From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 10 Jul 2015 05:14:47 +0000 (+0100)
Subject: JAL-1807 explicit imports (jalview.gui)
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=aa91e8c4561c2dd0f18760e18fb0052979733bf8;p=jalview.git

JAL-1807 explicit imports (jalview.gui)
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 68d7397..e656b0f 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -46,6 +46,7 @@ import jalview.commands.RemoveGapColCommand;
 import jalview.commands.RemoveGapsCommand;
 import jalview.commands.SlideSequencesCommand;
 import jalview.commands.TrimRegionCommand;
+import jalview.controller.AlignViewController;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -63,11 +64,13 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
+import jalview.io.AppletFormatAdapter;
 import jalview.io.BioJsHTMLOutput;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.JnetAnnotationMaker;
@@ -84,6 +87,7 @@ import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColour;
 import jalview.schemes.RNAHelicesColourChooser;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.StrandColourScheme;
@@ -94,10 +98,14 @@ import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.WSMenuEntryProviderI;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.rest.RestClient;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
@@ -146,6 +154,8 @@ import javax.swing.JRadioButtonMenuItem;
 import javax.swing.JScrollPane;
 import javax.swing.SwingUtilities;
 
+import ext.vamsas.ServiceHandle;
+
 /**
  * DOCUMENT ME!
  * 
@@ -341,7 +351,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
     }
 
-    avc = new jalview.controller.AlignViewController(this, viewport,
+    avc = new AlignViewController(this, viewport,
             alignPanel);
     if (viewport.getAlignmentConservationAnnotation() == null)
     {
@@ -353,7 +363,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // modifyPID.setEnabled(false);
     }
 
-    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+    String sortby = Cache.getDefault("SORT_ALIGNMENT",
             "No sort");
 
     if (sortby.equals("Id"))
@@ -381,7 +391,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       wrapMenuItem_actionPerformed(null);
     }
 
-    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+    if (Cache.getDefault("SHOW_OVERVIEW", false))
     {
       this.overviewMenuItem_actionPerformed(null);
     }
@@ -705,8 +715,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
   {
     ap.alignFrame = this;
-    avc = new jalview.controller.AlignViewController(this, viewport,
-            alignPanel);
+    avc = new AlignViewController(this, viewport, alignPanel);
 
     alignPanels.add(ap);
 
@@ -828,7 +837,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     purinePyrimidineColour.setEnabled(nucleotide);
     showComplementMenuItem.setText(MessageManager
             .getString(nucleotide ? "label.protein" : "label.nucleotide"));
-    setColourSelected(jalview.bin.Cache.getDefault(
+    setColourSelected(Cache.getDefault(
             nucleotide ? Preferences.DEFAULT_COLOUR_NUC
                     : Preferences.DEFAULT_COLOUR_PROT, "None"));
   }
@@ -894,7 +903,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     listenToViewSelections.setSelected(av.followSelection);
     rnahelicesColour.setEnabled(av.getAlignment().hasRNAStructure());
     rnahelicesColour
-            .setSelected(av.getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+            .setSelected(av.getGlobalColourScheme() instanceof RNAHelicesColour);
     setShowProductsEnabled();
     updateEditMenuBar();
   }
@@ -940,7 +949,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public String getVersion()
   {
-    return jalview.bin.Cache.getProperty("VERSION");
+    return Cache.getProperty("VERSION");
   }
 
   public FeatureRenderer getFeatureRenderer()
@@ -1043,7 +1052,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void save_actionPerformed(ActionEvent e)
   {
     if (fileName == null
-            || (currentFileFormat == null || !jalview.io.FormatAdapter
+            || (currentFileFormat == null || !FormatAdapter
                     .isValidIOFormat(currentFileFormat, true))
             || fileName.startsWith("http"))
     {
@@ -1065,9 +1074,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void saveAs_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS,
-            jalview.io.AppletFormatAdapter.WRITABLE_FNAMES,
+            Cache.getProperty("LAST_DIRECTORY"),
+            AppletFormatAdapter.WRITABLE_EXTENSIONS,
+            AppletFormatAdapter.WRITABLE_FNAMES,
             currentFileFormat, false);
 
     chooser.setFileView(new JalviewFileView());
@@ -1099,10 +1108,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       fileName = chooser.getSelectedFile().getPath();
 
