends GStructureChooser
    * @param fieldToFilterBy
    *          the field to filter by
    */
-  public void filterResultSet(final String fieldToFilterBy)
+  void filterResultSet(final String fieldToFilterBy)
   {
     Thread filterThread = new Thread(new Runnable()
     {
@@ -502,7 +563,7 @@ public class StructureChooser extends GStructureChooser
    * Handles action event for btn_pdbFromFile
    */
   @Override
-  public void pdbFromFile_actionPerformed()
+  protected void pdbFromFile_actionPerformed()
   {
     jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
@@ -603,28 +664,37 @@ public class StructureChooser extends GStructureChooser
   }
 
   /**
-   * Validates user selection and activates the view button if all parameters
-   * are correct
+   * Validates user selection and enables the 'Add' and 'New View' buttons if
+   * all parameters are correct (the Add button will only be visible if there is
+   * at least one existing structure viewer open). This basically means at least
+   * one structure selected and no error messages.
+   * <p>
+   * The 'Superpose Structures' option is enabled if either more than one
+   * structure is selected, or the 'Add' to existing view option is enabled, and
+   * disabled if the only option is to open a new view of a single structure.
    */
   @Override
-  public void validateSelections()
+  protected void validateSelections()
   {
     FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
             .getSelectedItem());
-    btn_view.setEnabled(false);
+    btn_add.setEnabled(false);
     String currentView = selectedFilterOpt.getView();
+    int selectedCount = 0;
     if (currentView == VIEWS_FILTER)
     {
-      if (getResultTable().getSelectedRows().length > 0)
+      selectedCount = getResultTable().getSelectedRows().length;
+      if (selectedCount > 0)
       {
-        btn_view.setEnabled(true);
+        btn_add.setEnabled(true);
       }
     }
     else if (currentView == VIEWS_LOCAL_PDB)
     {
-      if (tbl_local_pdb.getSelectedRows().length > 0)
+      selectedCount = tbl_local_pdb.getSelectedRows().length;
+      if (selectedCount > 0)
       {
-        btn_view.setEnabled(true);
+        btn_add.setEnabled(true);
       }
     }
     else if (currentView == VIEWS_ENTER_ID)
@@ -635,12 +705,21 @@ public class StructureChooser extends GStructureChooser
     {
       validateAssociationFromFile();
     }
+
+    btn_newView.setEnabled(btn_add.isEnabled());
+
+    /*
+     * enable 'Superpose' option if more than one structure is selected,
+     * or there are view(s) available to add structure(s) to
+     */
+    chk_superpose
+            .setEnabled(selectedCount > 1 || targetView.getItemCount() > 0);
   }
 
   /**
    * Validates inputs from the Manual PDB entry panel
    */
-  public void validateAssociationEnterPdb()
+  protected void validateAssociationEnterPdb()
   {
     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
             .getCmb_assSeq().getSelectedItem();
@@ -666,7 +745,7 @@ public class StructureChooser extends GStructureChooser
       txt_search.setEnabled(true);
       if (isValidPBDEntry)
       {
-        btn_view.setEnabled(true);
+        btn_add.setEnabled(true);
         lbl_pdbManualFetchStatus.setToolTipText("");
         lbl_pdbManualFetchStatus.setIcon(goodImage);
       }
@@ -681,7 +760,7 @@ public class StructureChooser extends GStructureChooser
   /**
    * Validates inputs for the manual PDB file selection options
    */
-  public void validateAssociationFromFile()
+  protected void validateAssociationFromFile()
   {
     AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) fileChooserAssSeqPanel
             .getCmb_assSeq().getSelectedItem();
@@ -692,7 +771,7 @@ public class StructureChooser extends GStructureChooser
       btn_pdbFromFile.setEnabled(true);
       if (selectedPdbFileName != null && selectedPdbFileName.length() > 0)
       {
-        btn_view.setEnabled(true);
+        btn_add.setEnabled(true);
         lbl_fromFileStatus.setIcon(goodImage);
       }
     }
@@ -704,7 +783,7 @@ public class StructureChooser extends GStructureChooser
   }
 
   @Override
-  public void cmbAssSeqStateChanged()
+  protected void cmbAssSeqStateChanged()
   {
     validateSelections();
   }
@@ -768,11 +847,22 @@ public class StructureChooser extends GStructureChooser
     }
     return found;
   }
+  
+  /**
+   * Handles the 'New View' action
+   */
+  @Override
+  protected void newView_ActionPerformed()
+  {
+    targetView.setSelectedItem(null);
+    showStructures(false);
+  }
+
   /**
-   * Handles action event for btn_ok
+   * Handles the 'Add to existing viewer' action
    */
   @Override
-  public void ok_ActionPerformed()
+  protected void add_ActionPerformed()
   {
     showStructures(false);
   }
@@ -957,6 +1047,30 @@ public class StructureChooser extends GStructureChooser
     return foundEntry;
   }
 
+  /**
+   * Answers a structure viewer (new or existing) configured to superimpose
+   * added structures or not according to the user's choice
+   * 
+   * @param ssm
+   * @return
+   */
+  StructureViewer getTargetedStructureViewer(
+          StructureSelectionManager ssm)
+  {
+    Object sv = targetView.getSelectedItem();
+
+    return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
+  }
+
+  /**
+   * Adds PDB structures to a new or existing structure viewer
+   * 
+   * @param ssm
+   * @param pdbEntriesToView
+   * @param alignPanel
+   * @param sequences
+   * @return
+   */
   private StructureViewer launchStructureViewer(
           StructureSelectionManager ssm,
           final PDBEntry[] pdbEntriesToView,
@@ -965,9 +1079,17 @@ public class StructureChooser extends GStructureChooser
     long progressId = sequences.hashCode();
     setProgressBar(MessageManager
             .getString("status.launching_3d_structure_viewer"), progressId);
-    final StructureViewer sViewer = new StructureViewer(ssm);
-    setProgressBar(null, progressId);
+    final StructureViewer theViewer = getTargetedStructureViewer(ssm);
+    boolean superimpose = chk_superpose.isSelected();
+    theViewer.setSuperpose(superimpose);
+
+    /*
+     * remember user's choice of superimpose or not
+     */
+    Cache.setProperty(AUTOSUPERIMPOSE,
+            Boolean.valueOf(superimpose).toString());
 
+    setProgressBar(null, progressId);
     if (SiftsSettings.isMapWithSifts())
     {
       List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
@@ -992,7 +1114,7 @@ public class StructureChooser extends GStructureChooser
             }
           }
         }
-        if (seq.getPrimaryDBRefs().size() == 0)
+        if (seq.getPrimaryDBRefs().isEmpty())
         {
           seqsWithoutSourceDBRef.add(seq);
           continue;
@@ -1004,13 +1126,8 @@ public class StructureChooser extends GStructureChooser
         setProgressBar(MessageManager.formatMessage(
                 "status.fetching_dbrefs_for_sequences_without_valid_refs",
                 y), progressId);
-        SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
-        int x = 0;
-        for (SequenceI fSeq : seqsWithoutSourceDBRef)
-        {
-          seqWithoutSrcDBRef[x++] = fSeq;
-        }
-
+        SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+                .toArray(new SequenceI[y]);
         DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
         dbRefFetcher.fetchDBRefs(true);
 
@@ -1022,17 +1139,19 @@ public class StructureChooser extends GStructureChooser
       setProgressBar(MessageManager.getString(
               "status.fetching_3d_structures_for_selected_entries"),
               progressId);
-      sViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
+      theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
     }
     else
     {
       setProgressBar(MessageManager.formatMessage(
               "status.fetching_3d_structures_for",
               pdbEntriesToView[0].getId()),progressId);
-      sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+      theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
     }
     setProgressBar(null, progressId);
-    return sViewer;
+    // remember the last viewer we used...
+    lastTargetedView = theViewer;
+    return theViewer;
   }
 
   /**
@@ -1040,7 +1159,7 @@ public class StructureChooser extends GStructureChooser
    * a unique sequence when more than one sequence selection is made.
    */
   @Override
-  public void populateCmbAssociateSeqOptions(
+  protected void populateCmbAssociateSeqOptions(
           JComboBox<AssociateSeqOptions> cmb_assSeq,
           JLabel lbl_associateSeq)
   {
@@ -1065,17 +1184,12 @@ public class StructureChooser extends GStructureChooser
     }
   }
 
-  public boolean isStructuresDiscovered()
+  protected boolean isStructuresDiscovered()
   {
     return discoveredStructuresSet != null
             && !discoveredStructuresSet.isEmpty();
   }
 
-  public Collection<FTSData> getDiscoveredStructuresSet()
-  {
-    return discoveredStructuresSet;
-  }
-
   @Override
   protected void txt_search_ActionPerformed()
   {
@@ -1125,7 +1239,7 @@ public class StructureChooser extends GStructureChooser
   }
 
   @Override
-  public void tabRefresh()
+  protected void tabRefresh()
   {
     if (selectedSequences != null)
     {
diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index f37df71..0c8354b 100644
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -49,6 +49,11 @@ public class StructureViewer
 
   StructureSelectionManager ssm;
 
+  /**
+   * decide if new structures are aligned to existing ones
+   */
+  private boolean superposeAdded = true;
+
   public enum ViewerType
   {
     JMOL, CHIMERA
@@ -64,6 +69,27 @@ public class StructureViewer
     ssm = structureSelectionManager;
   }
 
+  /**
+   * Factory to create a proxy for modifying existing structure viewer
+   * 
+   */
+  public static StructureViewer reconfigure(
+          JalviewStructureDisplayI display)
+  {
+    StructureViewer sv = new StructureViewer(display.getBinding().getSsm());
+    sv.sview = display;
+    return sv;
+  }
+
+  @Override
+  public String toString()
+  {
+    if (sview != null)
+    {
+      return sview.toString();
+    }
+    return "New View";
+  }
   public ViewerType getViewerType()
   {
     String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
@@ -104,14 +130,40 @@ public class StructureViewer
             new PDBEntry[seqsForPdbs.size()]);
     SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
             new SequenceI[seqsForPdbs.size()][]);
+    if (sview != null)
+    {
+      sview.setAlignAddedStructures(superposeAdded);
+      new Thread(new Runnable()
+      {
+        @Override
+        public void run()
+        {
+
+          for (int pdbep = 0; pdbep < pdbsForFile.length; pdbep++)
+          {
+            PDBEntry pdb = pdbsForFile[pdbep];
+            if (!sview.addAlreadyLoadedFile(theSeqs[pdbep], null, ap,
+                    pdb.getId()))
+            {
+              sview.addToExistingViewer(pdb, theSeqs[pdbep], null, ap,
+                      pdb.getId());
+            }
+          }
+
+          sview.updateTitleAndMenus();
+        }
+      }).start();
+      return sview;
+    }
 
     if (viewerType.equals(ViewerType.JMOL))
     {
-      sview = new AppJmol(ap, pdbsForFile, theSeqs);
+      sview = new AppJmol(ap, superposeAdded, pdbsForFile, theSeqs);
     }
     else if (viewerType.equals(ViewerType.CHIMERA))
     {
-      sview = new ChimeraViewFrame(pdbsForFile, theSeqs, ap);
+      sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
+              ap);
     }
     else
     {
@@ -232,6 +284,18 @@ public class StructureViewer
   public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
           SequenceI[] seqsForPdb, AlignmentPanel ap)
   {
+    if (sview != null)
+    {
+      sview.setAlignAddedStructures(superposeAdded);
+      String pdbId = pdb.getId();
+      if (!sview.addAlreadyLoadedFile(seqsForPdb, null, ap, pdbId))
+      {
+        sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
+      }
+      sview.updateTitleAndMenus();
+      sview.raiseViewer();
+      return sview;
+    }
     ViewerType viewerType = getViewerType();
     if (viewerType.equals(ViewerType.JMOL))
     {
@@ -299,4 +363,29 @@ public class StructureViewer
     return false;
   }
 
+  /**
+   * 
+   * @param pDBid
+   * @return true if view is already showing PDBid
+   */
+  public boolean hasPdbId(String pDBid)
+  {
+    if (sview == null)
+    {
+      return false;
+    }
+
+    return sview.getBinding().hasPdbId(pDBid);
+  }
+
+  public boolean isVisible()
+  {
+    return sview != null && sview.isVisible();
+  }
+
+  public void setSuperpose(boolean alignAddedStructures)
+  {
+    superposeAdded = alignAddedStructures;
+  }
+
 }
diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 93d675a..72b0bcc 100644
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -129,6 +130,26 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   /**
+   * @return true if added structures should be aligned to existing one(s)
+   */
+  @Override
+  public boolean isAlignAddedStructures()
+  {
+    return alignAddedStructures;
+  }
+
+  /**
+   * 
+   * @param true
+   *          if added structures should be aligned to existing one(s)
+   */
+  @Override
+  public void setAlignAddedStructures(boolean alignAdded)
+  {
+    alignAddedStructures = alignAdded;
+  }
+
+  /**
    * 
    * @param ap2
    * @return true if this Jmol instance is linked with the given alignPanel
@@ -334,7 +355,7 @@ public abstract class StructureViewerBase extends GStructureViewer
    */
   protected void addStructure(final PDBEntry pdbentry,
           final SequenceI[] seqs, final String[] chains,
-          final boolean align, final IProgressIndicator alignFrame)
+          final IProgressIndicator alignFrame)
   {
     if (pdbentry.getFile() == null)
     {
@@ -358,7 +379,7 @@ public abstract class StructureViewerBase extends GStructureViewer
               }
             }
             // and call ourselves again.
-            addStructure(pdbentry, seqs, chains, align, alignFrame);
+            addStructure(pdbentry, seqs, chains, alignFrame);
           }
         }).start();
         return;
@@ -370,87 +391,42 @@ public abstract class StructureViewerBase extends GStructureViewer
             { seqs }, new String[][] { chains });
     addingStructures = true;
     _started = false;
-    alignAddedStructures = align;
     worker = new Thread(this);
     worker.start();
     return;
   }
 
-  /**
-   * Presents a dialog with the option to add an align a structure to an
-   * existing structure view
-   * 
-   * @param pdbId
-   * @param view
-   * @return YES, NO or CANCEL JvOptionPane code
-   */
-  protected int chooseAlignStructureToViewer(String pdbId,
-          StructureViewerBase view)
-  {
-    int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
-            MessageManager.formatMessage("label.add_pdbentry_to_view",
-                    new Object[]
-                    { pdbId, view.getTitle() }),
-            MessageManager
-                    .getString("label.align_to_existing_structure_view"),
-            JvOptionPane.YES_NO_CANCEL_OPTION);
-    return option;
-  }
-
   protected boolean hasPdbId(String pdbId)
   {
     return getBinding().hasPdbId(pdbId);
   }
 
-  protected abstract List<StructureViewerBase> getViewersFor(
-          AlignmentPanel alp);
-
   /**
-   * Check for any existing views involving this alignment and give user the
-   * option to add and align this molecule to one of them
-   * 
-   * @param pdbentry
-   * @param seq
-   * @param chains
-   * @param apanel
-   * @param pdbId
-   * @return true if user adds to a view, or cancels entirely, else false
+   * Returns a list of any viewer of the instantiated type. The list is
+   * restricted to those linked to the given alignment panel if it is not null.
    */
-  protected boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
-          String[] chains, final AlignmentPanel apanel, String pdbId)
+  protected List<StructureViewerBase> getViewersFor(AlignmentPanel alp)
   {
-    for (StructureViewerBase view : getViewersFor(apanel))
-    {
-      // TODO: highlight the view somehow
-      /*
-       * JAL-1742 exclude view with this structure already mapped (don't offer
-       * to align chain B to chain A of the same structure)
-       */
-      if (view.hasPdbId(pdbId))
-      {
-        continue;
-      }
-      int option = chooseAlignStructureToViewer(pdbId, view);
-      if (option == JvOptionPane.CANCEL_OPTION)
-      {
-        return true;
-      }
-      else if (option == JvOptionPane.YES_OPTION)
-      {
-        view.useAlignmentPanelForSuperposition(apanel);
-        view.addStructure(pdbentry, seq, chains, true, apanel.alignFrame);
-        return true;
-      }
-      else
-      {
-        // NO_OPTION - offer the next viewer if any
-      }
-    }
+    return Desktop.instance.getStructureViewers(alp, this.getClass());
+  }
 
+  @Override
+  public void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+          String[] chains, final AlignmentViewPanel apanel, String pdbId)
+  {
     /*
-     * nothing offered and selected
+     * JAL-1742 exclude view with this structure already mapped (don't offer
+     * to align chain B to chain A of the same structure); code may defend
+     * against this possibility before we reach here
      */
-    return false;
+    if (hasPdbId(pdbId))
+    {
+      return;
+    }
+    AlignmentPanel alignPanel = (AlignmentPanel) apanel; // Implementation error if this
+                                                 // cast fails
+    useAlignmentPanelForSuperposition(alignPanel);
+    addStructure(pdbentry, seq, chains, alignPanel.alignFrame);
   }
 
   /**
@@ -462,9 +438,12 @@ public abstract class StructureViewerBase extends GStructureViewer
    * @param apanel
    * @param pdbFilename
    */
-  protected void addSequenceMappingsToStructure(SequenceI[] seq,
-          String[] chains, final AlignmentPanel apanel, String pdbFilename)
+  public void addSequenceMappingsToStructure(SequenceI[] seq,
+          String[] chains, final AlignmentViewPanel alpanel,
+          String pdbFilename)
   {
+    AlignmentPanel apanel = (AlignmentPanel) alpanel;
+
     // TODO : Fix multiple seq to one chain issue here.
     /*
      * create the mappings
@@ -511,47 +490,20 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
-  /**
-   * Check if the PDB file is already loaded, if so offer to add it to the
-   * existing viewer
-   * 
-   * @param seq
-   * @param chains
-   * @param apanel
-   * @param pdbId
-   * @return true if the user chooses to add to a viewer, or to cancel entirely
-   */
-  protected boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
-          final AlignmentPanel apanel, String pdbId)
+  @Override
+  public boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+          final AlignmentViewPanel apanel, String pdbId)
   {
-    boolean finished = false;
     String alreadyMapped = apanel.getStructureSelectionManager()
             .alreadyMappedToFile(pdbId);
 
-    if (alreadyMapped != null)
+    if (alreadyMapped == null)
     {
-      /*
-       * the PDB file is already loaded
-       */
-      int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
-              MessageManager.formatMessage(
-                      "label.pdb_entry_is_already_displayed", new Object[]
-                      { pdbId }),
-              MessageManager.formatMessage(
-                      "label.map_sequences_to_visible_window", new Object[]
-                      { pdbId }),
-              JvOptionPane.YES_NO_CANCEL_OPTION);
-      if (option == JvOptionPane.CANCEL_OPTION)
-      {
-        finished = true;
-      }
-      else if (option == JvOptionPane.YES_OPTION)
-      {
-        addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
-        finished = true;
-      }
+      return false;
     }
-    return finished;
+
+    addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+    return true;
   }
 
   void setChainMenuItems(List<String> chainNames)
@@ -831,11 +783,11 @@ public abstract class StructureViewerBase extends GStructureViewer
       int[] alm = new int[_alignwith.size()];
       int a = 0;
 
-      for (AlignmentPanel ap : _alignwith)
+      for (AlignmentPanel alignPanel : _alignwith)
       {
-        als[a] = ap.av.getAlignment();
+        als[a] = alignPanel.av.getAlignment();
         alm[a] = -1;
-        alc[a++] = ap.av.getAlignment().getHiddenColumns();
+        alc[a++] = alignPanel.av.getAlignment().getHiddenColumns();
       }
       reply = getBinding().superposeStructures(als, alm, alc);
       if (reply != null)
@@ -847,9 +799,9 @@ public abstract class StructureViewerBase extends GStructureViewer
     } catch (Exception e)
     {
       StringBuffer sp = new StringBuffer();
-      for (AlignmentPanel ap : _alignwith)
+      for (AlignmentPanel alignPanel : _alignwith)
       {
-        sp.append("'" + ap.alignFrame.getTitle() + "' ");
+        sp.append("'" + alignPanel.alignFrame.getTitle() + "' ");
       }
       Cache.log.info("Couldn't align structures with the " + sp.toString()
               + "associated alignment panels.", e);
@@ -913,9 +865,9 @@ public abstract class StructureViewerBase extends GStructureViewer
         }
       }
       // Set the colour using the current view for the associated alignframe
-      for (AlignmentPanel ap : _colourwith)
+      for (AlignmentPanel alignPanel : _colourwith)
       {
-        binding.colourBySequence(ap);
+        binding.colourBySequence(alignPanel);
       }
       seqColoursApplied = true;
     }
@@ -997,6 +949,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   /**
    * Configures the title and menu items of the viewer panel.
    */
+  @Override
   public void updateTitleAndMenus()
   {
     AAStructureBindingModel binding = getBinding();
@@ -1039,6 +992,12 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
+  public String toString()
+  {
+    return getTitle();
+  }
+
+  @Override
   public boolean hasMapping()
   {
     if (worker != null && (addingStructures || _started))
@@ -1075,4 +1034,10 @@ public abstract class StructureViewerBase extends GStructureViewer
     return seqColoursApplied;
   }
 
+  @Override
+  public void raiseViewer()
+  {
+    toFront();
+  }
+
 }
diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java
index d91775c..ab03d69 100644
--- a/src/jalview/gui/WsParamSetManager.java
+++ b/src/jalview/gui/WsParamSetManager.java
@@ -47,20 +47,21 @@ import java.util.StringTokenizer;
  */
 public class WsParamSetManager implements ParamManager
 {
-  Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<String, ParamDatastoreI>();
+  private static final String WS_PARAM_FILES = "WS_PARAM_FILES";
+  Hashtable<String, ParamDatastoreI> paramparsers = new Hashtable<>();
 
   @Override
   public WsParamSetI[] getParameterSet(String name, String serviceUrl,
           boolean modifiable, boolean unmodifiable)
   {
-    String files = Cache.getProperty("WS_PARAM_FILES");
+    String files = Cache.getProperty(WS_PARAM_FILES);
     if (files == null)
     {
       return null;
     }
     StringTokenizer st = new StringTokenizer(files, "|");
     String pfile = null;
-    ArrayList<WsParamSetI> params = new ArrayList<WsParamSetI>();
+    ArrayList<WsParamSetI> params = new ArrayList<>();
     while (st.hasMoreTokens())
     {
       pfile = st.nextToken();
@@ -98,7 +99,8 @@ public class WsParamSetManager implements ParamManager
       } catch (IOException e)
       {
         Cache.log.info("Failed to parse parameter file " + pfile
-                + " (Check that all JALVIEW_WSPARAMFILES entries are valid!)",
+                + " (Check that all " + WS_PARAM_FILES
+                + " entries are valid!)",
                 e);
       }
     }
@@ -107,7 +109,7 @@ public class WsParamSetManager implements ParamManager
 
   private WsParamSetI[] parseParamFile(String filename) throws IOException
   {
-    List<WsParamSetI> psets = new ArrayList<WsParamSetI>();
+    List<WsParamSetI> psets = new ArrayList<>();
     InputStreamReader is = new InputStreamReader(
             new java.io.FileInputStream(new File(filename)), "UTF-8");
 
@@ -202,7 +204,7 @@ public class WsParamSetManager implements ParamManager
     }
     if (outfile != null)
     {
-      String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES",
+      String paramFiles = jalview.bin.Cache.getDefault(WS_PARAM_FILES,
               filename);
       if (paramFiles.indexOf(filename) == -1)
       {
@@ -212,7 +214,7 @@ public class WsParamSetManager implements ParamManager
         }
         paramFiles = paramFiles.concat(filename);
       }
-      jalview.bin.Cache.setProperty("WS_PARAM_FILES", paramFiles);
+      jalview.bin.Cache.setProperty(WS_PARAM_FILES, paramFiles);
 
       jalview.schemabinding.version2.WebServiceParameterSet paramxml = new jalview.schemabinding.version2.WebServiceParameterSet();
 
@@ -266,7 +268,7 @@ public class WsParamSetManager implements ParamManager
     {
       return;
     }
-    String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES", "");
+    String paramFiles = jalview.bin.Cache.getDefault(WS_PARAM_FILES, "");
     if (paramFiles.indexOf(filename) > -1)
     {
       String nparamFiles = new String();
@@ -279,7 +281,7 @@ public class WsParamSetManager implements ParamManager
           nparamFiles = nparamFiles.concat("|").concat(fl);
         }
       }
-      jalview.bin.Cache.setProperty("WS_PARAM_FILES", nparamFiles);
+      jalview.bin.Cache.setProperty(WS_PARAM_FILES, nparamFiles);
     }
 
     try
diff --git a/src/jalview/hmmer/HMMBuild.java b/src/jalview/hmmer/HMMBuild.java
index 3c3bd40..6de7029 100644
--- a/src/jalview/hmmer/HMMBuild.java
+++ b/src/jalview/hmmer/HMMBuild.java
@@ -96,11 +96,14 @@ public class HMMBuild extends HmmerCommand
           AlignViewportI viewport)
   {
     List<AnnotatedCollectionI> runBuildFor = new ArrayList<>();
+    boolean foundArg = false;
+
     for (ArgumentI arg : params)
     {
       String name = arg.getName();
       if (MessageManager.getString("label.hmmbuild_for").equals(name))
       {
+        foundArg = true;
         String value = arg.getValue();
         if (MessageManager.getString("label.alignment").equals(value))
         {
@@ -134,6 +137,15 @@ public class HMMBuild extends HmmerCommand
         }
       }
     }
+
+    /*
+     * default is to build for the whole alignment
+     */
+    if (!foundArg)
+    {
+      runBuildFor.add(alignment);
+    }
+
     return runBuildFor;
   }
 
diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index 6f1f51f..fbab7a9 100644
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -9,6 +9,7 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.params.simple.BooleanOption;
+import jalview.ws.params.simple.DoubleParameter;
 import jalview.ws.params.simple.IntegerParameter;
 import jalview.ws.params.simple.LogarithmicParameter;
 import jalview.ws.params.simple.Option;
@@ -16,6 +17,7 @@ import jalview.ws.params.simple.StringParameter;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.List;
 import java.util.Scanner;
@@ -96,17 +98,16 @@ public final class HMMERParamStore implements ParamDatastoreI
    */
   private void getHMMSearchParams(List<ArgumentI> args)
   {
+    /*
+     * 'Options'
+     */
     addChoiceOfHmm(args);
 
-    args.add(new IntegerParameter(
-            MessageManager.getString("label.number_of_results"),
-            MessageManager.getString("label.number_of_results_desc"), true,
-            100, 0, 100000));
     String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
     if (names != null && !names.isEmpty())
     {
       List<String> databases = new ArrayList<>();
-      databases.add(MessageManager.getString("label.this_alignment"));
+      databases.add(MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY));
       Scanner nameScanner = new Scanner(names);
 
       if (nameScanner.hasNext())
@@ -126,45 +127,56 @@ public final class HMMERParamStore implements ParamDatastoreI
         }
       }
       nameScanner.close();
-      args.add(new Option(MessageManager.getString("label.database"),
+      args.add(new StringParameter(
+              MessageManager.getString(HMMSearch.DATABASE_KEY),
               MessageManager.getString("label.database_for_hmmsearch"),
-              true, MessageManager.getString("label.this_alignment"),
-              MessageManager.getString("label.this_alignment"), databases,
-              null));
+              true, MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY),
+              MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY),
+              databases));
     }
     args.add(new BooleanOption(
-            MessageManager.getString("label.auto_align_seqs"),
+            MessageManager.getString(HMMSearch.AUTO_ALIGN_SEQS_KEY),
             MessageManager.getString("label.auto_align_seqs_desc"), false,
             false, true, null));
     args.add(new BooleanOption(
-            MessageManager.getString("label.use_accessions"),
+            MessageManager.getString(HMMSearch.USE_ACCESSIONS_KEY),
             MessageManager.getString("label.use_accessions_desc"), false,
             false, true, null));
     args.add(new BooleanOption(
-            MessageManager.getString("label.trim_termini"),
+            MessageManager.getString(HMMSearch.TRIM_TERMINI_KEY),
             MessageManager.getString("label.trim_termini_desc"), false,
             false, true, null));
+
+    /*
+     * 'Parameters'
+     */
+    args.add(new IntegerParameter(
+            MessageManager.getString(HMMSearch.NUMBER_OF_RESULTS_KEY),
+            MessageManager.getString("label.number_of_results_desc"), true,
+            100, 0, 100000));
+    args.add(new StringParameter(
+            MessageManager.getString(HMMSearch.REPORTING_CUTOFF_KEY), null,
+            true, HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_NONE,
+            Arrays.asList(HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_EVALUE,
+                    HMMSearch.CUTOFF_SCORE)));
     args.add(new LogarithmicParameter(
-            MessageManager.getString("label.seq_e_value"),
+            MessageManager.getString(HMMSearch.SEQ_EVALUE_KEY),
             MessageManager.getString("label.seq_e_value_desc"), false, 1D,
-            1E-38, 10D, 10D));
-    /*
-    args.add(new DoubleParameter(
-            MessageManager.getString("label.seq_score"),
-            MessageManager.getString("label.seq_score_desc"), false,
-            0d, 0d, 10000d));
-       */
+            1E-38, 10D));
     args.add(new LogarithmicParameter(
-            MessageManager.getString("label.dom_e_value"),
+            MessageManager.getString(HMMSearch.DOM_EVALUE_KEY),
             MessageManager.getString("label.dom_e_value_desc"), false, 1D,
-            1E-38, 10D, 10D));
-    /*
-    args.add(new DoubleParameter(
-            MessageManager.getString("label.dom_score"),
-            MessageManager.getString("label.dom_score_desc"), false, 0d,
-            0d,
-            10000d));
-            */
+            1E-38, 10D));
+    args.add(
+            new DoubleParameter(
+                    MessageManager.getString(HMMSearch.SEQ_SCORE_KEY),
+                    MessageManager.getString("label.seq_score_desc"), false,
+                    0d, 0d, 1000d));
+    args.add(
+            new DoubleParameter(
+                    MessageManager.getString(HMMSearch.DOM_SCORE_KEY),
+                    MessageManager.getString("label.dom_score_desc"), false,
+                    0d, 0d, 1000d));
   }
 
   /**
@@ -187,7 +199,7 @@ public final class HMMERParamStore implements ParamDatastoreI
 
   /**
    * Adds an argument representing the choice of HMM sequences (profiles)
-   * against which to perform align or search, provided more than one is found
+   * against which to perform align or search, provided at least one is found
    * 
    * @param args
    */
@@ -202,9 +214,10 @@ public final class HMMERParamStore implements ParamDatastoreI
         options.add(hmmSeq.getName());
       }
       String defseq = options.get(0);
-      Option option = new Option(MessageManager.getString("label.use_hmm"),
-              "", true, defseq, defseq, options, null);
-      args.add(option);
+      ArgumentI arg = new StringParameter(
+              MessageManager.getString("label.use_hmm"), null, true, defseq,
+              defseq, options);
+      args.add(arg);
     }
   }
 
@@ -239,16 +252,20 @@ public final class HMMERParamStore implements ParamDatastoreI
 
     /*
      * choice of whether to compute HMM for alignment and/or group(s)
+     * - only if there are any groups
      */
-    Collection<String> options = new ArrayList<>();
-    options.add(MessageManager.getString("label.alignment"));
-    options.add(MessageManager.getString("label.groups_and_alignment"));
-    options.add(MessageManager.getString("label.groups"));
-    options.add(MessageManager.getString("label.selected_group"));
-    args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
-            MessageManager.getString("label.hmmbuild_for_desc"), true,
-            MessageManager.getString("label.alignment"),
-            MessageManager.getString("label.alignment"), options, null));
+    if (!viewport.getAlignment().getGroups().isEmpty())
+    {
+      Collection<String> options = new ArrayList<>();
+      options.add(MessageManager.getString("label.alignment"));
+      options.add(MessageManager.getString("label.groups_and_alignment"));
+      options.add(MessageManager.getString("label.groups"));
+      options.add(MessageManager.getString("label.selected_group"));
+      args.add(new Option(MessageManager.getString("label.hmmbuild_for"),
+              MessageManager.getString("label.hmmbuild_for_desc"), true,
+              MessageManager.getString("label.alignment"),
+              MessageManager.getString("label.alignment"), options, null));
+    }
   }
 
   @Override
diff --git a/src/jalview/hmmer/HMMSearch.java b/src/jalview/hmmer/HMMSearch.java
index d4c9656..efc34ae 100644
--- a/src/jalview/hmmer/HMMSearch.java
+++ b/src/jalview/hmmer/HMMSearch.java
@@ -31,10 +31,39 @@ import javax.swing.JOptionPane;
 
 public class HMMSearch extends HmmerCommand
 {
-  private static final String PARAMNAME_NO_OF_RESULTS = MessageManager.getString("label.number_of_results");
-
   static final String HMMSEARCH = "hmmsearch";
 
+  /*
+   * constants for i18n lookup of passed parameter names
+   */
+  static final String DATABASE_KEY = "label.database";
+
+  static final String THIS_ALIGNMENT_KEY = "label.this_alignment";
+
+  static final String USE_ACCESSIONS_KEY = "label.use_accessions";
+
+  static final String AUTO_ALIGN_SEQS_KEY = "label.auto_align_seqs";
+
+  static final String NUMBER_OF_RESULTS_KEY = "label.number_of_results";
+
+  static final String TRIM_TERMINI_KEY = "label.trim_termini";
+
+  static final String REPORTING_CUTOFF_KEY = "label.reporting_cutoff";
+
+  static final String CUTOFF_NONE = "None";
+
+  static final String CUTOFF_SCORE = "Score";
+
+  static final String CUTOFF_EVALUE = "E-Value";
+
+  static final String SEQ_EVALUE_KEY = "label.seq_evalue";
+
+  static final String DOM_EVALUE_KEY = "label.dom_evalue";
+
+  static final String SEQ_SCORE_KEY = "label.seq_score";
+
+  static final String DOM_SCORE_KEY = "label.dom_score";
+
   boolean realign = false;
 
   boolean trim = false;
@@ -138,57 +167,72 @@ public class HMMSearch extends HmmerCommand
     String dbPath = "";
     File databaseFile = null;
 
+    boolean useEvalueCutoff = false;
+    boolean useScoreCutoff = false;
+    String seqEvalueCutoff = null;
+    String domEvalueCutoff = null;
+    String seqScoreCutoff = null;
+    String domScoreCutoff = null;
+
     if (params != null)
     {
       for (ArgumentI arg : params)
       {
         String name = arg.getName();
-        if (MessageManager.getString("label.number_of_results")
+        if (MessageManager.getString(NUMBER_OF_RESULTS_KEY)
                 .equals(name))
         {
           seqsToReturn = Integer.parseInt(arg.getValue());
         }
-        else if (MessageManager.getString("label.auto_align_seqs")
+        else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY)
                 .equals(name))
         {
           realign = true; // TODO: not used
         }
-        else if (MessageManager.getString("label.use_accessions")
+        else if (MessageManager.getString(USE_ACCESSIONS_KEY)
                 .equals(name))
         {
           args.add("--acc");
         }
-        else if (MessageManager.getString("label.seq_e_value").equals(name))
+        else if (MessageManager.getString(REPORTING_CUTOFF_KEY)
+                .equals(name))
+        {
+          if (CUTOFF_EVALUE.equals(arg.getValue()))
+          {
+            useEvalueCutoff = true;
+          }
+          else if (CUTOFF_SCORE.equals(arg.getValue()))
+          {
+            useScoreCutoff = true;
+          }
+        }
+        else if (MessageManager.getString(SEQ_EVALUE_KEY).equals(name))
         {
-          args.add("-E");
-          args.add(arg.getValue());
+          seqEvalueCutoff = arg.getValue();
         }
-        else if (MessageManager.getString("label.seq_score").equals(name))
+        else if (MessageManager.getString(SEQ_SCORE_KEY).equals(name))
         {
-          args.add("-incT");
-          args.add(arg.getValue());
+          seqScoreCutoff = arg.getValue();
         }
-        else if (MessageManager.getString("label.dom_e_value")
+        else if (MessageManager.getString(DOM_EVALUE_KEY)
                 .equals(name))
         {
-          args.add("--domE");
-          args.add(arg.getValue());
+          domEvalueCutoff = arg.getValue();
         }
-        else if (MessageManager.getString("label.dom_score").equals(name))
+        else if (MessageManager.getString(DOM_SCORE_KEY).equals(name))
         {
-          args.add("--incdomT");
-          args.add(arg.getValue());
+          domScoreCutoff = arg.getValue();
         }
-        else if (MessageManager.getString("label.trim_termini")
+        else if (MessageManager.getString(TRIM_TERMINI_KEY)
                 .equals(name))
         {
           trim = true;
         }
-        else if (MessageManager.getString("label.database").equals(name))
+        else if (MessageManager.getString(DATABASE_KEY).equals(name))
         {
           dbFound = true;
           dbPath = arg.getValue();
-          if (!MessageManager.getString("label.this_alignment")
+          if (!MessageManager.getString(THIS_ALIGNMENT_KEY)
                   .equals(dbPath))
           {
             databaseFile = new File(dbPath);
@@ -197,7 +241,22 @@ public class HMMSearch extends HmmerCommand
       }
     }
 