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
+      Cache.setProperty("DEFAULT_FILE_FORMAT",
               currentFileFormat);
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
+      Cache.setProperty("LAST_DIRECTORY", fileName);
       if (currentFileFormat.indexOf(" ") > -1)
       {
         currentFileFormat = currentFileFormat.substring(0,
@@ -1135,7 +1144,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true))
+      if (!AppletFormatAdapter.isValidFormat(format, true))
       {
         warningMessage("Cannot save file " + fileName + " using format "
                 + format, "Alignment output format not supported");
@@ -1201,7 +1210,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   private void warningMessage(String warning, String title)
   {
-    if (new jalview.util.Platform().isHeadless())
+    if (Platform.isHeadless())
     {
       System.err.println("Warning: " + title + "\nWarning: " + warning);
 
@@ -1441,7 +1450,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.load_jalview_annotations"));
@@ -1453,7 +1462,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      Cache.setProperty("LAST_DIRECTORY", choice);
       loadJalviewDataFile(choice, null, null, null);
     }
 
@@ -1883,7 +1892,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     try
     {
-      jalview.gui.Desktop.internalCopy = true;
+      Desktop.internalCopy = true;
       // Its really worth setting the clipboard contents
       // to empty before setting the large StringSelection!!
       Toolkit.getDefaultToolkit().getSystemClipboard()
@@ -3706,9 +3715,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         iSize--;
       }
     }
-    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    if (UserDefinedColours.getUserColourSchemes() != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+      Enumeration userColours = UserDefinedColours
               .getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
@@ -3727,7 +3736,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               radioItem.removeActionListener(radioItem.getActionListeners()[0]);
 
               int option = JOptionPane.showInternalConfirmDialog(
-                      jalview.gui.Desktop.desktop,
+                      Desktop.desktop,
                       MessageManager
                               .getString("label.remove_from_default_list"),
                       MessageManager
@@ -3735,8 +3744,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       JOptionPane.YES_NO_OPTION);
               if (option == JOptionPane.YES_OPTION)
               {
-                jalview.gui.UserDefinedColours
-                        .removeColourFromDefaults(radioItem.getText());
+                UserDefinedColours.removeColourFromDefaults(radioItem
+                        .getText());
                 colourMenu.remove(radioItem);
               }
               else
@@ -4303,7 +4312,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * be submitted for multiple alignment.
    * 
    */
-  public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
+  public AlignmentView gatherSequencesForAlignment()
   {
     // Now, check we have enough sequences
     AlignmentView msa = null;
@@ -4387,7 +4396,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.select_newick_like_tree_file"));
@@ -4398,11 +4407,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-      jalview.io.NewickFile fin = null;
+      Cache.setProperty("LAST_DIRECTORY", choice);
+      NewickFile fin = null;
       try
       {
-        fin = new jalview.io.NewickFile(choice, "File");
+        fin = new NewickFile(choice, "File");
         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
       } catch (Exception ex)
       {
@@ -4575,10 +4584,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               // Add any secondary structure prediction services
               for (int i = 0, j = secstrpr.size(); i < j; i++)
               {
-                final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
-                        .get(i);
-                jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
-                        .getServiceClient(sh);
+                final ServiceHandle sh = (ServiceHandle) secstrpr.get(i);
+                WSMenuEntryProviderI impl = Discoverer.getServiceClient(sh);
                 int p = secstrmenu.getItemCount();
                 impl.attachWSMenuEntry(secstrmenu, me);
                 int q = secstrmenu.getItemCount();
@@ -4705,8 +4712,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // SHmmr test client - still being implemented.
     // DEBUG - alignmentView
 