-    if (!dbFound || MessageManager.getString("label.this_alignment")
+    if (useEvalueCutoff)
+    {
+      args.add("-E");
+      args.add(seqEvalueCutoff);
+      args.add("--domE");
+      args.add(domEvalueCutoff);
+    }
+    else if (useScoreCutoff)
+    {
+      args.add("-T");
+      args.add(seqScoreCutoff);
+      args.add("--domT");
+      args.add(domScoreCutoff);
+    }
+
+    if (!dbFound || MessageManager.getString(THIS_ALIGNMENT_KEY)
             .equals(dbPath))
     {
       /*
@@ -214,12 +273,6 @@ public class HMMSearch extends HmmerCommand
         copy.deleteSequence(hmmSeq);
       }
       exportStockholm(copy.getSequencesArray(), databaseFile, null);
-      // StockholmFile stoFile = new StockholmFile(copy);
-      // stoFile.setSeqs(copy.getSequencesArray());
-      // String alignmentString = stoFile.print();
-      // PrintWriter writer = new PrintWriter(databaseFile);
-      // writer.print(alignmentString);
-      // writer.close();
     }
 
     args.add(getFilePath(hmmFile));
@@ -273,7 +326,7 @@ public class HMMSearch extends HmmerCommand
       if (trim)
       {
         alignArgs.add(new BooleanOption(
-                MessageManager.getString("label.trim_termini"),
+                MessageManager.getString(TRIM_TERMINI_KEY),
                 MessageManager.getString("label.trim_termini_desc"), true,
                 true, true, null));
       }
diff --git a/src/jalview/io/HMMFile.java b/src/jalview/io/HMMFile.java
index 2a17915..07f29c8 100644
--- a/src/jalview/io/HMMFile.java
+++ b/src/jalview/io/HMMFile.java
@@ -140,7 +140,6 @@ public class HMMFile extends AlignFile
    * Constructor for HMMFile used for exporting
    * 
    * @param hmm
-   * @param exportImmediately
    */
   public HMMFile(HiddenMarkovModel markov)
   {
diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java
index 9bcaa5a..a30be66 100644
--- a/src/jalview/jbgui/GStructureChooser.java
+++ b/src/jalview/jbgui/GStructureChooser.java
@@ -29,6 +29,7 @@ import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 import jalview.gui.JvSwingUtils;
+import jalview.gui.StructureViewer;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -36,6 +37,7 @@ import java.awt.CardLayout;
 import java.awt.Component;
 import java.awt.Dimension;
 import java.awt.FlowLayout;
+import java.awt.Font;
 import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ItemEvent;
@@ -70,6 +72,8 @@ import javax.swing.event.DocumentListener;
 import javax.swing.event.InternalFrameEvent;
 import javax.swing.table.TableColumn;
 
+import net.miginfocom.swing.MigLayout;
+
 @SuppressWarnings("serial")
 /**
  * GUI layout for structure chooser
@@ -80,12 +84,23 @@ import javax.swing.table.TableColumn;
 public abstract class GStructureChooser extends JPanel
         implements ItemListener
 {
+  private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
+
+  protected static final String VIEWS_FILTER = "VIEWS_FILTER";
+
+  protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
+
+  protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID";
+
+  /*
+   * 'cached' structure view
+   */
+  protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
+
   protected JPanel statusPanel = new JPanel();
 
   public JLabel statusBar = new JLabel();
 
-  private JPanel pnl_actionsAndStatus = new JPanel(new BorderLayout());
-
   protected String frameTitle = MessageManager
           .getString("label.structure_chooser");
 
@@ -97,41 +112,22 @@ public abstract class GStructureChooser extends JPanel
 
   protected StringBuilder errorWarning = new StringBuilder();
 
-  protected JLabel lbl_result = new JLabel(
-          MessageManager.getString("label.select"));
-
-  protected JButton btn_view = new JButton();
+  protected JButton btn_add;
 
-  protected JButton btn_cancel = new JButton();
+  protected JButton btn_newView;
 
   protected JButton btn_pdbFromFile = new JButton();
 
-  protected JTextField txt_search = new JTextField(14);
-
-  private JPanel pnl_actions = new JPanel();
-
-  private JPanel pnl_main = new JPanel();
-
-  private JPanel pnl_idInput = new JPanel(new FlowLayout());
+  protected JCheckBox chk_superpose = new JCheckBox(
+          MessageManager.getString("label.superpose_structures"));
 
-  private JPanel pnl_fileChooser = new JPanel(new FlowLayout());
-
-  private JPanel pnl_idInputBL = new JPanel(new BorderLayout());
-
-  private JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
-
-  private JPanel pnl_locPDB = new JPanel(new BorderLayout());
+  protected JTextField txt_search = new JTextField(14);
 
   protected JPanel pnl_switchableViews = new JPanel(new CardLayout());
 
   protected CardLayout layout_switchableViews = (CardLayout) (pnl_switchableViews
           .getLayout());
 
-  private BorderLayout mainLayout = new BorderLayout();
-
-  protected JCheckBox chk_rememberSettings = new JCheckBox(
-          MessageManager.getString("label.dont_ask_me_again"));
-
   protected JCheckBox chk_invertFilter = new JCheckBox(
           MessageManager.getString("label.invert"));
 
@@ -147,33 +143,20 @@ public abstract class GStructureChooser extends JPanel
   protected ImageIcon warningImage = new ImageIcon(
           getClass().getResource("/images/warning.gif"));
 
-  protected JLabel lbl_warning = new JLabel(warningImage);
-
   protected JLabel lbl_loading = new JLabel(loadingImage);
 
   protected JLabel lbl_pdbManualFetchStatus = new JLabel(errorImage);
 
   protected JLabel lbl_fromFileStatus = new JLabel(errorImage);
 
-  protected AssciateSeqPanel idInputAssSeqPanel = new AssciateSeqPanel();
-
-  protected AssciateSeqPanel fileChooserAssSeqPanel = new AssciateSeqPanel();
-
-  protected static final String VIEWS_FILTER = "VIEWS_FILTER";
+  protected AssociateSeqPanel idInputAssSeqPanel = new AssociateSeqPanel();
 
-  protected static final String VIEWS_FROM_FILE = "VIEWS_FROM_FILE";
+  protected AssociateSeqPanel fileChooserAssSeqPanel = new AssociateSeqPanel();
 
-  protected static final String VIEWS_ENTER_ID = "VIEWS_ENTER_ID";
-
-  /**
-   * 'cached' structure view
-   */
-  protected static final String VIEWS_LOCAL_PDB = "VIEWS_LOCAL_PDB";
+  protected JComboBox<StructureViewer> targetView = new JComboBox<>();
 
   protected JTable tbl_local_pdb = new JTable();
 
-  protected JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
-
   protected JTabbedPane pnl_filter = new JTabbedPane();
 
   protected FTSDataColumnPreferences pdbDocFieldPrefs = new FTSDataColumnPreferences(
@@ -262,8 +245,6 @@ public abstract class GStructureChooser extends JPanel
     }
   };
 
-  protected JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
-
   public GStructureChooser()
   {
     try
@@ -319,9 +300,9 @@ public abstract class GStructureChooser extends JPanel
           mainFrame.dispose();
           break;
         case KeyEvent.VK_ENTER: // enter key
-          if (btn_view.isEnabled())
+          if (btn_add.isEnabled())
           {
-            ok_ActionPerformed();
+            add_ActionPerformed();
           }
           break;
         case KeyEvent.VK_TAB: // tab key
@@ -331,7 +312,7 @@ public abstract class GStructureChooser extends JPanel
           }
           else
           {
-            btn_view.requestFocus();
+            btn_add.requestFocus();
           }
           evt.consume();
           break;
@@ -340,6 +321,30 @@ public abstract class GStructureChooser extends JPanel
         }
       }
     });
+
+    JButton btn_cancel = new JButton(
+            MessageManager.getString("action.cancel"));
+    btn_cancel.setFont(VERDANA_12);
+    btn_cancel.addActionListener(new java.awt.event.ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        closeAction(pnl_filter.getHeight());
+      }
+    });
+    btn_cancel.addKeyListener(new KeyAdapter()
+    {
+      @Override
+      public void keyPressed(KeyEvent evt)
+      {
+        if (evt.getKeyCode() == KeyEvent.VK_ENTER)
+        {
+          closeAction(pnl_filter.getHeight());
+        }
+      }
+    });
+
     tbl_local_pdb.setAutoCreateRowSorter(true);
     tbl_local_pdb.getTableHeader().setReorderingAllowed(false);
     tbl_local_pdb.addMouseListener(new MouseAdapter()
@@ -368,9 +373,9 @@ public abstract class GStructureChooser extends JPanel
           mainFrame.dispose();
           break;
         case KeyEvent.VK_ENTER: // enter key
-          if (btn_view.isEnabled())
+          if (btn_add.isEnabled())
           {
-            ok_ActionPerformed();
+            add_ActionPerformed();
           }
           break;
         case KeyEvent.VK_TAB: // tab key
@@ -380,9 +385,9 @@ public abstract class GStructureChooser extends JPanel
           }
           else
           {
-            if (btn_view.isEnabled())
+            if (btn_add.isEnabled())
             {
-              btn_view.requestFocus();
+              btn_add.requestFocus();
             }
             else
             {
@@ -396,51 +401,52 @@ public abstract class GStructureChooser extends JPanel
         }
       }
     });
-    btn_view.setFont(new java.awt.Font("Verdana", 0, 12));
-    btn_view.setText(MessageManager.getString("action.view"));
-    btn_view.addActionListener(new java.awt.event.ActionListener()
+
+    btn_newView = new JButton(MessageManager.getString("action.new_view"));
+    btn_newView.setFont(VERDANA_12);
+    btn_newView.addActionListener(new java.awt.event.ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        ok_ActionPerformed();
+        newView_ActionPerformed();
       }
     });
-    btn_view.addKeyListener(new KeyAdapter()
+    btn_newView.addKeyListener(new KeyAdapter()
     {
       @Override
       public void keyPressed(KeyEvent evt)
       {
         if (evt.getKeyCode() == KeyEvent.VK_ENTER)
         {
-          ok_ActionPerformed();
+          newView_ActionPerformed();
         }
       }
     });
 
-    btn_cancel.setFont(new java.awt.Font("Verdana", 0, 12));
-    btn_cancel.setText(MessageManager.getString("action.cancel"));
-    btn_cancel.addActionListener(new java.awt.event.ActionListener()
+    btn_add = new JButton(MessageManager.getString("action.add"));
+    btn_add.setFont(VERDANA_12);
+    btn_add.addActionListener(new java.awt.event.ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        closeAction(pnl_filter.getHeight());
+        add_ActionPerformed();
       }
     });
-    btn_cancel.addKeyListener(new KeyAdapter()
+    btn_add.addKeyListener(new KeyAdapter()
     {
       @Override
       public void keyPressed(KeyEvent evt)
       {
         if (evt.getKeyCode() == KeyEvent.VK_ENTER)
         {
-          closeAction(pnl_filter.getHeight());
+          add_ActionPerformed();
         }
       }
     });
 
-    btn_pdbFromFile.setFont(new java.awt.Font("Verdana", 0, 12));
+    btn_pdbFromFile.setFont(VERDANA_12);
     String btn_title = MessageManager.getString("label.select_pdb_file");
     btn_pdbFromFile.setText(btn_title + "              ");
     btn_pdbFromFile.addActionListener(new java.awt.event.ActionListener()
@@ -463,20 +469,17 @@ public abstract class GStructureChooser extends JPanel
       }
     });
 
+    JScrollPane scrl_foundStructures = new JScrollPane(tbl_summary);
     scrl_foundStructures.setPreferredSize(new Dimension(width, height));
 
+    JScrollPane scrl_localPDB = new JScrollPane(tbl_local_pdb);
     scrl_localPDB.setPreferredSize(new Dimension(width, height));
     scrl_localPDB.setHorizontalScrollBarPolicy(
             JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
 
-    cmb_filterOption.setFont(new java.awt.Font("Verdana", 0, 12));
-    chk_invertFilter.setFont(new java.awt.Font("Verdana", 0, 12));
-    chk_rememberSettings.setFont(new java.awt.Font("Verdana", 0, 12));
-    chk_rememberSettings.setVisible(false);
+    chk_invertFilter.setFont(VERDANA_12);
     txt_search.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.enter_pdb_id_tip")));
-    cmb_filterOption.setToolTipText(
-            MessageManager.getString("info.select_filter_option"));
     txt_search.getDocument().addDocumentListener(new DocumentListener()
     {
       @Override
@@ -498,8 +501,10 @@ public abstract class GStructureChooser extends JPanel
       }
     });
 
+    cmb_filterOption.setFont(VERDANA_12);
+    cmb_filterOption.setToolTipText(
+            MessageManager.getString("info.select_filter_option"));
     cmb_filterOption.addItemListener(this);
-
     // add CustomComboSeparatorsRenderer to filter option combo-box
     cmb_filterOption.setRenderer(new CustomComboSeparatorsRenderer(
             (ListCellRenderer<Object>) cmb_filterOption.getRenderer())
@@ -514,23 +519,33 @@ public abstract class GStructureChooser extends JPanel
 
     chk_invertFilter.addItemListener(this);
 
-    pnl_actions.add(chk_rememberSettings);
-    pnl_actions.add(btn_view);
-    pnl_actions.add(btn_cancel);
+    targetView.setVisible(false);
 
-    // pnl_filter.add(lbl_result);
+    JPanel actionsPanel = new JPanel(new MigLayout());
+    actionsPanel.add(targetView, "left");
+    actionsPanel.add(btn_add, "wrap");
+    actionsPanel.add(chk_superpose, "left");
+    actionsPanel.add(btn_newView);
+    actionsPanel.add(btn_cancel, "right");
+
+    JPanel pnl_main = new JPanel();
     pnl_main.add(cmb_filterOption);
     pnl_main.add(lbl_loading);
     pnl_main.add(chk_invertFilter);
     lbl_loading.setVisible(false);
 
+    JPanel pnl_fileChooser = new JPanel(new FlowLayout());
     pnl_fileChooser.add(btn_pdbFromFile);
     pnl_fileChooser.add(lbl_fromFileStatus);
+    JPanel pnl_fileChooserBL = new JPanel(new BorderLayout());
     pnl_fileChooserBL.add(fileChooserAssSeqPanel, BorderLayout.NORTH);
     pnl_fileChooserBL.add(pnl_fileChooser, BorderLayout.CENTER);
 
+    JPanel pnl_idInput = new JPanel(new FlowLayout());
     pnl_idInput.add(txt_search);
     pnl_idInput.add(lbl_pdbManualFetchStatus);
+
+    JPanel pnl_idInputBL = new JPanel(new BorderLayout());
     pnl_idInputBL.add(idInputAssSeqPanel, BorderLayout.NORTH);
     pnl_idInputBL.add(pnl_idInput, BorderLayout.CENTER);
 
@@ -546,13 +561,15 @@ public abstract class GStructureChooser extends JPanel
         JTabbedPane sourceTabbedPane = (JTabbedPane) changeEvent
                 .getSource();
         int index = sourceTabbedPane.getSelectedIndex();
-        btn_view.setVisible(true);
+        btn_add.setVisible(targetView.isVisible());
+        btn_newView.setVisible(true);
         btn_cancel.setVisible(true);
         if (sourceTabbedPane.getTitleAt(index).equals(configureCols))
         {
-          btn_view.setEnabled(false);
+          btn_add.setEnabled(false);
           btn_cancel.setEnabled(false);
-          btn_view.setVisible(false);
+          btn_add.setVisible(false);
+          btn_newView.setEnabled(false);
           btn_cancel.setVisible(false);
           previousWantedFields = pdbDocFieldPrefs
                   .getStructureSummaryFields()
@@ -578,6 +595,7 @@ public abstract class GStructureChooser extends JPanel
     pnl_filter.add(foundStructureSummary, scrl_foundStructures);
     pnl_filter.add(configureCols, pdbDocFieldPrefs);
 
+    JPanel pnl_locPDB = new JPanel(new BorderLayout());
     pnl_locPDB.add(scrl_localPDB);
 
     pnl_switchableViews.add(pnl_fileChooserBL, VIEWS_FROM_FILE);
@@ -585,12 +603,14 @@ public abstract class GStructureChooser extends JPanel
     pnl_switchableViews.add(pnl_filter, VIEWS_FILTER);
     pnl_switchableViews.add(pnl_locPDB, VIEWS_LOCAL_PDB);
 
-    this.setLayout(mainLayout);
+    this.setLayout(new BorderLayout());
     this.add(pnl_main, java.awt.BorderLayout.NORTH);
     this.add(pnl_switchableViews, java.awt.BorderLayout.CENTER);
     // this.add(pnl_actions, java.awt.BorderLayout.SOUTH);
     statusPanel.setLayout(new GridLayout());
-    pnl_actionsAndStatus.add(pnl_actions, BorderLayout.CENTER);
+
+    JPanel pnl_actionsAndStatus = new JPanel(new BorderLayout());
+    pnl_actionsAndStatus.add(actionsPanel, BorderLayout.CENTER);
     pnl_actionsAndStatus.add(statusPanel, BorderLayout.SOUTH);
     statusPanel.add(statusBar, null);
     this.add(pnl_actionsAndStatus, java.awt.BorderLayout.SOUTH);
@@ -801,13 +821,13 @@ public abstract class GStructureChooser extends JPanel
    * @author tcnofoegbu
    *
    */
-  public class AssciateSeqPanel extends JPanel implements ItemListener
+  public class AssociateSeqPanel extends JPanel implements ItemListener
   {
     private JComboBox<AssociateSeqOptions> cmb_assSeq = new JComboBox<>();
 
     private JLabel lbl_associateSeq = new JLabel();
 
-    public AssciateSeqPanel()
+    public AssociateSeqPanel()
     {
       this.setLayout(new FlowLayout());
       this.add(cmb_assSeq);
@@ -901,19 +921,21 @@ public abstract class GStructureChooser extends JPanel
 
   protected abstract void stateChanged(ItemEvent e);
 
-  protected abstract void ok_ActionPerformed();
+  protected abstract void add_ActionPerformed();
+
+  protected abstract void newView_ActionPerformed();
 
   protected abstract void pdbFromFile_actionPerformed();
 
   protected abstract void txt_search_ActionPerformed();
 
-  public abstract void populateCmbAssociateSeqOptions(
+  protected abstract void populateCmbAssociateSeqOptions(
           JComboBox<AssociateSeqOptions> cmb_assSeq,
           JLabel lbl_associateSeq);
 