-    for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
-            .getRestClients())
+    for (RestClient client : RestClient.getRestClients())
     {
       client.attachWSMenuEntry(
               JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
@@ -4716,7 +4722,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   /*
    * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser
-   * chooser = new JalviewFileChooser(jalview.bin.Cache.
+   * chooser = new JalviewFileChooser(Cache.
    * getProperty("LAST_DIRECTORY"));
    * 
    * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export
@@ -4796,7 +4802,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showProducts.setEnabled(showp);
     } catch (Exception e)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .warn("canTranslate threw an exception - please report to help@jalview.org",
                       e);
       return false;
@@ -4911,14 +4917,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
         } catch (Exception e)
         {
-          jalview.bin.Cache.log.error(
+          Cache.log.error(
                   "Exception when finding crossreferences", e);
         } catch (OutOfMemoryError e)
         {
           new OOMWarning("whilst fetching crossreferences", e);
         } catch (Error e)
         {
-          jalview.bin.Cache.log.error("Error when finding crossreferences",
+          Cache.log.error("Error when finding crossreferences",
                   e);
         }
         AlignFrame.this.setProgressBar(MessageManager.formatMessage(
@@ -4939,11 +4945,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // old way
     try
     {
-      return (jalview.analysis.Dna.canTranslate(selection,
+      return (Dna.canTranslate(selection,
               viewport.getViewAsVisibleContigs(true)));
     } catch (Exception e)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .warn("canTranslate threw an exception - please report to help@jalview.org",
                       e);
       return false;
@@ -4965,7 +4971,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       al = dna.translateCdna();
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log.error(
+      Cache.log.error(
               "Exception during translation. Please report this !", ex);
       final String msg = MessageManager
               .getString("label.error_when_translating_sequences_submit_bug_report");
@@ -5029,7 +5035,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public boolean parseFeaturesFile(String file, String type)
   {
     return avc.parseFeaturesFile(file, type,
-            jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+            Cache.getDefault("RELAXEDSEQIDMATCHING", false));
     
   }
 
@@ -5136,12 +5142,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           String file = files.get(i).toString();
           String pdbfn = "";
           String protocol = FormatAdapter.checkProtocol(file);
-          if (protocol == jalview.io.FormatAdapter.FILE)
+          if (protocol == FormatAdapter.FILE)
           {
             File fl = new File(file);
             pdbfn = fl.getName();
           }
-          else if (protocol == jalview.io.FormatAdapter.URL)
+          else if (protocol == FormatAdapter.URL)
           {
             URL url = new URL(file);
             pdbfn = url.getFile();
@@ -5280,7 +5286,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (protocol == null)
       {
-        protocol = jalview.io.FormatAdapter.checkProtocol(file);
+        protocol = FormatAdapter.checkProtocol(file);
       }
       // if the file isn't identified, or not positively identified as some
       // other filetype (PFAM is default unidentified alignment file type) then
@@ -5346,8 +5352,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (format.equalsIgnoreCase("JnetFile"))
           {
-            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
-                    file, protocol);
+            JPredFile predictions = new JPredFile(file, protocol);
             new JnetAnnotationMaker();
             JnetAnnotationMaker.add_annotation(predictions,
                     viewport.getAlignment(), 0, false);
@@ -5364,9 +5369,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
              * if (format.equalsIgnoreCase("PDB")) {
              * 
              * String pdbfn = ""; // try to match up filename with sequence id
-             * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl =
+             * try { if (protocol == FormatAdapter.FILE) { File fl =
              * new File(file); pdbfn = fl.getName(); } else if (protocol ==
-             * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn =
+             * FormatAdapter.URL) { URL url = new URL(file); pdbfn =
              * url.getFile(); } } catch (Exception e) { } ; if (assocSeq ==
              * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport
              * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) {
@@ -5491,8 +5496,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   protected void extractScores_actionPerformed(ActionEvent e)
   {
-    ParseProperties pp = new jalview.analysis.ParseProperties(
-            viewport.getAlignment());
+    ParseProperties pp = new ParseProperties(viewport.getAlignment());
     // TODO: verify regex and introduce GUI dialog for version 2.5
     // if (pp.getScoresFromDescription("col", "score column ",
     // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
@@ -5602,7 +5606,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           @Override
           public void run()
           {
-            new jalview.ws.DBRefFetcher(alignPanel.av
+            new DBRefFetcher(alignPanel.av
                     .getSequenceSelection(), alignPanel.alignFrame)
                     .fetchDBRefs(false);
           }
@@ -5620,7 +5624,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         final jalview.ws.SequenceFetcher sf = SequenceFetcher
                 .getSequenceFetcherSingleton(me);
-        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        SwingUtilities.invokeLater(new Runnable()
         {
           @Override
           public void run()
@@ -5672,7 +5676,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       @Override
                       public void run()
                       {
-                        new jalview.ws.DBRefFetcher(alignPanel.av
+                        new DBRefFetcher(alignPanel.av
                                 .getSequenceSelection(),
                                 alignPanel.alignFrame, dassource)
                                 .fetchDBRefs(false);
@@ -5705,7 +5709,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       @Override
                       public void run()
                       {
-                        new jalview.ws.DBRefFetcher(alignPanel.av
+                        new DBRefFetcher(alignPanel.av
                                 .getSequenceSelection(),
                                 alignPanel.alignFrame, dassource)
                                 .fetchDBRefs(false);
@@ -5748,7 +5752,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         @Override
                         public void run()
                         {
-                          new jalview.ws.DBRefFetcher(alignPanel.av
+                          new DBRefFetcher(alignPanel.av
                                   .getSequenceSelection(),
                                   alignPanel.alignFrame, dassrc)
                                   .fetchDBRefs(false);
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index c18c989..062fa82 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -573,7 +573,7 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public void sendSelection()
   {
-    jalview.structure.StructureSelectionManager
+    StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance).sendSelection(
                     new SequenceGroup(getSelectionGroup()),
                     new ColumnSelection(getColumnSelection()), this);
@@ -900,7 +900,7 @@ public class AlignViewport extends AlignmentViewport implements
 
     try
     {
-      newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
+      newAlignFrame.setMaximum(Cache.getDefault(
               "SHOW_FULLSCREEN",
               false));
     } catch (java.beans.PropertyVetoException ex)
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ad7e75c..4c66214 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -29,10 +29,12 @@ import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.HTMLOutput;
 import jalview.jbgui.GAlignmentPanel;
 import jalview.math.AlignmentDimension;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
@@ -1237,7 +1239,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     return idwidth.intValue() + 4;
   }
 
-  void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
+  void makeAlignmentImage(ImageMaker.TYPE type, File file)
   {
     long progress = System.currentTimeMillis();
     headless = (System.getProperty("java.awt.headless") != null && System
@@ -1253,14 +1255,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
       AlignmentDimension aDimension = getAlignmentDimension();
       try
       {
-        jalview.util.ImageMaker im;
+        ImageMaker im;
         final String imageAction, imageTitle;
-        if (type == jalview.util.ImageMaker.TYPE.PNG)
+        if (type == ImageMaker.TYPE.PNG)
         {
           imageAction = "Create PNG image from alignment";
           imageTitle = null;
         }
-        else if (type == jalview.util.ImageMaker.TYPE.EPS)
+        else if (type == ImageMaker.TYPE.EPS)
         {
           imageAction = "Create EPS file from alignment";
           imageTitle = alignFrame.getTitle();
@@ -1271,7 +1273,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           imageTitle = alignFrame.getTitle();
         }
 
-        im = new jalview.util.ImageMaker(this, type, imageAction,
+        im = new ImageMaker(this, type, imageAction,
                 aDimension.getWidth(), aDimension.getHeight(), file,
                 imageTitle);
         if (av.getWrapAlignment())
@@ -1357,7 +1359,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void makeEPS(File epsFile)
   {
-    makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
+    makeAlignmentImage(ImageMaker.TYPE.EPS, epsFile);
   }
 