-  public abstract void cmbAssSeqStateChanged();
+  protected abstract void cmbAssSeqStateChanged();
 
-  public abstract void tabRefresh();
+  protected abstract void tabRefresh();
 
-  public abstract void validateSelections();
+  protected abstract void validateSelections();
 }
\ No newline at end of file
diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 7c6308e..8414e28 100644
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-//---------------------------------/
-//- Imported classes and packages -/
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,1079 +19,1048 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class JSeq implements java.io.Serializable
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * Field _colour.
-   */
-  private int _colour;
-
-  /**
-   * keeps track of state for field: _colour
-   */
-  private boolean _has_colour;
-
-  /**
-   * Field _start.
-   */
-  private int _start;
-
-  /**
-   * keeps track of state for field: _start
-   */
-  private boolean _has_start;
-
-  /**
-   * Field _end.
-   */
-  private int _end;
-
-  /**
-   * keeps track of state for field: _end
-   */
-  private boolean _has_end;
-
-  /**
-   * Field _id.
-   */
-  private java.lang.String _id;
-
-  /**
-   * Field _hidden.
-   */
-  private boolean _hidden;
-
-  /**
-   * keeps track of state for field: _hidden
-   */
-  private boolean _has_hidden;
-
-  /**
-   * Field _viewreference.
-   */
-  private boolean _viewreference;
-
-  /**
-   * keeps track of state for field: _viewreference
-   */
-  private boolean _has_viewreference;
-
-  /**
-   * Field _featuresList.
-   */
-  private java.util.Vector _featuresList;
-
-  /**
-   * Field _pdbidsList.
-   */
-  private java.util.Vector _pdbidsList;
-
-  /**
-   * Field _hiddenSequencesList.
-   */
-  private java.util.Vector _hiddenSequencesList;
-
-  /**
-   * Reference to a viewer showing RNA structure for this sequence. Schema
-   * supports one viewer showing multiple annotations for multiple sequences,
-   * though currently only one annotation for one sequence (gapped or trimmed)
-   * is used
-   * 
-   */
-  private java.util.Vector _rnaViewerList;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public JSeq()
-  {
-    super();
-    this._featuresList = new java.util.Vector();
-    this._pdbidsList = new java.util.Vector();
-    this._hiddenSequencesList = new java.util.Vector();
-    this._rnaViewerList = new java.util.Vector();
-  }
-
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-   * 
-   * 
-   * @param vFeatures
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addFeatures(
-          final jalview.schemabinding.version2.Features vFeatures)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._featuresList.addElement(vFeatures);
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vFeatures
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addFeatures(final int index,
-          final jalview.schemabinding.version2.Features vFeatures)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._featuresList.add(index, vFeatures);
-  }
-
-  /**
-   * 
-   * 
-   * @param vHiddenSequences
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addHiddenSequences(final int vHiddenSequences)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._hiddenSequencesList.addElement(new java.lang.Integer(
-            vHiddenSequences));
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vHiddenSequences
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addHiddenSequences(final int index, final int vHiddenSequences)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._hiddenSequencesList.add(index, new java.lang.Integer(
-            vHiddenSequences));
-  }
-
-  /**
-   * 
-   * 
-   * @param vPdbids
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addPdbids(final jalview.schemabinding.version2.Pdbids vPdbids)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._pdbidsList.addElement(vPdbids);
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vPdbids
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addPdbids(final int index,
-          final jalview.schemabinding.version2.Pdbids vPdbids)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._pdbidsList.add(index, vPdbids);
-  }
-
-  /**
-   * 
-   * 
-   * @param vRnaViewer
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addRnaViewer(
-          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._rnaViewerList.addElement(vRnaViewer);
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vRnaViewer
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void addRnaViewer(final int index,
-          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    this._rnaViewerList.add(index, vRnaViewer);
-  }
-
-  /**
-     */
-  public void deleteColour()
-  {
-    this._has_colour = false;
-  }
-
-  /**
-     */
-  public void deleteEnd()
-  {
-    this._has_end = false;
-  }
-
-  /**
-     */
-  public void deleteHidden()
-  {
-    this._has_hidden = false;
-  }
-
-  /**
-     */
-  public void deleteStart()
-  {
-    this._has_start = false;
-  }
-
-  /**
-     */
-  public void deleteViewreference()
-  {
-    this._has_viewreference = false;
-  }
-
-  /**
-   * Method enumerateFeatures.
-   * 
-   * @return an Enumeration over all jalview.schemabinding.version2.Features
-   *         elements
-   */
-  public java.util.Enumeration enumerateFeatures()
-  {
-    return this._featuresList.elements();
-  }
-
-  /**
-   * Method enumerateHiddenSequences.
-   * 
-   * @return an Enumeration over all int elements
-   */
-  public java.util.Enumeration enumerateHiddenSequences()
-  {
-    return this._hiddenSequencesList.elements();
-  }
-
-  /**
-   * Method enumeratePdbids.
-   * 
-   * @return an Enumeration over all jalview.schemabinding.version2.Pdbids
-   *         elements
-   */
-  public java.util.Enumeration enumeratePdbids()
-  {
-    return this._pdbidsList.elements();
-  }
-
-  /**
-   * Method enumerateRnaViewer.
-   * 
-   * @return an Enumeration over all jalview.schemabinding.version2.RnaViewer
-   *         elements
-   */
-  public java.util.Enumeration enumerateRnaViewer()
-  {
-    return this._rnaViewerList.elements();
-  }
-
-  /**
-   * Returns the value of field 'colour'.
-   * 
-   * @return the value of field 'Colour'.
-   */
-  public int getColour()
-  {
-    return this._colour;
-  }
-
-  /**
-   * Returns the value of field 'end'.
-   * 
-   * @return the value of field 'End'.
-   */
-  public int getEnd()
-  {
-    return this._end;
-  }
-
-  /**
-   * Method getFeatures.
-   * 
-   * @param index
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   * @return the value of the jalview.schemabinding.version2.Features at the
-   *         given index
-   */
-  public jalview.schemabinding.version2.Features getFeatures(final int index)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._featuresList.size())
-    {
-      throw new IndexOutOfBoundsException("getFeatures: Index value '"
-              + index + "' not in range [0.."
-              + (this._featuresList.size() - 1) + "]");
-    }
-
-    return (jalview.schemabinding.version2.Features) _featuresList
-            .get(index);
-  }
-
-  /**
-   * Method getFeatures.Returns the contents of the collection in an Array.
-   * <p>
-   * Note: Just in case the collection contents are changing in another thread,
-   * we pass a 0-length Array of the correct type into the API call. This way we
-   * <i>know</i> that the Array returned is of exactly the correct length.
-   * 
-   * @return this collection as an Array
-   */
-  public jalview.schemabinding.version2.Features[] getFeatures()
-  {
-    jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
-    return (jalview.schemabinding.version2.Features[]) this._featuresList
-            .toArray(array);
-  }
-
-  /**
-   * Method getFeaturesCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getFeaturesCount()
-  {
-    return this._featuresList.size();
-  }
-
-  /**
-   * Returns the value of field 'hidden'.
-   * 
-   * @return the value of field 'Hidden'.
-   */
-  public boolean getHidden()
-  {
-    return this._hidden;
-  }
-
-  /**
-   * Method getHiddenSequences.
-   * 
-   * @param index
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   * @return the value of the int at the given index
-   */
-  public int getHiddenSequences(final int index)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._hiddenSequencesList.size())
-    {
-      throw new IndexOutOfBoundsException(
-              "getHiddenSequences: Index value '" + index
-                      + "' not in range [0.."
-                      + (this._hiddenSequencesList.size() - 1) + "]");
-    }
-
-    return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
-  }
-
-  /**
-   * Method getHiddenSequences.Returns the contents of the collection in an
-   * Array.
-   * 
-   * @return this collection as an Array
-   */
-  public int[] getHiddenSequences()
-  {
-    int size = this._hiddenSequencesList.size();
-    int[] array = new int[size];
-    java.util.Iterator iter = _hiddenSequencesList.iterator();
-    for (int index = 0; index < size; index++)
-    {
-      array[index] = ((java.lang.Integer) iter.next()).intValue();
-    }
-    return array;
-  }
-
-  /**
-   * Method getHiddenSequencesCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getHiddenSequencesCount()
-  {
-    return this._hiddenSequencesList.size();
-  }
-
-  /**
-   * Returns the value of field 'id'.
-   * 
-   * @return the value of field 'Id'.
-   */
-  public java.lang.String getId()
-  {
-    return this._id;
-  }
-
-  /**
-   * Method getPdbids.
-   * 
-   * @param index
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   * @return the value of the jalview.schemabinding.version2.Pdbids at the given
-   *         index
-   */
-  public jalview.schemabinding.version2.Pdbids getPdbids(final int index)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._pdbidsList.size())
-    {
-      throw new IndexOutOfBoundsException("getPdbids: Index value '"
-              + index + "' not in range [0.."
-              + (this._pdbidsList.size() - 1) + "]");
-    }
-
-    return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
-  }
-
-  /**
-   * Method getPdbids.Returns the contents of the collection in an Array.
-   * <p>
-   * Note: Just in case the collection contents are changing in another thread,
-   * we pass a 0-length Array of the correct type into the API call. This way we
-   * <i>know</i> that the Array returned is of exactly the correct length.
-   * 
-   * @return this collection as an Array
-   */
-  public jalview.schemabinding.version2.Pdbids[] getPdbids()
-  {
-    jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
-    return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList
-            .toArray(array);
-  }
-
-  /**
-   * Method getPdbidsCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getPdbidsCount()
-  {
-    return this._pdbidsList.size();
-  }
-
-  /**
-   * Method getRnaViewer.
-   * 
-   * @param index
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   * @return the value of the jalview.schemabinding.version2.RnaViewer at the
-   *         given index
-   */
-  public jalview.schemabinding.version2.RnaViewer getRnaViewer(
-          final int index) throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._rnaViewerList.size())
-    {
-      throw new IndexOutOfBoundsException("getRnaViewer: Index value '"
-              + index + "' not in range [0.."
-              + (this._rnaViewerList.size() - 1) + "]");
-    }
-
-    return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList
-            .get(index);
-  }
-
-  /**
-   * Method getRnaViewer.Returns the contents of the collection in an Array.
-   * <p>
-   * Note: Just in case the collection contents are changing in another thread,
-   * we pass a 0-length Array of the correct type into the API call. This way we
-   * <i>know</i> that the Array returned is of exactly the correct length.
-   * 
-   * @return this collection as an Array
-   */
-  public jalview.schemabinding.version2.RnaViewer[] getRnaViewer()
-  {
-    jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0];
-    return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList
-            .toArray(array);
-  }
-
-  /**
-   * Method getRnaViewerCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getRnaViewerCount()
-  {
-    return this._rnaViewerList.size();
-  }
-
-  /**
-   * Returns the value of field 'start'.
-   * 
-   * @return the value of field 'Start'.
-   */
-  public int getStart()
-  {
-    return this._start;
-  }
-
-  /**
-   * Returns the value of field 'viewreference'.
-   * 
-   * @return the value of field 'Viewreference'.
-   */
-  public boolean getViewreference()
-  {
-    return this._viewreference;
-  }
-
-  /**
-   * Method hasColour.
-   * 
-   * @return true if at least one Colour has been added
-   */
-  public boolean hasColour()
-  {
-    return this._has_colour;
-  }
-
-  /**
-   * Method hasEnd.
-   * 
-   * @return true if at least one End has been added
-   */
-  public boolean hasEnd()
-  {
-    return this._has_end;
-  }
-
-  /**
-   * Method hasHidden.
-   * 
-   * @return true if at least one Hidden has been added
-   */
-  public boolean hasHidden()
-  {
-    return this._has_hidden;
-  }
-
-  /**
-   * Method hasStart.
-   * 
-   * @return true if at least one Start has been added
-   */
-  public boolean hasStart()
-  {
-    return this._has_start;
-  }
-
-  /**
-   * Method hasViewreference.
-   * 
-   * @return true if at least one Viewreference has been added
-   */
-  public boolean hasViewreference()
-  {
-    return this._has_viewreference;
-  }
-
-  /**
-   * Returns the value of field 'hidden'.
-   * 
-   * @return the value of field 'Hidden'.
-   */
-  public boolean isHidden()
-  {
-    return this._hidden;
-  }
-
-  /**
-   * Method isValid.
-   * 
-   * @return true if this object is valid according to the schema
-   */
-  public boolean isValid()
-  {
-    try
-    {
-      validate();
-    } catch (org.exolab.castor.xml.ValidationException vex)
-    {
-      return false;
-    }
-    return true;
-  }
-
-  /**
-   * Returns the value of field 'viewreference'.
-   * 
-   * @return the value of field 'Viewreference'.
-   */
-  public boolean isViewreference()
-  {
-    return this._viewreference;
-  }
-
-  /**
-   * 
-   * 
-   * @param out
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   */
-  public void marshal(final java.io.Writer out)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    Marshaller.marshal(this, out);
-  }
-
-  /**
-   * 
-   * 
-   * @param handler
-   * @throws java.io.IOException
-   *           if an IOException occurs during marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   */
-  public void marshal(final org.xml.sax.ContentHandler handler)
-          throws java.io.IOException,
-          org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    Marshaller.marshal(this, handler);
-  }
-
-  /**
-     */
-  public void removeAllFeatures()
-  {
-    this._featuresList.clear();
-  }
-
-  /**
-     */
-  public void removeAllHiddenSequences()
-  {
-    this._hiddenSequencesList.clear();
-  }
-
-  /**
-     */
-  public void removeAllPdbids()
-  {
-    this._pdbidsList.clear();
-  }
-
-  /**
-     */
-  public void removeAllRnaViewer()
-  {
-    this._rnaViewerList.clear();
-  }
-
-  /**
-   * Method removeFeatures.
-   * 
-   * @param vFeatures
-   * @return true if the object was removed from the collection.
-   */
-  public boolean removeFeatures(
-          final jalview.schemabinding.version2.Features vFeatures)
-  {
-    boolean removed = _featuresList.remove(vFeatures);
-    return removed;
-  }
-
-  /**
-   * Method removeFeaturesAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public jalview.schemabinding.version2.Features removeFeaturesAt(
-          final int index)
-  {
-    java.lang.Object obj = this._featuresList.remove(index);
-    return (jalview.schemabinding.version2.Features) obj;
-  }
-
-  /**
-   * Method removeHiddenSequences.
-   * 
-   * @param vHiddenSequences
-   * @return true if the object was removed from the collection.
-   */
-  public boolean removeHiddenSequences(final int vHiddenSequences)
-  {
-    boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(
-            vHiddenSequences));
-    return removed;
-  }
-
-  /**
-   * Method removeHiddenSequencesAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public int removeHiddenSequencesAt(final int index)
-  {
-    java.lang.Object obj = this._hiddenSequencesList.remove(index);
-    return ((java.lang.Integer) obj).intValue();
-  }
-
-  /**
-   * Method removePdbids.
-   * 
-   * @param vPdbids
-   * @return true if the object was removed from the collection.
-   */
-  public boolean removePdbids(
-          final jalview.schemabinding.version2.Pdbids vPdbids)
-  {
-    boolean removed = _pdbidsList.remove(vPdbids);
-    return removed;
-  }
-
-  /**
-   * Method removePdbidsAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public jalview.schemabinding.version2.Pdbids removePdbidsAt(
-          final int index)
-  {
-    java.lang.Object obj = this._pdbidsList.remove(index);
-    return (jalview.schemabinding.version2.Pdbids) obj;
-  }
-
-  /**
-   * Method removeRnaViewer.
-   * 
-   * @param vRnaViewer
-   * @return true if the object was removed from the collection.
-   */
-  public boolean removeRnaViewer(
-          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
-  {
-    boolean removed = _rnaViewerList.remove(vRnaViewer);
-    return removed;
-  }
-
-  /**
-   * Method removeRnaViewerAt.
-   * 
-   * @param index
-   * @return the element removed from the collection
-   */
-  public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(
-          final int index)
-  {
-    java.lang.Object obj = this._rnaViewerList.remove(index);
-    return (jalview.schemabinding.version2.RnaViewer) obj;
-  }
-
-  /**
-   * Sets the value of field 'colour'.
-   * 
-   * @param colour
-   *          the value of field 'colour'.
-   */
-  public void setColour(final int colour)
-  {
-    this._colour = colour;
-    this._has_colour = true;
-  }
-
-  /**
-   * Sets the value of field 'end'.
-   * 
-   * @param end
-   *          the value of field 'end'.
-   */
-  public void setEnd(final int end)
-  {
-    this._end = end;
-    this._has_end = true;
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vFeatures
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void setFeatures(final int index,
-          final jalview.schemabinding.version2.Features vFeatures)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._featuresList.size())
-    {
-      throw new IndexOutOfBoundsException("setFeatures: Index value '"
-              + index + "' not in range [0.."
-              + (this._featuresList.size() - 1) + "]");
-    }
-
-    this._featuresList.set(index, vFeatures);
-  }
-
-  /**
-   * 
-   * 
-   * @param vFeaturesArray
-   */
-  public void setFeatures(
-          final jalview.schemabinding.version2.Features[] vFeaturesArray)
-  {
-    // -- copy array
-    _featuresList.clear();
-
-    for (int i = 0; i < vFeaturesArray.length; i++)
-    {
-      this._featuresList.add(vFeaturesArray[i]);
-    }
-  }
-
-  /**
-   * Sets the value of field 'hidden'.
-   * 
-   * @param hidden
-   *          the value of field 'hidden'.
-   */
-  public void setHidden(final boolean hidden)
-  {
-    this._hidden = hidden;
-    this._has_hidden = true;
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vHiddenSequences
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void setHiddenSequences(final int index, final int vHiddenSequences)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._hiddenSequencesList.size())
-    {
-      throw new IndexOutOfBoundsException(
-              "setHiddenSequences: Index value '" + index
-                      + "' not in range [0.."
-                      + (this._hiddenSequencesList.size() - 1) + "]");
-    }
-
-    this._hiddenSequencesList.set(index, new java.lang.Integer(
-            vHiddenSequences));
-  }
-
-  /**
-   * 
-   * 
-   * @param vHiddenSequencesArray
-   */
-  public void setHiddenSequences(final int[] vHiddenSequencesArray)
-  {
-    // -- copy array
-    _hiddenSequencesList.clear();
-
-    for (int i = 0; i < vHiddenSequencesArray.length; i++)
-    {
-      this._hiddenSequencesList.add(new java.lang.Integer(
-              vHiddenSequencesArray[i]));
-    }
-  }
-
-  /**
-   * Sets the value of field 'id'.
-   * 
-   * @param id
-   *          the value of field 'id'.
-   */
-  public void setId(final java.lang.String id)
-  {
-    this._id = id;
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vPdbids
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void setPdbids(final int index,
-          final jalview.schemabinding.version2.Pdbids vPdbids)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._pdbidsList.size())
-    {
-      throw new IndexOutOfBoundsException("setPdbids: Index value '"
-              + index + "' not in range [0.."
-              + (this._pdbidsList.size() - 1) + "]");
-    }
-
-    this._pdbidsList.set(index, vPdbids);
-  }
-
-  /**
-   * 
-   * 
-   * @param vPdbidsArray
-   */
-  public void setPdbids(
-          final jalview.schemabinding.version2.Pdbids[] vPdbidsArray)
-  {
-    // -- copy array
-    _pdbidsList.clear();
-
-    for (int i = 0; i < vPdbidsArray.length; i++)
-    {
-      this._pdbidsList.add(vPdbidsArray[i]);
-    }
-  }
-
-  /**
-   * 
-   * 
-   * @param index
-   * @param vRnaViewer
-   * @throws java.lang.IndexOutOfBoundsException
-   *           if the index given is outside the bounds of the collection
-   */
-  public void setRnaViewer(final int index,
-          final jalview.schemabinding.version2.RnaViewer vRnaViewer)
-          throws java.lang.IndexOutOfBoundsException
-  {
-    // check bounds for index
-    if (index < 0 || index >= this._rnaViewerList.size())
-    {
-      throw new IndexOutOfBoundsException("setRnaViewer: Index value '"
-              + index + "' not in range [0.."
-              + (this._rnaViewerList.size() - 1) + "]");
-    }
-
-    this._rnaViewerList.set(index, vRnaViewer);
-  }
-
-  /**
-   * 
-   * 
-   * @param vRnaViewerArray
-   */
-  public void setRnaViewer(
-          final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray)
-  {
-    // -- copy array
-    _rnaViewerList.clear();
-
-    for (int i = 0; i < vRnaViewerArray.length; i++)
-    {
-      this._rnaViewerList.add(vRnaViewerArray[i]);
-    }
-  }
-
-  /**
-   * Sets the value of field 'start'.
-   * 
-   * @param start
-   *          the value of field 'start'.
-   */
-  public void setStart(final int start)
-  {
-    this._start = start;
-    this._has_start = true;
-  }
-
-  /**
-   * Sets the value of field 'viewreference'.
-   * 
-   * @param viewreference
-   *          the value of field 'viewreference'.
-   */
-  public void setViewreference(final boolean viewreference)
-  {
-    this._viewreference = viewreference;
-    this._has_viewreference = true;
-  }
-
-  /**
-   * Method unmarshal.
-   * 
-   * @param reader
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   * @return the unmarshaled jalview.schemabinding.version2.JSeq
-   */
-  public static jalview.schemabinding.version2.JSeq unmarshal(
-          final java.io.Reader reader)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(
-            jalview.schemabinding.version2.JSeq.class, reader);
-  }
-
-  /**
-   * 
-   * 
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   */
-  public void validate() throws org.exolab.castor.xml.ValidationException
-  {
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-    validator.validate(this);
-  }
+public class JSeq implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _colour.