   /**
@@ -1365,12 +1367,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void makePNG(File pngFile)
   {
-    makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
+    makeAlignmentImage(ImageMaker.TYPE.PNG, pngFile);
   }
 
   public void makeSVG(File svgFile)
   {
-    makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
+    makeAlignmentImage(ImageMaker.TYPE.SVG, svgFile);
   }
   public void makePNGImageMap(File imgMapFile, String imageName)
   {
@@ -1390,7 +1392,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 .getAlignment().getWidth(), g, gSize, f, fSize, sy;
         StringBuffer text = new StringBuffer();
         PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
-        out.println(jalview.io.HTMLOutput.getImageMapHTML());
+        out.println(HTMLOutput.getImageMapHTML());
         out.println("<img src=\"" + imageName
                 + "\" border=\"0\" usemap=\"#Map\" >"
                 + "<map name=\"Map\">");
@@ -1566,7 +1568,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.RemoveComponent(this);
     if (av != null)
     {
-      jalview.structure.StructureSelectionManager ssm = av
+      StructureSelectionManager ssm = av
               .getStructureSelectionManager();
       ssm.removeStructureViewerListener(getSeqPanel(), null);
       ssm.removeSelectionListener(getSeqPanel());
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index c8dd889..37205a7 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.bin.Cache;
+import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
@@ -449,7 +450,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
             && getCurrentAnnotation().threshold == null)
     {
       getCurrentAnnotation()
-              .setThreshold(new jalview.datamodel.GraphLine(
+              .setThreshold(
+                      new GraphLine(
                       (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
                       "Threshold", Color.black));
     }
diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index e87be35..62a6f96 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -23,6 +23,7 @@ package jalview.gui;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.GraphLine;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
@@ -387,7 +388,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       {
         getCurrentAnnotation()
                 .setThreshold(
-                        new jalview.datamodel.GraphLine(
+                        new GraphLine(
                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
                                 "Threshold", Color.black));
       }
diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 9b25388..b67a2f7 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.io.AnnotationFile;
 import jalview.io.FeaturesFile;
@@ -117,7 +118,7 @@ public class AnnotationExporter extends JPanel
   public void toFile_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(features ? MessageManager.getString("label.save_features_to_file")
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index fad9dcd..13f2723 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -20,6 +20,18 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Font;
@@ -50,16 +62,6 @@ import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
 
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
-import jalview.util.MessageManager;
-
 /**
  * DOCUMENT ME!
  * 
@@ -862,8 +864,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     if (dseqs[0] == null)
     {
       dseqs[0] = new Sequence(sq);
-      dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
+      dseqs[0].setSequence(AlignSeq.extractGaps(
+              Comparison.GapChars, sq.getSequenceAsString()));
 
       sq.setDatasetSequence(dseqs[0]);
     }
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 97752f2..3b405d8 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -27,6 +27,7 @@ import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.AlphaComposite;
 import java.awt.Color;
@@ -139,7 +140,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   public AnnotationPanel(AlignmentPanel ap)
   {
 
-    MAC = jalview.util.Platform.isAMac();
+    MAC = Platform.isAMac();
 
     ToolTipManager.sharedInstance().registerComponent(this);
     ToolTipManager.sharedInstance().setInitialDelay(0);
diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 21c91d8..6551228 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -32,7 +32,7 @@ public abstract class AnnotationRowFilter extends JPanel
 
   protected boolean enableSeqAss = false;
 
-  private jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  private AlignmentAnnotation currentAnnotation;
 
   protected boolean adjusting = false;
 
@@ -365,13 +365,13 @@ public abstract class AnnotationRowFilter extends JPanel
   }
 
 
-  public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
+  public AlignmentAnnotation getCurrentAnnotation()
   {
     return currentAnnotation;
   }
 
   public void setCurrentAnnotation(
-          jalview.datamodel.AlignmentAnnotation currentAnnotation)
+          AlignmentAnnotation currentAnnotation)
   {
     this.currentAnnotation = currentAnnotation;
   }
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index a16ea68..900d3be 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -40,8 +40,11 @@ import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.ZappoColourScheme;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -147,7 +150,7 @@ public class AppJmol extends StructureViewerBase
     this.setBounds(bounds);
     initMenus();
     setViewId(viewid);
-    // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
+    // Desktop.addInternalFrame(this, "Loading File",
     // bounds.width,bounds.height);
 
     this.addInternalFrameListener(new InternalFrameAdapter()
@@ -477,7 +480,7 @@ public class AppJmol extends StructureViewerBase
     // TODO: consider waiting until the structure/view is fully loaded before
     // displaying
     this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
-    jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
+    Desktop.addInternalFrame(this, jmb.getViewerTitle(),
             getBounds().width, getBounds().height);
     if (scriptWindow == null)
     {
@@ -595,7 +598,7 @@ public class AppJmol extends StructureViewerBase
       String[] curfiles = jmb.getPdbFile(); // files currently in viewer
       // TODO: replace with reference fetching/transfer code (validate PDBentry
       // as a DBRef?)
-      jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
+      Pdb pdbclient = new Pdb();
       for (int pi = 0; pi < jmb.getPdbCount(); pi++)
       {
         String file = jmb.getPdbEntry(pi).getFile();
@@ -765,7 +768,7 @@ public class AppJmol extends StructureViewerBase
   public void pdbFile_actionPerformed(ActionEvent actionEvent)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
@@ -815,7 +818,7 @@ public class AppJmol extends StructureViewerBase
   @Override
   public void viewMapping_actionPerformed(ActionEvent actionEvent)
   {
-    jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
     try
     {
       cap.appendText(jmb.printMappings());
@@ -827,7 +830,7 @@ public class AppJmol extends StructureViewerBase
       cap.dispose();
       return;
     }
-    jalview.gui.Desktop.addInternalFrame(cap,
+    Desktop.addInternalFrame(cap,
             MessageManager.getString("label.pdb_sequence_mapping"), 550,
             600);
   }
@@ -835,40 +838,38 @@ public class AppJmol extends StructureViewerBase
   @Override
   public void eps_actionPerformed(ActionEvent e)
   {
-    makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
+    makePDBImage(ImageMaker.TYPE.EPS);
   }
 
   @Override
   public void png_actionPerformed(ActionEvent e)
   {
-    makePDBImage(jalview.util.ImageMaker.TYPE.PNG);
+    makePDBImage(ImageMaker.TYPE.PNG);
   }
 
-  void makePDBImage(jalview.util.ImageMaker.TYPE type)
+  void makePDBImage(ImageMaker.TYPE type)
   {
     int width = getWidth();
     int height = getHeight();
 
-    jalview.util.ImageMaker im;
+    ImageMaker im;
 
-    if (type == jalview.util.ImageMaker.TYPE.PNG)
+    if (type == ImageMaker.TYPE.PNG)
     {
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.PNG,
+      im = new ImageMaker(this, ImageMaker.TYPE.PNG,
               "Make PNG image from view", width, height, null, null);
     }
-    else if (type == jalview.util.ImageMaker.TYPE.EPS)
+    else if (type == ImageMaker.TYPE.EPS)
     {
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.EPS,
+      im = new ImageMaker(this, ImageMaker.TYPE.EPS,
               "Make EPS file from view", width, height, null,
               this.getTitle());
     }
     else
     {
 
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+      im = new ImageMaker(this, ImageMaker.TYPE.SVG,
+              "Make SVG file from PCA",
               width, height, null, this.getTitle());
     }
 