+     */
+    private int _colour;
+
+    /**
+     * keeps track of state for field: _colour
+     */
+    private boolean _has_colour;
+
+    /**
+     * Field _start.
+     */
+    private int _start;
+
+    /**
+     * keeps track of state for field: _start
+     */
+    private boolean _has_start;
+
+    /**
+     * Field _end.
+     */
+    private int _end;
+
+    /**
+     * keeps track of state for field: _end
+     */
+    private boolean _has_end;
+
+    /**
+     * Field _id.
+     */
+    private java.lang.String _id;
+
+    /**
+     * Field _hidden.
+     */
+    private boolean _hidden;
+
+    /**
+     * keeps track of state for field: _hidden
+     */
+    private boolean _has_hidden;
+
+    /**
+     * Field _viewreference.
+     */
+    private boolean _viewreference;
+
+    /**
+     * keeps track of state for field: _viewreference
+     */
+    private boolean _has_viewreference;
+
+    /**
+     * Field _featuresList.
+     */
+    private java.util.Vector _featuresList;
+
+    /**
+     * Field _pdbidsList.
+     */
+    private java.util.Vector _pdbidsList;
+
+    /**
+     * Field _hiddenSequencesList.
+     */
+    private java.util.Vector _hiddenSequencesList;
+
+    /**
+     * Reference to a viewer showing RNA structure
+     *  for this sequence. Schema supports one viewer showing
+     * multiple
+     *  annotations for multiple sequences, though currently only
+     * one
+     *  annotation for one sequence (gapped or trimmed) is used
+     *  
+     */
+    private java.util.Vector _rnaViewerList;
+
+    /**
+     * name of the project jar entry that holds the HMM file with
+     * the profile for the sequence
+     */
+    private java.lang.String _hmmerProfile;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JSeq() {
+        super();
+        this._featuresList = new java.util.Vector();
+        this._pdbidsList = new java.util.Vector();
+        this._hiddenSequencesList = new java.util.Vector();
+        this._rnaViewerList = new java.util.Vector();
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * 
+     * 
+     * @param vFeatures
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addFeatures(
+            final jalview.schemabinding.version2.Features vFeatures)
+    throws java.lang.IndexOutOfBoundsException {
+        this._featuresList.addElement(vFeatures);
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vFeatures
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addFeatures(
+            final int index,
+            final jalview.schemabinding.version2.Features vFeatures)
+    throws java.lang.IndexOutOfBoundsException {
+        this._featuresList.add(index, vFeatures);
+    }
+
+    /**
+     * 
+     * 
+     * @param vHiddenSequences
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addHiddenSequences(
+            final int vHiddenSequences)
+    throws java.lang.IndexOutOfBoundsException {
+        this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vHiddenSequences
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addHiddenSequences(
+            final int index,
+            final int vHiddenSequences)
+    throws java.lang.IndexOutOfBoundsException {
+        this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences));
+    }
+
+    /**
+     * 
+     * 
+     * @param vPdbids
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addPdbids(
+            final jalview.schemabinding.version2.Pdbids vPdbids)
+    throws java.lang.IndexOutOfBoundsException {
+        this._pdbidsList.addElement(vPdbids);
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vPdbids
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addPdbids(
+            final int index,
+            final jalview.schemabinding.version2.Pdbids vPdbids)
+    throws java.lang.IndexOutOfBoundsException {
+        this._pdbidsList.add(index, vPdbids);
+    }
+
+    /**
+     * 
+     * 
+     * @param vRnaViewer
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addRnaViewer(
+            final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+    throws java.lang.IndexOutOfBoundsException {
+        this._rnaViewerList.addElement(vRnaViewer);
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vRnaViewer
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addRnaViewer(
+            final int index,
+            final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+    throws java.lang.IndexOutOfBoundsException {
+        this._rnaViewerList.add(index, vRnaViewer);
+    }
+
+    /**
+     */
+    public void deleteColour(
+    ) {
+        this._has_colour= false;
+    }
+
+    /**
+     */
+    public void deleteEnd(
+    ) {
+        this._has_end= false;
+    }
+
+    /**
+     */
+    public void deleteHidden(
+    ) {
+        this._has_hidden= false;
+    }
+
+    /**
+     */
+    public void deleteStart(
+    ) {
+        this._has_start= false;
+    }
+
+    /**
+     */
+    public void deleteViewreference(
+    ) {
+        this._has_viewreference= false;
+    }
+
+    /**
+     * Method enumerateFeatures.
+     * 
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.Features elements
+     */
+    public java.util.Enumeration enumerateFeatures(
+    ) {
+        return this._featuresList.elements();
+    }
+
+    /**
+     * Method enumerateHiddenSequences.
+     * 
+     * @return an Enumeration over all int elements
+     */
+    public java.util.Enumeration enumerateHiddenSequences(
+    ) {
+        return this._hiddenSequencesList.elements();
+    }
+
+    /**
+     * Method enumeratePdbids.
+     * 
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.Pdbids elements
+     */
+    public java.util.Enumeration enumeratePdbids(
+    ) {
+        return this._pdbidsList.elements();
+    }
+
+    /**
+     * Method enumerateRnaViewer.
+     * 
+     * @return an Enumeration over all
+     * jalview.schemabinding.version2.RnaViewer elements
+     */
+    public java.util.Enumeration enumerateRnaViewer(
+    ) {
+        return this._rnaViewerList.elements();
+    }
+
+    /**
+     * Returns the value of field 'colour'.
+     * 
+     * @return the value of field 'Colour'.
+     */
+    public int getColour(
+    ) {
+        return this._colour;
+    }
+
+    /**
+     * Returns the value of field 'end'.
+     * 
+     * @return the value of field 'End'.
+     */
+    public int getEnd(
+    ) {
+        return this._end;
+    }
+
+    /**
+     * Method getFeatures.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the
+     * jalview.schemabinding.version2.Features at the given index
+     */
+    public jalview.schemabinding.version2.Features getFeatures(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._featuresList.size()) {
+            throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
+        }
+        
+        return (jalview.schemabinding.version2.Features) _featuresList.get(index);
+    }
+
+    /**
+     * Method getFeatures.Returns the contents of the collection in
+     * an Array.  <p>Note:  Just in case the collection contents
+     * are changing in another thread, we pass a 0-length Array of
+     * the correct type into the API call.  This way we <i>know</i>
+     * that the Array returned is of exactly the correct length.
+     * 
+     * @return this collection as an Array
+     */
+    public jalview.schemabinding.version2.Features[] getFeatures(
+    ) {
+        jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0];
+        return (jalview.schemabinding.version2.Features[]) this._featuresList.toArray(array);
+    }
+
+    /**
+     * Method getFeaturesCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getFeaturesCount(
+    ) {
+        return this._featuresList.size();
+    }
+
+    /**
+     * Returns the value of field 'hidden'.
+     * 
+     * @return the value of field 'Hidden'.
+     */
+    public boolean getHidden(
+    ) {
+        return this._hidden;
+    }
+
+    /**
+     * Method getHiddenSequences.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the int at the given index
+     */
+    public int getHiddenSequences(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._hiddenSequencesList.size()) {
+            throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
+        }
+        
+        return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue();
+    }
+
+    /**
+     * Method getHiddenSequences.Returns the contents of the
+     * collection in an Array.  
+     * 
+     * @return this collection as an Array
+     */
+    public int[] getHiddenSequences(
+    ) {
+        int size = this._hiddenSequencesList.size();
+        int[] array = new int[size];
+        java.util.Iterator iter = _hiddenSequencesList.iterator();
+        for (int index = 0; index < size; index++) {
+            array[index] = ((java.lang.Integer) iter.next()).intValue();
+        }
+        return array;
+    }
+
+    /**
+     * Method getHiddenSequencesCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getHiddenSequencesCount(
+    ) {
+        return this._hiddenSequencesList.size();
+    }
+
+    /**
+     * Returns the value of field 'hmmerProfile'. The field
+     * 'hmmerProfile' has the following description: name of the
+     * project jar entry that holds the HMM file with the profile
+     * for the sequence
+     * 
+     * @return the value of field 'HmmerProfile'.
+     */
+    public java.lang.String getHmmerProfile(
+    ) {
+        return this._hmmerProfile;
+    }
+
+    /**
+     * Returns the value of field 'id'.
+     * 
+     * @return the value of field 'Id'.
+     */
+    public java.lang.String getId(
+    ) {
+        return this._id;
+    }
+
+    /**
+     * Method getPdbids.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the
+     * jalview.schemabinding.version2.Pdbids at the given index
+     */
+    public jalview.schemabinding.version2.Pdbids getPdbids(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._pdbidsList.size()) {
+            throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
+        }
+        
+        return (jalview.schemabinding.version2.Pdbids) _pdbidsList.get(index);
+    }
+
+    /**
+     * Method getPdbids.Returns the contents of the collection in
+     * an Array.  <p>Note:  Just in case the collection contents
+     * are changing in another thread, we pass a 0-length Array of
+     * the correct type into the API call.  This way we <i>know</i>
+     * that the Array returned is of exactly the correct length.
+     * 
+     * @return this collection as an Array
+     */
+    public jalview.schemabinding.version2.Pdbids[] getPdbids(
+    ) {
+        jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0];
+        return (jalview.schemabinding.version2.Pdbids[]) this._pdbidsList.toArray(array);
+    }
+
+    /**
+     * Method getPdbidsCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getPdbidsCount(
+    ) {
+        return this._pdbidsList.size();
+    }
+
+    /**
+     * Method getRnaViewer.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the
+     * jalview.schemabinding.version2.RnaViewer at the given index
+     */
+    public jalview.schemabinding.version2.RnaViewer getRnaViewer(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._rnaViewerList.size()) {
+            throw new IndexOutOfBoundsException("getRnaViewer: Index value '" + index + "' not in range [0.." + (this._rnaViewerList.size() - 1) + "]");
+        }
+        
+        return (jalview.schemabinding.version2.RnaViewer) _rnaViewerList.get(index);
+    }
+
+    /**
+     * Method getRnaViewer.Returns the contents of the collection
+     * in an Array.  <p>Note:  Just in case the collection contents
+     * are changing in another thread, we pass a 0-length Array of
+     * the correct type into the API call.  This way we <i>know</i>
+     * that the Array returned is of exactly the correct length.
+     * 
+     * @return this collection as an Array
+     */
+    public jalview.schemabinding.version2.RnaViewer[] getRnaViewer(
+    ) {
+        jalview.schemabinding.version2.RnaViewer[] array = new jalview.schemabinding.version2.RnaViewer[0];
+        return (jalview.schemabinding.version2.RnaViewer[]) this._rnaViewerList.toArray(array);
+    }
+
+    /**
+     * Method getRnaViewerCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getRnaViewerCount(
+    ) {
+        return this._rnaViewerList.size();
+    }
+
+    /**
+     * Returns the value of field 'start'.
+     * 
+     * @return the value of field 'Start'.
+     */
+    public int getStart(
+    ) {
+        return this._start;
+    }
+
+    /**
+     * Returns the value of field 'viewreference'.
+     * 
+     * @return the value of field 'Viewreference'.
+     */
+    public boolean getViewreference(
+    ) {
+        return this._viewreference;
+    }
+
+    /**
+     * Method hasColour.
+     * 
+     * @return true if at least one Colour has been added
+     */
+    public boolean hasColour(
+    ) {
+        return this._has_colour;
+    }
+
+    /**
+     * Method hasEnd.
+     * 
+     * @return true if at least one End has been added
+     */
+    public boolean hasEnd(
+    ) {
+        return this._has_end;
+    }
+
+    /**
+     * Method hasHidden.
+     * 
+     * @return true if at least one Hidden has been added
+     */
+    public boolean hasHidden(
+    ) {
+        return this._has_hidden;
+    }
+
+    /**
+     * Method hasStart.
+     * 
+     * @return true if at least one Start has been added
+     */
+    public boolean hasStart(
+    ) {
+        return this._has_start;
+    }
+
+    /**
+     * Method hasViewreference.
+     * 
+     * @return true if at least one Viewreference has been added
+     */
+    public boolean hasViewreference(
+    ) {
+        return this._has_viewreference;
+    }
+
+    /**
+     * Returns the value of field 'hidden'.
+     * 
+     * @return the value of field 'Hidden'.
+     */
+    public boolean isHidden(
+    ) {
+        return this._hidden;
+    }
+
+    /**
+     * Method isValid.
+     * 
+     * @return true if this object is valid according to the schema
+     */
+    public boolean isValid(
+    ) {
+        try {
+            validate();
+        } catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    }
+
+    /**
+     * Returns the value of field 'viewreference'.
+     * 
+     * @return the value of field 'Viewreference'.
+     */
+    public boolean isViewreference(
+    ) {
+        return this._viewreference;
+    }
+
+    /**
+     * 
+     * 
+     * @param out
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     */
+    public void marshal(
+            final java.io.Writer out)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        Marshaller.marshal(this, out);
+    }
+
+    /**
+     * 
+     * 
+     * @param handler
+     * @throws java.io.IOException if an IOException occurs during
+     * marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     */
+    public void marshal(
+            final org.xml.sax.ContentHandler handler)
+    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        Marshaller.marshal(this, handler);
+    }
+
+    /**
+     */
+    public void removeAllFeatures(
+    ) {
+        this._featuresList.clear();
+    }
+
+    /**
+     */
+    public void removeAllHiddenSequences(
+    ) {
+        this._hiddenSequencesList.clear();
+    }
+
+    /**
+     */
+    public void removeAllPdbids(
+    ) {
+        this._pdbidsList.clear();
+    }
+
+    /**
+     */
+    public void removeAllRnaViewer(
+    ) {
+        this._rnaViewerList.clear();
+    }
+
+    /**
+     * Method removeFeatures.
+     * 
+     * @param vFeatures
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeFeatures(
+            final jalview.schemabinding.version2.Features vFeatures) {
+        boolean removed = _featuresList.remove(vFeatures);
+        return removed;
+    }
+
+    /**
+     * Method removeFeaturesAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.schemabinding.version2.Features removeFeaturesAt(
+            final int index) {
+        java.lang.Object obj = this._featuresList.remove(index);
+        return (jalview.schemabinding.version2.Features) obj;
+    }
+
+    /**
+     * Method removeHiddenSequences.
+     * 
+     * @param vHiddenSequences
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeHiddenSequences(
+            final int vHiddenSequences) {
+        boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences));
+        return removed;
+    }
+
+    /**
+     * Method removeHiddenSequencesAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public int removeHiddenSequencesAt(
+            final int index) {
+        java.lang.Object obj = this._hiddenSequencesList.remove(index);
+        return ((java.lang.Integer) obj).intValue();
+    }
+
+    /**
+     * Method removePdbids.
+     * 
+     * @param vPdbids
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removePdbids(
+            final jalview.schemabinding.version2.Pdbids vPdbids) {
+        boolean removed = _pdbidsList.remove(vPdbids);
+        return removed;
+    }
+
+    /**
+     * Method removePdbidsAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.schemabinding.version2.Pdbids removePdbidsAt(
+            final int index) {
+        java.lang.Object obj = this._pdbidsList.remove(index);
+        return (jalview.schemabinding.version2.Pdbids) obj;
+    }
+
+    /**
+     * Method removeRnaViewer.
+     * 
+     * @param vRnaViewer
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeRnaViewer(
+            final jalview.schemabinding.version2.RnaViewer vRnaViewer) {
+        boolean removed = _rnaViewerList.remove(vRnaViewer);
+        return removed;
+    }
+
+    /**
+     * Method removeRnaViewerAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.schemabinding.version2.RnaViewer removeRnaViewerAt(
+            final int index) {
+        java.lang.Object obj = this._rnaViewerList.remove(index);
+        return (jalview.schemabinding.version2.RnaViewer) obj;
+    }
+
+    /**
+     * Sets the value of field 'colour'.
+     * 
+     * @param colour the value of field 'colour'.
+     */
+    public void setColour(
+            final int colour) {
+        this._colour = colour;
+        this._has_colour = true;
+    }
+
+    /**
+     * Sets the value of field 'end'.
+     * 
+     * @param end the value of field 'end'.
+     */
+    public void setEnd(
+            final int end) {
+        this._end = end;
+        this._has_end = true;
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vFeatures
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setFeatures(
+            final int index,
+            final jalview.schemabinding.version2.Features vFeatures)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._featuresList.size()) {
+            throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
+        }
+        
+        this._featuresList.set(index, vFeatures);
+    }
+
+    /**
+     * 
+     * 
+     * @param vFeaturesArray
+     */
+    public void setFeatures(
+            final jalview.schemabinding.version2.Features[] vFeaturesArray) {
+        //-- copy array
+        _featuresList.clear();
+        
+        for (int i = 0; i < vFeaturesArray.length; i++) {
+                this._featuresList.add(vFeaturesArray[i]);
+        }
+    }
+
+    /**
+     * Sets the value of field 'hidden'.
+     * 
+     * @param hidden the value of field 'hidden'.
+     */
+    public void setHidden(
+            final boolean hidden) {
+        this._hidden = hidden;
+        this._has_hidden = true;
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vHiddenSequences
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setHiddenSequences(
+            final int index,
+            final int vHiddenSequences)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._hiddenSequencesList.size()) {
+            throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]");
+        }
+        
+        this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences));
+    }
+
+    /**
+     * 
+     * 
+     * @param vHiddenSequencesArray
+     */
+    public void setHiddenSequences(
+            final int[] vHiddenSequencesArray) {
+        //-- copy array
+        _hiddenSequencesList.clear();
+        
+        for (int i = 0; i < vHiddenSequencesArray.length; i++) {
+                this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i]));
+        }
+    }
+
+    /**
+     * Sets the value of field 'hmmerProfile'. The field
+     * 'hmmerProfile' has the following description: name of the
+     * project jar entry that holds the HMM file with the profile
+     * for the sequence
+     * 
+     * @param hmmerProfile the value of field 'hmmerProfile'.
+     */
+    public void setHmmerProfile(
+            final java.lang.String hmmerProfile) {
+        this._hmmerProfile = hmmerProfile;
+    }
+
+    /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(
+            final java.lang.String id) {
+        this._id = id;
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vPdbids
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setPdbids(
+            final int index,
+            final jalview.schemabinding.version2.Pdbids vPdbids)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._pdbidsList.size()) {
+            throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
+        }
+        
+        this._pdbidsList.set(index, vPdbids);
+    }
+
+    /**
+     * 
+     * 
+     * @param vPdbidsArray
+     */
+    public void setPdbids(
+            final jalview.schemabinding.version2.Pdbids[] vPdbidsArray) {
+        //-- copy array
+        _pdbidsList.clear();
+        
+        for (int i = 0; i < vPdbidsArray.length; i++) {
+                this._pdbidsList.add(vPdbidsArray[i]);
+        }
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vRnaViewer
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setRnaViewer(
+            final int index,
+            final jalview.schemabinding.version2.RnaViewer vRnaViewer)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._rnaViewerList.size()) {
+            throw new IndexOutOfBoundsException("setRnaViewer: Index value '" + index + "' not in range [0.." + (this._rnaViewerList.size() - 1) + "]");
+        }
+        
+        this._rnaViewerList.set(index, vRnaViewer);
+    }
+
+    /**
+     * 
+     * 
+     * @param vRnaViewerArray
+     */
+    public void setRnaViewer(
+            final jalview.schemabinding.version2.RnaViewer[] vRnaViewerArray) {
+        //-- copy array
+        _rnaViewerList.clear();
+        
+        for (int i = 0; i < vRnaViewerArray.length; i++) {
+                this._rnaViewerList.add(vRnaViewerArray[i]);
+        }
+    }
+
+    /**
+     * Sets the value of field 'start'.
+     * 
+     * @param start the value of field 'start'.
+     */
+    public void setStart(
+            final int start) {
+        this._start = start;
+        this._has_start = true;
+    }
+
+    /**
+     * Sets the value of field 'viewreference'.
+     * 
+     * @param viewreference the value of field 'viewreference'.
+     */
+    public void setViewreference(
+            final boolean viewreference) {
+        this._viewreference = viewreference;
+        this._has_viewreference = true;
+    }
+
+    /**
+     * Method unmarshal.
+     * 
+     * @param reader
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @return the unmarshaled jalview.schemabinding.version2.JSeq
+     */
+    public static jalview.schemabinding.version2.JSeq unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.JSeq.class, reader);
+    }
+
+    /**
+     * 
+     * 
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     */
+    public void validate(
+    )
+    throws org.exolab.castor.xml.ValidationException {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    }
 
 }
diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
index 28f23b26..b6becc0 100644
--- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-//---------------------------------/
-//- Imported classes and packages -/
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.JSeq;
@@ -18,697 +18,607 @@ import jalview.schemabinding.version2.JSeq;
  * 
  * @version $Revision$ $Date$
  */
-public class JSeqDescriptor extends
-        org.exolab.castor.xml.util.XMLClassDescriptorImpl
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * Field _elementDefinition.
-   */
-  private boolean _elementDefinition;
-
-  /**
-   * Field _nsPrefix.
-   */
-  private java.lang.String _nsPrefix;
-
-  /**
-   * Field _nsURI.
-   */
-  private java.lang.String _nsURI;
-
-  /**
-   * Field _xmlName.
-   */
-  private java.lang.String _xmlName;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public JSeqDescriptor()
-  {
-    super();
-    _nsURI = "www.jalview.org";
-    _xmlName = "JSeq";
-    _elementDefinition = true;
-
-    // -- set grouping compositor
-    setCompositorAsSequence();
-    org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
-    org.exolab.castor.mapping.FieldHandler handler = null;
-    org.exolab.castor.xml.FieldValidator fieldValidator = null;
-    // -- initialize attribute descriptors
-
-    // -- _colour
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_colour", "colour",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasColour())
-        {
-          return null;
+public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _elementDefinition.
+     */
+    private boolean _elementDefinition;
+
+    /**
+     * Field _nsPrefix.
+     */
+    private java.lang.String _nsPrefix;
+
+    /**
+     * Field _nsURI.
+     */
+    private java.lang.String _nsURI;
+
+    /**
+     * Field _xmlName.
+     */
+    private java.lang.String _xmlName;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public JSeqDescriptor() {
+        super();
+        _nsURI = "www.jalview.org";
+        _xmlName = "JSeq";
+        _elementDefinition = true;
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _colour
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                if (!target.hasColour()) { return null; }
+                return new java.lang.Integer(target.getColour());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteColour();
+                        return;
+                    }
+                    target.setColour( ((java.lang.Integer) value).intValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _colour
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.IntValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setMinInclusive(-2147483648);
+            typeValidator.setMaxInclusive(2147483647);
         }
-        return new java.lang.Integer(target.getColour());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteColour();
-            return;
-          }
-          target.setColour(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+        desc.setValidator(fieldValidator);
+        //-- _start
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                if (!target.hasStart()) { return null; }
+                return new java.lang.Integer(target.getStart());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) { return; }
+                    
+                    target.setStart( ((java.lang.Integer) value).intValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _start
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            org.exolab.castor.xml.validators.IntValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setMinInclusive(-2147483648);
+            typeValidator.setMaxInclusive(2147483647);
         }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _colour
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _start
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_start", "start",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasStart())
-        {
-          return null;
+        desc.setValidator(fieldValidator);
+        //-- _end
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                if (!target.hasEnd()) { return null; }
+                return new java.lang.Integer(target.getEnd());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) { return; }
+                    
+                    target.setEnd( ((java.lang.Integer) value).intValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _end
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            org.exolab.castor.xml.validators.IntValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setMinInclusive(-2147483648);
+            typeValidator.setMaxInclusive(2147483647);
         }
-        return new java.lang.Integer(target.getStart());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // ignore null values for non optional primitives
-          if (value == null)
-          {
-            return;
-          }
-
-          target.setStart(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+        desc.setValidator(fieldValidator);
+        //-- _id
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                return target.getId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.setId( (java.lang.String) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            org.exolab.castor.xml.validators.StringValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setWhiteSpace("preserve");
         }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _start
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _end
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_end", "end",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasEnd())
-        {
-          return null;
+        desc.setValidator(fieldValidator);
+        //-- _hidden
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                if (!target.hasHidden()) { return null; }
+                return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteHidden();
+                        return;
+                    }
+                    target.setHidden( ((java.lang.Boolean) value).booleanValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _hidden
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
         }
-        return new java.lang.Integer(target.getEnd());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // ignore null values for non optional primitives
-          if (value == null)
-          {
-            return;
-          }
-
-          target.setEnd(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+        desc.setValidator(fieldValidator);
+        //-- _viewreference
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_viewreference", "viewreference", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                if (!target.hasViewreference()) { return null; }
+                return (target.getViewreference() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteViewreference();
+                        return;
+                    }
+                    target.setViewreference( ((java.lang.Boolean) value).booleanValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _viewreference
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
         }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _end
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _id
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.String.class, "_id", "id",
-            org.exolab.castor.xml.NodeType.Attribute);
-    desc.setImmutable(true);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getId();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.setId((java.lang.String) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _featuresList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                return target.getFeatures();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.addFeatures( (jalview.schemabinding.version2.Features) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.removeAllFeatures();
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return new jalview.schemabinding.version2.Features();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _featuresList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
         }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _id
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.StringValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setWhiteSpace("preserve");
-    }
-    desc.setValidator(fieldValidator);
-    // -- _hidden
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Boolean.TYPE, "_hidden", "hidden",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasHidden())
-        {
-          return null;
+        desc.setValidator(fieldValidator);
+        //-- _pdbidsList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                return target.getPdbids();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.addPdbids( (jalview.schemabinding.version2.Pdbids) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.removeAllPdbids();
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return new jalview.schemabinding.version2.Pdbids();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _pdbidsList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
         }
-        return (target.getHidden() ? java.lang.Boolean.TRUE
-                : java.lang.Boolean.FALSE);
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteHidden();
-            return;
-          }
-          target.setHidden(((java.lang.Boolean) value).booleanValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+        desc.setValidator(fieldValidator);
+        //-- _hiddenSequencesList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                return target.getHiddenSequences();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) { return; }
+                    
+                    target.addHiddenSequences( ((java.lang.Integer) value).intValue());
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.removeAllHiddenSequences();
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _hiddenSequencesList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+            org.exolab.castor.xml.validators.IntValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setMinInclusive(-2147483648);
+            typeValidator.setMaxInclusive(2147483647);
         }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _hidden
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-      fieldValidator.setValidator(typeValidator);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _viewreference
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Boolean.TYPE, "_viewreference", "viewreference",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasViewreference())
-        {
-          return null;
+        desc.setValidator(fieldValidator);
+        //-- _rnaViewerList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.RnaViewer.class, "_rnaViewerList", "rnaViewer", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                return target.getRnaViewer();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.addRnaViewer( (jalview.schemabinding.version2.RnaViewer) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.removeAllRnaViewer();
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return new jalview.schemabinding.version2.RnaViewer();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _rnaViewerList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
         }
-        return (target.getViewreference() ? java.lang.Boolean.TRUE
-                : java.lang.Boolean.FALSE);
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteViewreference();
-            return;
-          }
-          target.setViewreference(((java.lang.Boolean) value)
-                  .booleanValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+        desc.setValidator(fieldValidator);
+        //-- _hmmerProfile
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_hmmerProfile", "hmmerProfile", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                JSeq target = (JSeq) object;
+                return target.getHmmerProfile();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    JSeq target = (JSeq) object;
+                    target.setHmmerProfile( (java.lang.String) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _hmmerProfile
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.StringValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setWhiteSpace("preserve");
         }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _viewreference
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-      fieldValidator.setValidator(typeValidator);
+        desc.setValidator(fieldValidator);
     }
-    desc.setValidator(fieldValidator);
-    // -- initialize element descriptors
 
-    // -- _featuresList
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.Features.class, "_featuresList",
-            "features", org.exolab.castor.xml.NodeType.Element);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getFeatures();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.addFeatures((jalview.schemabinding.version2.Features) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.removeAllFeatures();
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
 
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return new jalview.schemabinding.version2.Features();
-      }
-    };
-    desc.setHandler(handler);
-    desc.setNameSpaceURI("www.jalview.org");
-    desc.setMultivalued(true);
-    addFieldDescriptor(desc);
+      //-----------/
+     //- Methods -/
+    //-----------/
 
-    // -- validation code for: _featuresList
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(0);
-    { // -- local scope
+    /**
+     * Method getAccessMode.
+     * 
+     * @return the access mode specified for this class.
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode(
+    ) {
+        return null;
     }
-    desc.setValidator(fieldValidator);
-    // -- _pdbidsList
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.Pdbids.class, "_pdbidsList",
-            "pdbids", org.exolab.castor.xml.NodeType.Element);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getPdbids();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.addPdbids((jalview.schemabinding.version2.Pdbids) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.removeAllPdbids();
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
 
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return new jalview.schemabinding.version2.Pdbids();
-      }
-    };
-    desc.setHandler(handler);
-    desc.setNameSpaceURI("www.jalview.org");
-    desc.setMultivalued(true);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _pdbidsList
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(0);
-    { // -- local scope
+    /**
+     * Method getIdentity.
+     * 
+     * @return the identity field, null if this class has no
+     * identity.
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+    ) {
+        return super.getIdentity();
     }
-    desc.setValidator(fieldValidator);
-    // -- _hiddenSequencesList
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_hiddenSequencesList",
-            "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getHiddenSequences();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // ignore null values for non optional primitives
-          if (value == null)
-          {
-            return;
-          }
-
-          target.addHiddenSequences(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
 
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.removeAllHiddenSequences();
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setNameSpaceURI("www.jalview.org");
-    desc.setMultivalued(true);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _hiddenSequencesList
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(0);
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
+    /**
+     * Method getJavaClass.
+     * 
+     * @return the Java class represented by this descriptor.
+     */
+    public java.lang.Class getJavaClass(
+    ) {
+        return jalview.schemabinding.version2.JSeq.class;
     }
-    desc.setValidator(fieldValidator);
-    // -- _rnaViewerList
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.RnaViewer.class,
-            "_rnaViewerList", "rnaViewer",
-            org.exolab.castor.xml.NodeType.Element);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getRnaViewer();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.addRnaViewer((jalview.schemabinding.version2.RnaViewer) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.removeAllRnaViewer();
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return new jalview.schemabinding.version2.RnaViewer();
-      }
-    };
-    desc.setHandler(handler);
-    desc.setNameSpaceURI("www.jalview.org");
-    desc.setMultivalued(true);
-    addFieldDescriptor(desc);
 
-    // -- validation code for: _rnaViewerList
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(0);
-    { // -- local scope
+    /**
+     * Method getNameSpacePrefix.
+     * 
+     * @return the namespace prefix to use when marshaling as XML.
+     */
+    public java.lang.String getNameSpacePrefix(
+    ) {
+        return _nsPrefix;
     }
-    desc.setValidator(fieldValidator);
-  }
 
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-   * Method getAccessMode.
-   * 
-   * @return the access mode specified for this class.
-   */
-  public org.exolab.castor.mapping.AccessMode getAccessMode()
-  {
-    return null;
-  }
-
-  /**
-   * Method getIdentity.
-   * 
-   * @return the identity field, null if this class has no identity.
-   */
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-  {
-    return super.getIdentity();
-  }
-
-  /**
-   * Method getJavaClass.
-   * 
-   * @return the Java class represented by this descriptor.
-   */
-  public java.lang.Class getJavaClass()
-  {
-    return jalview.schemabinding.version2.JSeq.class;
-  }
-
-  /**
-   * Method getNameSpacePrefix.
-   * 
-   * @return the namespace prefix to use when marshaling as XML.
-   */
-  public java.lang.String getNameSpacePrefix()
-  {
-    return _nsPrefix;
-  }
-
-  /**
-   * Method getNameSpaceURI.
-   * 
-   * @return the namespace URI used when marshaling and unmarshaling as XML.
-   */
-  public java.lang.String getNameSpaceURI()
-  {
-    return _nsURI;
-  }
+    /**
+     * Method getNameSpaceURI.
+     * 
+     * @return the namespace URI used when marshaling and
+     * unmarshaling as XML.
+     */
+    public java.lang.String getNameSpaceURI(
+    ) {
+        return _nsURI;
+    }
 
-  /**
-   * Method getValidator.
-   * 
-   * @return a specific validator for the class described by this
-   *         ClassDescriptor.
-   */
-  public org.exolab.castor.xml.TypeValidator getValidator()
-  {
-    return this;
-  }
+    /**
+     * Method getValidator.
+     * 
+     * @return a specific validator for the class described by this
+     * ClassDescriptor.
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator(
+    ) {
+        return this;
+    }
 
-  /**
-   * Method getXMLName.
-   * 
-   * @return the XML Name for the Class being described.
-   */
-  public java.lang.String getXMLName()
-  {
-    return _xmlName;
-  }
+    /**
+     * Method getXMLName.
+     * 
+     * @return the XML Name for the Class being described.
+     */
+    public java.lang.String getXMLName(
+    ) {
+        return _xmlName;
+    }
 
-  /**
-   * Method isElementDefinition.
-   * 
-   * @return true if XML schema definition of this Class is that of a global
-   *         element or element with anonymous type definition.
-   */
-  public boolean isElementDefinition()
-  {
-    return _elementDefinition;
-  }
+    /**
+     * Method isElementDefinition.
+     * 
+     * @return true if XML schema definition of this Class is that
+     * of a global
+     * element or element with anonymous type definition.
+     */
+    public boolean isElementDefinition(
+    ) {
+        return _elementDefinition;
+    }
 
 }
diff --git a/src/jalview/structure/StructureMapping.java b/src/jalview/structure/StructureMapping.java
index fcf322d..4174f5b 100644
--- a/src/jalview/structure/StructureMapping.java
+++ b/src/jalview/structure/StructureMapping.java
@@ -30,6 +30,12 @@ import java.util.List;
 
 public class StructureMapping
 {
+  public static final int UNASSIGNED_VALUE = Integer.MIN_VALUE;
+
+  private static final int PDB_RES_NUM_INDEX = 0;
+
+  private static final int PDB_ATOM_NUM_INDEX = 1;
+
   String mappingDetails;
 
   SequenceI sequence;
@@ -40,17 +46,12 @@ public class StructureMapping
 
   String pdbchain;
 
-  public static final int UNASSIGNED_VALUE = Integer.MIN_VALUE;
-
-  private static final int PDB_RES_NUM_INDEX = 0;
-
-  private static final int PDB_ATOM_NUM_INDEX = 1;
-
   // Mapping key is residue index while value is an array containing PDB resNum,
   // and atomNo
   HashMap<Integer, int[]> mapping;
 
   jalview.datamodel.Mapping seqToPdbMapping = null;
+
   /**
    * Constructor
    * 
@@ -145,7 +146,7 @@ public class StructureMapping
    */
   public List<int[]> getPDBResNumRanges(int fromSeqPos, int toSeqPos)
   {
-    List<int[]> result = new ArrayList<int[]>();
+    List<int[]> result = new ArrayList<>();
     int startRes = -1;
     int endRes = -1;
 
@@ -263,4 +264,105 @@ public class StructureMapping
   {
     return seqToPdbMapping;
   }
+
+  /**
+   * A hash function that satisfies the contract that if two mappings are
+   * equal(), they have the same hashCode
+   */
+  @Override
+  public int hashCode()
+  {
+    final int prime = 31;
+    int result = 1;
+    result = prime * result
+            + ((mappingDetails == null) ? 0 : mappingDetails.hashCode());
+    result = prime * result
+            + ((pdbchain == null) ? 0 : pdbchain.hashCode());
+    result = prime * result + ((pdbfile == null) ? 0 : pdbfile.hashCode());
+    result = prime * result + ((pdbid == null) ? 0 : pdbid.hashCode());
+    result = prime * result
+            + ((seqToPdbMapping == null) ? 0 : seqToPdbMapping.hashCode());
+    result = prime * result
+            + ((sequence == null) ? 0 : sequence.hashCode());
+    return result;
+  }
+
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (this == obj)
+    {
+      return true;
+    }
+    if (obj == null)
+    {
+      return false;
+    }
+    if (getClass() != obj.getClass())
+    {
+      return false;
+    }
+    StructureMapping other = (StructureMapping) obj;
+    if (mappingDetails == null)
+    {
+      if (other.mappingDetails != null)
+      {
+        return false;
+      }
+    }
+    else if (!mappingDetails.equals(other.mappingDetails))
+    {
+      return false;
+    }
+    if (pdbchain == null)
+    {
+      if (other.pdbchain != null)
+      {
+        return false;
+      }
+    }
+    else if (!pdbchain.equals(other.pdbchain))
+    {
+      return false;
+    }
+    if (pdbfile == null)
+    {
+      if (other.pdbfile != null)
+      {
+        return false;
+      }
+    }
+    else if (!pdbfile.equals(other.pdbfile))
+    {
+      return false;
+    }
+    if (pdbid == null)
+    {
+      if (other.pdbid != null)
+      {
+        return false;
+      }
+    }
+    else if (!pdbid.equals(other.pdbid))
+    {
+      return false;
+    }
+    if (seqToPdbMapping == null)
+    {
+      if (other.seqToPdbMapping != null)
+      {
+        return false;
+      }
+    }
+    else if (!seqToPdbMapping.equals(other.seqToPdbMapping))
+    {
+      return false;
+    }
+    if (sequence != other.sequence)
+    {
+      return false;
+    }
+
+    return true;
+  }
 }
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 10fe836..ad259fd 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -285,7 +285,8 @@ public class StructureSelectionManager
   }
 
   /**
-   * Returns the file name for a mapped PDB id (or null if not mapped).
+   * Returns the filename the PDB id is already mapped to if known, or null if
+   * it is not mapped
    * 
    * @param pdbid
    * @return
@@ -294,7 +295,7 @@ public class StructureSelectionManager
   {
     for (StructureMapping sm : mappings)
     {
-      if (sm.getPdbId().equals(pdbid))
+      if (sm.getPdbId().equalsIgnoreCase(pdbid))
       {
         return sm.pdbfile;
       }
@@ -572,6 +573,13 @@ public class StructureSelectionManager
             {
               System.err.println(e.getMessage());
             }
+            catch (Exception e)
+            {
+              System.err
+                      .println(
+                              "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
+              System.err.println(e.getMessage());
+            }
           }
           if (!foundSiftsMappings.isEmpty())
           {
@@ -605,7 +613,10 @@ public class StructureSelectionManager
       }
       if (forStructureView)
       {
-        mappings.addAll(seqToStrucMapping);
+        for (StructureMapping sm : seqToStrucMapping)
+        {
+          addStructureMapping(sm); // not addAll!
+        }
       }
       if (progress != null)
       {
@@ -657,7 +668,10 @@ public class StructureSelectionManager
 
   public void addStructureMapping(StructureMapping sm)
   {
-    mappings.add(sm);
+    if (!mappings.contains(sm))
+    {
+      mappings.add(sm);
+    }
   }
 
   /**
diff --git a/src/jalview/util/MapList.java b/src/jalview/util/MapList.java
index 81b9964..60054f1 100644
--- a/src/jalview/util/MapList.java
+++ b/src/jalview/util/MapList.java
@@ -116,8 +116,17 @@ public class MapList
   {
     int hashCode = 31 * fromRatio;
     hashCode = 31 * hashCode + toRatio;
-    hashCode = 31 * hashCode + fromShifts.toArray().hashCode();
-    hashCode = 31 * hashCode + toShifts.toArray().hashCode();
+    for (int[] shift : fromShifts)
+    {
+      hashCode = 31 * hashCode + shift[0];
+      hashCode = 31 * hashCode + shift[1];
+    }
+    for (int[] shift : toShifts)
+    {
+      hashCode = 31 * hashCode + shift[0];
+      hashCode = 31 * hashCode + shift[1];
+    }
+
     return hashCode;
   }
 
diff --git a/src/jalview/workers/InformationThread.java b/src/jalview/workers/InformationThread.java
index cf42425..d719189 100644
--- a/src/jalview/workers/InformationThread.java
+++ b/src/jalview/workers/InformationThread.java
@@ -44,6 +44,10 @@ public class InformationThread extends AlignCalcWorker
   @Override
   public void run()
   {
+    if (alignViewport.getAlignment().getHmmSequences().isEmpty())
+    {
+      return;
+    }
     if (calcMan.isPending(this))
     {
       return;
diff --git a/src/jalview/ws/params/simple/LogarithmicParameter.java b/src/jalview/ws/params/simple/LogarithmicParameter.java
index 01744e7..af80181 100644
--- a/src/jalview/ws/params/simple/LogarithmicParameter.java
+++ b/src/jalview/ws/params/simple/LogarithmicParameter.java
@@ -17,8 +17,6 @@ public class LogarithmicParameter extends Option implements ParameterI
 
   final double max;
 
-  final double base; // todo is this even needed?
-
   @Override
   public ValueConstrainI getValidValue()
   {
@@ -51,31 +49,27 @@ public class LogarithmicParameter extends Option implements ParameterI
     max = parm.max;
     min = parm.min;
     defval = 0D;
-    base = parm.base;
   }
 
   public LogarithmicParameter(String name, String description,
-          boolean required, Double defValue, double min, double max,
-          double base)
+          boolean required, Double defValue, double min, double max)
   {
     super(name, description, required, String.valueOf(defValue), null, null,
             null);
     defval = defValue;
     this.min = min;
     this.max = max;
-    this.base = base;
   }
 
   public LogarithmicParameter(String name, String description,
           boolean required, Double defValue, double value, double min,
-          double max, double base)
+          double max)
   {
     super(name, description, required, String.valueOf(defValue),
             String.valueOf(value), null, null);
     defval = defValue;
     this.min = min;
     this.max = max;
-    this.base = base;
   }
 
   @Override
@@ -83,9 +77,4 @@ public class LogarithmicParameter extends Option implements ParameterI
   {
     return new LogarithmicParameter(this);
   }
-
-  public double getBase()
-  {
-    return base;
-  }
 }
diff --git a/src/jalview/ws/params/simple/StringChoiceParameter.java b/src/jalview/ws/params/simple/StringChoiceParameter.java
index d613d58..254eb80 100644
--- a/src/jalview/ws/params/simple/StringChoiceParameter.java
+++ b/src/jalview/ws/params/simple/StringChoiceParameter.java
@@ -20,7 +20,25 @@
  */
 package jalview.ws.params.simple;
 
+import java.util.List;
+
+/**
+ * A parameter with options intended to be rendered as radio buttons
+ */
 public class StringChoiceParameter extends Option
 {
 
+  /**
+   * Constructor
+   * 
+   * @param name
+   * @param description
+   * @param options
+   * @param def
+   */
+  public StringChoiceParameter(String name, String description,
+          List<String> options, String def)
+  {
+    super(name, description, true, def, def, options, null);
+  }
 }
diff --git a/src/jalview/ws/params/simple/StringParameter.java b/src/jalview/ws/params/simple/StringParameter.java
index 1d6a37e..b61836a 100644
--- a/src/jalview/ws/params/simple/StringParameter.java
+++ b/src/jalview/ws/params/simple/StringParameter.java
@@ -3,65 +3,13 @@ package jalview.ws.params.simple;
 import jalview.ws.params.ParameterI;
 import jalview.ws.params.ValueConstrainI;
 
-import java.net.URL;
-import java.util.List;
+import java.util.Collection;
 
 public class StringParameter extends Option implements ParameterI
 {
-
-  @Override
-  public URL getFurtherDetails()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public boolean isRequired()
-  {
-    // TODO Auto-generated method stub
-    return false;
-  }
-
-  @Override
-  public String getDescription()
-  {
-    // TODO Auto-generated method stub
-    return description;
-  }
-
-  @Override
-  public List<String> getPossibleValues()
-  {
-    // TODO Auto-generated method stub
-    return null;
-  }
-
-  @Override
-  public String getName()
-  {
-    // TODO Auto-generated method stub
-    return name;
-  }
-
-  @Override
-  public String getValue()
-  {
-    // TODO Auto-generated method stub
-    return value;
-  }
-
-  @Override
-  public void setValue(String selectedItem)
-  {
-    value = selectedItem;
-
-  }
-
   @Override
   public ValueConstrainI getValidValue()
   {
-    // TODO Auto-generated method stub
     return new StringValueConstrain();
   }
 
@@ -115,4 +63,22 @@ public class StringParameter extends Option implements ParameterI
             String.valueOf(value), null, null);
     this.defvalue = defValue;
   }
+
+  /**
+   * Constructor for a parameter with a list of possible values
+   * 
+   * @param name2
+   * @param description2
+   * @param isrequired
+   * @param defValue
+   * @param value
+   * @param possibleVals
+   */
+  public StringParameter(String name2, String description2,
+          boolean isrequired, String defValue, String value,
+          Collection<String> possibleVals)
+  {
+    super(name2, description2, isrequired, defValue, value, possibleVals,
+            null);
+  }
 }
diff --git a/test/MCview/PDBChainTest.java b/test/MCview/PDBChainTest.java
index defcdbc..533c0af 100644
--- a/test/MCview/PDBChainTest.java
+++ b/test/MCview/PDBChainTest.java
@@ -91,7 +91,7 @@ public class PDBChainTest
     a3.resName = "ASP";
     a3.resNumber = 41;
 
-    Vector<Bond> v = new Vector<Bond>();
+    Vector<Bond> v = new Vector<>();
     v.add(new Bond(a1, a2));
     v.add(new Bond(a2, a3));
     v.add(new Bond(a3, a1));
@@ -234,7 +234,7 @@ public class PDBChainTest
   @Test(groups = { "Functional" })
   public void testMakeResidueList_noAnnotation()
   {
-    Vector<Atom> atoms = new Vector<Atom>();
+    Vector<Atom> atoms = new Vector<>();
     c.atoms = atoms;
     c.isNa = true;
     atoms.add(makeAtom(4, "N", "MET"));
@@ -292,7 +292,7 @@ public class PDBChainTest
   @Test(groups = { "Functional" })
   public void testMakeResidueList_withTempFactor()
   {
-    Vector<Atom> atoms = new Vector<Atom>();
+    Vector<Atom> atoms = new Vector<>();
     c.atoms = atoms;
     atoms.add(makeAtom(4, "N", "MET"));
     atoms.get(atoms.size() - 1).tfactor = 1f;
@@ -307,7 +307,7 @@ public class PDBChainTest
     atoms.add(makeAtom(5, "CA", "LYS"));
     atoms.get(atoms.size() - 1).tfactor = 9f;
     atoms.add(makeAtom(6, "O", "LEU"));
-    atoms.get(atoms.size() - 1).tfactor = 4f;
+    atoms.get(atoms.size() - 1).tfactor = -4f;
     atoms.add(makeAtom(6, "N", "LEU"));
     atoms.get(atoms.size() - 1).tfactor = 5f;
     atoms.add(makeAtom(6, "CA", "LEU"));
@@ -320,7 +320,7 @@ public class PDBChainTest
 
     /*
      * Verify annotations; note the tempFactor is read from the first atom in
-     * each residue i.e. we expect values 1, 7, 4 for the residues
+     * each residue i.e. we expect values 1, 7, -4 for the residues
      */
     AlignmentAnnotation[] ann = c.sequence.getAnnotation();
     assertEquals(1, ann.length);
@@ -328,12 +328,12 @@ public class PDBChainTest
     assertEquals("Temperature Factor for 1gaqA", ann[0].description);
     assertSame(c.sequence, ann[0].sequenceRef);
     assertEquals(AlignmentAnnotation.LINE_GRAPH, ann[0].graph);
-    assertEquals(0f, ann[0].graphMin, 0.001f);
+    assertEquals(-4f, ann[0].graphMin, 0.001f);
     assertEquals(7f, ann[0].graphMax, 0.001f);
     assertEquals(3, ann[0].annotations.length);
     assertEquals(1f, ann[0].annotations[0].value, 0.001f);
     assertEquals(7f, ann[0].annotations[1].value, 0.001f);
-    assertEquals(4f, ann[0].annotations[2].value, 0.001f);
+    assertEquals(-4f, ann[0].annotations[2].value, 0.001f);
   }
 
   /**
@@ -344,7 +344,7 @@ public class PDBChainTest
   public void testMakeCaBondList()
   {
     c.isNa = true;
-    Vector<Atom> atoms = new Vector<Atom>();
+    Vector<Atom> atoms = new Vector<>();
     c.atoms = atoms;
     atoms.add(makeAtom(4, "N", "MET"));
     atoms.add(makeAtom(4, "CA", "MET"));
@@ -375,7 +375,7 @@ public class PDBChainTest
   public void testMakeCaBondList_nucleotide()
   {
     c.isNa = false;
-    Vector<Atom> atoms = new Vector<Atom>();
+    Vector<Atom> atoms = new Vector<>();
     c.atoms = atoms;
     atoms.add(makeAtom(4, "N", "G"));
     atoms.add(makeAtom(4, "P", "G"));
@@ -406,7 +406,7 @@ public class PDBChainTest
   @Test(groups = { "Functional" })
   public void testMakeExactMapping()
   {
-    Vector<Atom> atoms = new Vector<Atom>();
+    Vector<Atom> atoms = new Vector<>();
     c.atoms = atoms;
     atoms.add(makeAtom(4, "N", "MET"));
     atoms.add(makeAtom(4, "CA", "MET"));
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 5a14514..79bb2bb 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -247,7 +247,9 @@ public class SequenceTest
     sq.sequenceChanged();
     assertEquals(6, sq.findIndex(9));
 
-    sq = new Sequence("test/8-13", "-A--B-C-D-E-F--");
+    final String aligned = "-A--B-C-D-E-F--";
+    assertEquals(15, aligned.length());
+    sq = new Sequence("test/8-13", aligned);
     assertEquals(2, sq.findIndex(8));
     sq.sequenceChanged();
     assertEquals(5, sq.findIndex(9));
@@ -263,6 +265,29 @@ public class SequenceTest
     // beyond end returns last residue column
     sq.sequenceChanged();
     assertEquals(13, sq.findIndex(99));
+
+    /*
+     * residue before sequence 'end' but beyond end of sequence returns 
+     * length of sequence (last column) (rightly or wrongly!)
+     */
+    sq = new Sequence("test/8-15", "A-B-C-"); // trailing gap case
+    assertEquals(6, sq.getLength());
+    sq.sequenceChanged();
+    assertEquals(sq.getLength(), sq.findIndex(14));
+    sq = new Sequence("test/8-99", "-A--B-C-D"); // trailing residue case
+    sq.sequenceChanged();
+    assertEquals(sq.getLength(), sq.findIndex(65));
+
+    /*
+     * residue after sequence 'start' but before first residue returns 
+     * zero (before first column) (rightly or wrongly!)
+     */
+    sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
+    sq.sequenceChanged();
+    assertEquals(0, sq.findIndex(3));
+    sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
+    sq.sequenceChanged();
+    assertEquals(0, sq.findIndex(2));
   }
 
   /**
@@ -1402,14 +1427,61 @@ public class SequenceTest
   {
     Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
 
-    // find F given A
+    // find F given A, check cursor is now at the found position
     assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, 0)));
+    SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(13, cursor.residuePosition);
+    assertEquals(10, cursor.columnPosition);
 
     // find A given F
     assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, 0)));
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(8, cursor.residuePosition);
+    assertEquals(2, cursor.columnPosition);
 
-    // find C given C
+    // find C given C (no cursor update is done for this case)
     assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0)));
+    SequenceCursor cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertSame(cursor2, cursor);
+
+    /*
+     * sequence 'end' beyond end of sequence returns length of sequence 
+     *  (for compatibility with pre-cursor code)
+     *  - also verify the cursor is left in a valid state
+     */
+    sq = new Sequence("test/8-99", "-A--B-C-D-E-F--"); // trailing gap case
+    assertEquals(7, sq.findIndex(10)); // establishes a cursor
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(10, cursor.residuePosition);
+    assertEquals(7, cursor.columnPosition);
+    assertEquals(sq.getLength(), sq.findIndex(65));
+    cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertSame(cursor, cursor2); // not updated for this case!
+
+    sq = new Sequence("test/8-99", "-A--B-C-D-E-F"); // trailing residue case
+    sq.findIndex(10); // establishes a cursor
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(sq.getLength(), sq.findIndex(65));
+    cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertSame(cursor, cursor2); // not updated for this case!
+
+    /*
+     * residue after sequence 'start' but before first residue should return 
+     * zero (for compatibility with pre-cursor code)
+     */
+    sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
+    sq.findIndex(10); // establishes a cursor
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(0, sq.findIndex(3));
+    cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertSame(cursor, cursor2); // not updated for this case!
+
+    sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
+    sq.findIndex(10); // establishes a cursor
+    cursor = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertEquals(0, sq.findIndex(2));
+    cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
+    assertSame(cursor, cursor2); // not updated for this case!
   }
 
   @Test(groups = { "Functional" })
diff --git a/test/jalview/datamodel/features/FeatureAttributesTest.java b/test/jalview/datamodel/features/FeatureAttributesTest.java
index e47c787..686cd2f 100644
--- a/test/jalview/datamodel/features/FeatureAttributesTest.java
+++ b/test/jalview/datamodel/features/FeatureAttributesTest.java
@@ -23,7 +23,7 @@ public class FeatureAttributesTest
   /**
    * clear down attributes map before tests
    */
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     FeatureAttributes fa = FeatureAttributes.getInstance();
@@ -33,7 +33,7 @@ public class FeatureAttributesTest
   /**
    * clear down attributes map after tests
    */
-  @AfterMethod
+  @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
     FeatureAttributes fa = FeatureAttributes.getInstance();
diff --git a/test/jalview/ext/jmol/JmolViewerTest.java b/test/jalview/ext/jmol/JmolViewerTest.java
index 792f7ad..e451ed2 100644
--- a/test/jalview/ext/jmol/JmolViewerTest.java
+++ b/test/jalview/ext/jmol/JmolViewerTest.java
@@ -20,11 +20,15 @@
  */
 package jalview.ext.jmol;
 
+import static org.junit.Assert.assertNotNull;
+import static org.testng.Assert.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.JvOptionPane;
@@ -32,6 +36,10 @@ import jalview.gui.Preferences;
 import jalview.gui.StructureViewer;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileLoader;
+
+import java.lang.reflect.InvocationTargetException;
 
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
@@ -54,8 +62,10 @@ public class JmolViewerTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    Jalview.main(new String[] { "-noquestionnaire", "-nonews", "-props",
-        "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
+    Jalview.main(
+            new String[]
+            { "-noquestionnaire", "-nonews", "-props",
+                "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
   }
 
   /**
@@ -70,10 +80,11 @@ public class JmolViewerTest
   @Test(groups = { "Functional" })
   public void testSingleSeqViewJMol()
   {
-    Cache.setProperty(Preferences.STRUCTURE_DISPLAY, ViewerType.JMOL.name());
+    Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+            ViewerType.JMOL.name());
     String inFile = "examples/1gaq.txt";
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, DataSourceType.FILE);
+    AlignFrame af = new jalview.io.FileLoader()
+            .LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
     assertTrue("Didn't read input file " + inFile, af != null);
     for (SequenceI sq : af.getViewport().getAlignment().getSequences())
     {
@@ -87,13 +98,13 @@ public class JmolViewerTest
       {
         for (int q = 0; q < dsq.getAllPDBEntries().size(); q++)
         {
-          final StructureViewer structureViewer = new StructureViewer(af
-                  .getViewport().getStructureSelectionManager());
+          final StructureViewer structureViewer = new StructureViewer(
+                  af.getViewport().getStructureSelectionManager());
           structureViewer.setViewerType(ViewerType.JMOL);
           JalviewStructureDisplayI jmolViewer = structureViewer
                   .viewStructures(dsq.getAllPDBEntries().elementAt(q),
-                          new SequenceI[] { sq }, af.getCurrentView()
-                                  .getAlignPanel());
+                          new SequenceI[]
+                          { sq }, af.getCurrentView().getAlignPanel());
           /*
            * Wait for viewer load thread to complete
            */
@@ -116,5 +127,86 @@ public class JmolViewerTest
     }
   }
 
+  @Test(groups = { "Functional" })
+  public void testAddStrToSingleSeqViewJMol()
+          throws InvocationTargetException, InterruptedException
+  {
+    Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
+            ViewerType.JMOL.name());
+    String inFile = "examples/1gaq.txt";
+    AlignFrame af = new jalview.io.FileLoader(true)
+            .LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
+    assertTrue("Didn't read input file " + inFile, af != null);
+    // show a structure for 4th Sequence
+    SequenceI sq1 = af.getViewport().getAlignment().getSequences().get(0);
+    final StructureViewer structureViewer = new StructureViewer(
+            af.getViewport().getStructureSelectionManager());
+    structureViewer.setViewerType(ViewerType.JMOL);
+    JalviewStructureDisplayI jmolViewer = structureViewer.viewStructures(
+            sq1.getDatasetSequence().getAllPDBEntries().elementAt(0),
+            new SequenceI[]
+            { sq1 }, af.getCurrentView().getAlignPanel());
+    /*
+     * Wait for viewer load thread to complete
+     */
+    try
+    {
+      while (!jmolViewer.getBinding().isFinishedInit())
+      {
+        Thread.sleep(500);
+      }
+    } catch (InterruptedException e)
+    {
+    }
+
+    assertTrue(jmolViewer.isVisible());
+
+    // add another pdb file and add it to view
+    final String _inFile = "examples/3W5V.pdb";
+    inFile = _inFile;
+    FileLoader fl = new FileLoader();
+    fl.LoadFile(af.getCurrentView(), _inFile, DataSourceType.FILE,
+            FileFormat.PDB);
+    try
+    {
+      int time = 0;
+      do
+      {
+        Thread.sleep(50); // hope we can avoid race condition
+
+      } while (++time < 30
+              && af.getViewport().getAlignment().getHeight() == 3);
+    } catch (Exception q)
+    {
+    }
+    ;
+    assertTrue("Didn't paste additional structure" + inFile,
+            af.getViewport().getAlignment().getHeight() > 3);
+    SequenceI sq2 = af.getViewport().getAlignment().getSequenceAt(3);
+    PDBEntry pdbe = sq2.getDatasetSequence().getAllPDBEntries().get(0);
+    assertTrue(pdbe.getFile().contains(inFile));
+    structureViewer.viewStructures(pdbe, new SequenceI[] { sq2 },
+            af.alignPanel);
+    /*
+     * Wait for viewer load thread to complete
+     */
+    try
+    {
+      while (structureViewer.isBusy())
+      {
+        Thread.sleep(500);
+      }
+    } catch (InterruptedException e)
+    {
+    }
+    assertEquals(jmolViewer.getBinding().getPdbCount(), 2);
+    String mouseOverTest = "[GLY]293:A.CA/2.1 #2164";
+    ((JalviewJmolBinding) jmolViewer.getBinding()).mouseOverStructure(2164,
+            mouseOverTest);
+    SearchResultsI highlight = af.alignPanel.getSeqPanel()
+            .getLastSearchResults();
+    assertNotNull("Didn't find highlight from second structure mouseover",
+            highlight.getResults(sq2, sq2.getStart(), sq2.getEnd()));
+  }
 
 }
diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 91fe602..f69e6b5 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.DBRefEntry;
@@ -28,8 +29,10 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
 import jalview.jbgui.GStructureChooser.FilterOption;
 
+import java.util.Collection;
 import java.util.Vector;
 
 import org.testng.annotations.AfterMethod;
@@ -37,6 +40,8 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class StructureChooserTest
 {
 
@@ -142,8 +147,10 @@ public class StructureChooserTest
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
     sc.fetchStructuresMetaData();
-    assertTrue(sc.getDiscoveredStructuresSet() != null);
-    assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
+    Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
+            "discoveredStructuresSet");
+    assertNotNull(ss);
+    assertTrue(ss.size() > 0);
 
   }
 
diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 41a6b89..3a727b4 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -33,7 +33,9 @@ import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceCollectionI;
@@ -78,6 +80,8 @@ import org.testng.AssertJUnit;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 @Test(singleThreaded = true)
 public class Jalview2xmlTests extends Jalview2xmlBase
 {
@@ -256,6 +260,31 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
   }
 
+  /**
+   * Test for JAL-2223 - multiple mappings in View Mapping report
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" })
+  public void noDuplicatePdbMappingsMade() throws Exception
+  {
+    StructureImportSettings.setProcessSecondaryStructure(true);
+    StructureImportSettings.setVisibleChainAnnotation(true);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile_2_7.jar", DataSourceType.FILE);
+    assertNotNull(af, "Didn't read in the example file correctly.");
+
+    // locate Jmol viewer
+    // count number of PDB mappings the structure selection manager holds -
+    String pdbFile = af.getCurrentView().getStructureSelectionManager()
+            .findFileForPDBId("1A70");
+    assertEquals(
+            af.getCurrentView().getStructureSelectionManager()
+                    .getMapping(pdbFile).length,
+            2, "Expected only two mappings for 1A70");
+
+  }
+
   @Test(groups = { "Functional" })
   public void viewRefPdbAnnotation() throws Exception
   {
@@ -857,7 +886,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
    * @throws IOException
    */
   @Test(groups = { "Functional" })
-  public void testSaveLoadFeatureColoursAndFilters() throws IOException
+  public void testStoreAndRecoverFeatureColoursAndFilters()
+          throws IOException
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
@@ -1009,4 +1039,57 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     addFeature(seq, featureType, score++);
     addFeature(seq, featureType, score);
   }
+
+  /**
+   * Load an HMM profile to an alignment, and confirm it is correctly restored
+   * when reloaded from project
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
+  public void testStoreAndRecoverHmmProfile() throws IOException
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+  
+    AlignViewportI av = af.getViewport();
+    AlignmentI al = av.getAlignment();
+
+    /*
+     * mimic drag and drop of hmm file on to alignment
+     */
+    AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.hmm", DataSourceType.FILE);
+    al.insertSequenceAt(0,
+            af2.getViewport().getAlignment().getSequenceAt(0));
+
+    /*
+     * check it loaded in
+     */
+    SequenceI hmmSeq = al.getSequenceAt(0);
+    assertTrue(hmmSeq.hasHMMProfile());
+    HiddenMarkovModel hmm = hmmSeq.getHMM();
+    assertSame(hmm.getConsensusSequence(), hmmSeq);
+
+    /*
+     * save project, close windows, reload project, verify
+     */
+    File tfile = File.createTempFile("testStoreAndRecoverHmmProfile",
+            ".jvp");
+    tfile.deleteOnExit();
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.instance.closeAll_actionPerformed(null);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+    Assert.assertNotNull(af, "Failed to reload project");
+
+    hmmSeq = al.getSequenceAt(0);
+    assertTrue(hmmSeq.hasHMMProfile());
+    assertSame(hmm.getConsensusSequence(), hmmSeq);
+    Mapping mapToHmmConsensus = (Mapping) PA.getValue(hmm,
+            "mapToHmmConsensus");
+    assertNotNull(mapToHmmConsensus);
+    assertSame(mapToHmmConsensus.getTo(), hmmSeq.getDatasetSequence());
+  }
 }
diff --git a/test/jalview/structure/StructureMappingTest.java b/test/jalview/structure/StructureMappingTest.java
index f26c5f1..036aeaa 100644
--- a/test/jalview/structure/StructureMappingTest.java
+++ b/test/jalview/structure/StructureMappingTest.java
@@ -1,8 +1,14 @@
 package jalview.structure;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertTrue;
 
+import jalview.datamodel.Mapping;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MapList;
+
 import java.util.HashMap;
 import java.util.List;
 
@@ -11,9 +17,9 @@ import org.testng.annotations.Test;
 public class StructureMappingTest
 {
   @Test(groups = "Functional")
-  public void testgetPDBResNumRanges()
+  public void testGetPDBResNumRanges()
   {
-    HashMap<Integer, int[]> map = new HashMap<Integer, int[]>();
+    HashMap<Integer, int[]> map = new HashMap<>();
 
     StructureMapping mapping = new StructureMapping(null, null, null, null,
             map, null);
@@ -43,4 +49,75 @@ public class StructureMappingTest
     assertEquals(ranges.get(1)[0], 15);
     assertEquals(ranges.get(1)[1], 15);
   }
+
+  @Test(groups = "Functional")
+  public void testEquals()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDE");
+    SequenceI seq2 = new Sequence("seq1", "ABCDE");
+    String pdbFile = "a/b/file1.pdb";
+    String pdbId = "1a70";
+    String chain = "A";
+    String mappingDetails = "these are the mapping details, honest";
+    HashMap<Integer, int[]> map = new HashMap<>();
+
+    Mapping seqToPdbMapping = new Mapping(seq1,
+            new MapList(new int[]
+            { 1, 5 }, new int[] { 2, 6 }, 1, 1));
+    StructureMapping sm1 = new StructureMapping(seq1, pdbFile, pdbId, chain,
+            map, mappingDetails, seqToPdbMapping);
+    assertFalse(sm1.equals(null));
+    assertFalse(sm1.equals("x"));
+
+    StructureMapping sm2 = new StructureMapping(seq1, pdbFile, pdbId, chain,
+            map, mappingDetails, seqToPdbMapping);
+    assertTrue(sm1.equals(sm2));
+    assertTrue(sm2.equals(sm1));
+    assertEquals(sm1.hashCode(), sm2.hashCode());
+
+    // with different sequence
+    sm2 = new StructureMapping(seq2, pdbFile, pdbId, chain, map,
+            mappingDetails, seqToPdbMapping);
+    assertFalse(sm1.equals(sm2));
+    assertFalse(sm2.equals(sm1));
+
+    // with different file
+    sm2 = new StructureMapping(seq1, "a/b/file2.pdb", pdbId, chain, map,
+            mappingDetails, seqToPdbMapping);
+    assertFalse(sm1.equals(sm2));
+    assertFalse(sm2.equals(sm1));
+
+    // with different pdbid (case sensitive)
+    sm2 = new StructureMapping(seq1, pdbFile, "1A70", chain, map,
+            mappingDetails, seqToPdbMapping);
+    assertFalse(sm1.equals(sm2));
+    assertFalse(sm2.equals(sm1));
+
+    // with different chain
+    sm2 = new StructureMapping(seq1, pdbFile, pdbId, "B", map,
+            mappingDetails, seqToPdbMapping);
+    assertFalse(sm1.equals(sm2));
+    assertFalse(sm2.equals(sm1));
+
+    // map is ignore for this test
+    sm2 = new StructureMapping(seq1, pdbFile, pdbId, chain, null,
+            mappingDetails, seqToPdbMapping);
+    assertTrue(sm1.equals(sm2));
+    assertTrue(sm2.equals(sm1));
+
+    // with different mapping details
+    sm2 = new StructureMapping(seq1, pdbFile, pdbId, chain, map,
+            "different details!", seqToPdbMapping);
+    assertFalse(sm1.equals(sm2));
+    assertFalse(sm2.equals(sm1));
+
+    // with different seq to pdb mapping
+    Mapping map2 = new Mapping(seq1,
+            new MapList(new int[]
+            { 1, 5 }, new int[] { 3, 7 }, 1, 1));
+    sm2 = new StructureMapping(seq1, pdbFile, pdbId, chain, map,
+            mappingDetails, map2);
+    assertFalse(sm1.equals(sm2));
+    assertFalse(sm2.equals(sm1));
+  }
 }
diff --git a/test/jalview/util/MapListTest.java b/test/jalview/util/MapListTest.java
index fd68e96..cd3e124 100644
--- a/test/jalview/util/MapListTest.java
+++ b/test/jalview/util/MapListTest.java
@@ -391,7 +391,9 @@ public class MapListTest
     MapList ml7 = new MapList(codons, protein, 3, 1); // toShifts differ
 
     assertTrue(ml.equals(ml));
+    assertEquals(ml.hashCode(), ml.hashCode());
     assertTrue(ml.equals(ml1));
+    assertEquals(ml.hashCode(), ml1.hashCode());
     assertTrue(ml1.equals(ml));
 
     assertFalse(ml.equals(null));
diff --git a/utils/InstallAnywhere/Jalview.iap_xml b/utils/InstallAnywhere/Jalview.iap_xml
index a649cb4..20726f5 100755
--- a/utils/InstallAnywhere/Jalview.iap_xml
+++ b/utils/InstallAnywhere/Jalview.iap_xml
@@ -2320,6 +2320,58 @@ and any path to a file to save to the file]]></string>
 						</object>
 					</method>
 					<method name="addElement">
+            <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="9a1f46efeef911a">
+              <property name="belongsToUninstallPhase">
+                <boolean>false</boolean>
+              </property>
+              <property name="rollbackEnabledCancel">
+                <boolean>true</boolean>
+              </property>
+              <property name="rollbackEnabledError">
+                <boolean>true</boolean>
+              </property>
+              <property name="ruleExpression">
+                <string><![CDATA[]]></string>
+              </property>
+              <property name="unixPermissions">
+                <string><![CDATA[664]]></string>
+              </property>
+              <property name="sourceName">
+                <string><![CDATA[VAqua4.jar]]></string>
+              </property>
+              <property name="overrideUnixPermissions">
+                <boolean>false</boolean>
+              </property>
+              <property name="sourcePath">
+                <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+              </property>
+              <property name="shouldUninstall">
+                <boolean>true</boolean>
+              </property>
+              <property name="rollbackEnabledCancel">
+                <boolean>true</boolean>
+              </property>
+              <property name="rollbackEnabledError">
+                <boolean>true</boolean>
+              </property>
+              <property name="destinationName">
+                <string><![CDATA[VAqua4.jar]]></string>
+              </property>
+              <property name="fileSize">
+                <long>1355141</long>
+              </property>
+              <property name="macBinary">
+                <boolean>false</boolean>
+              </property>
+              <property name="targetCheckKind">
+                <int>0</int>
+              </property>
+              <property name="ruleExpression">
+                <string><![CDATA[]]></string>
+              </property>
+            </object>
+          </method>
+          <method name="addElement">
 						<object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1936efeefab93">
 							<property name="belongsToUninstallPhase">
 								<boolean>false</boolean>
@@ -7230,6 +7282,7 @@ and any path to a file to read from that file]]></string>
 										<object refID="24485f8ca673"/>
 										<object refID="24485f8ba674"/>
 										<object refID="24485f8ca674"/>
+										<object refID="9a1f46efeef911a"/>
 										<object class="com.zerog.ia.installer.actions.CreateShortcut" objectID="3cd8e2ffa672">
 											<property name="belongsToUninstallPhase">
 												<boolean>false</boolean>
@@ -7981,6 +8034,7 @@ and any path to a file to read from that file]]></string>
 												<object refID="24485f8ca673"/>
 												<object refID="24485f8ba674"/>
 												<object refID="24485f8ca674"/>
+												<object refID="9a1f46efeef911a"/>
 												<object refID="b1a16838a449"/>
 												<object refID="b1a16839a449"/>
 												<object refID="495aeddb8b3d"/>