@@ -1007,7 +1008,7 @@ public class AppJmol extends StructureViewerBase
   {
     try
     {
-      jalview.util.BrowserLauncher
+      BrowserLauncher
               .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
     } catch (Exception ex)
     {
diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 99bcff4..c6836d3 100644
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -252,7 +252,7 @@ public class AppVarna extends JInternalFrame implements SelectionListener,
     getContentPane().add(split, BorderLayout.CENTER);
 
     varnaPanel.addSelectionListener(this);
-    jalview.gui.Desktop.addInternalFrame(this, "", getBounds().width,
+    Desktop.addInternalFrame(this, "", getBounds().width,
             getBounds().height);
     this.pack();
     showPanel(true);
diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index a3e695a..8b4c281 100644
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -252,9 +252,9 @@ public class BlogReader extends JPanel
     _channelModel = new ChannelListModel();
     // Construct our jalview news channel
     Channel chan = new Channel();
-    chan.setURL(jalview.bin.Cache.getDefault(
+    chan.setURL(Cache.getDefault(
             "JALVIEW_NEWS_RSS",
-            jalview.bin.Cache.getDefault("www.jalview.org",
+            Cache.getDefault("www.jalview.org",
                     "http://www.jalview.org") + "/feeds/desktop/rss"));
     loadLastM();
     _channelModel.addChannel(chan);
@@ -419,10 +419,10 @@ public class BlogReader extends JPanel
       }
       if (lastDate != null)
       {
-        jalview.bin.Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED",
+        Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED",
                 lastDate);
-        jalview.bin.Cache.log.debug("Saved last read date as "
-                + jalview.bin.Cache.date_format.format(lastDate));
+        Cache.log.debug("Saved last read date as "
+                + Cache.date_format.format(lastDate));
 
       }
     }
@@ -743,8 +743,8 @@ public class BlogReader extends JPanel
   {
     // this tests the detection of new news based on the last read date stored
     // in jalview properties
-    jalview.bin.Cache.loadProperties(null);
-    jalview.bin.Cache.initLogger();
+    Cache.loadProperties(null);
+    Cache.initLogger();
     // test will advance read date each time
     Calendar today = Calendar.getInstance(), lastread = Calendar
             .getInstance();
@@ -755,7 +755,7 @@ public class BlogReader extends JPanel
               lastread.getTime());
       BlogReader me = new BlogReader();
       System.out.println("Set last date to "
-              + jalview.bin.Cache.date_format.format(lastread.getTime()));
+              + Cache.date_format.format(lastread.getTime()));
       if (me.isNewsNew())
       {
         Cache.log.debug("There is news to read.");
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index f644e95..b81de3d 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -20,6 +20,32 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
+
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
@@ -50,31 +76,6 @@ import javax.swing.event.InternalFrameEvent;
 import javax.swing.event.MenuEvent;
 import javax.swing.event.MenuListener;
 
-import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.AppletFormatAdapter;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.dbsources.Pdb;
-
 /**
  * GUI elements for handling an external chimera display
  * 
@@ -601,7 +602,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   void initChimera()
   {
     jmb.setFinishedInit(false);
-    jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
+    Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true),
             getBounds().width, getBounds().height);
 
     if (!jmb.launchChimera())
@@ -995,7 +996,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   public void pdbFile_actionPerformed(ActionEvent actionEvent)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
@@ -1044,7 +1045,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   @Override
   public void viewMapping_actionPerformed(ActionEvent actionEvent)
   {
-    jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+    CutAndPasteTransfer cap = new CutAndPasteTransfer();
     try
     {
       cap.appendText(jmb.printMappings());
@@ -1056,7 +1057,7 @@ public class ChimeraViewFrame extends StructureViewerBase
       cap.dispose();
       return;
     }
-    jalview.gui.Desktop.addInternalFrame(cap,
+    Desktop.addInternalFrame(cap,
             MessageManager.getString("label.pdb_sequence_mapping"), 550,
             600);
   }
@@ -1206,7 +1207,7 @@ public class ChimeraViewFrame extends StructureViewerBase
   {
     try
     {
-      jalview.util.BrowserLauncher
+      BrowserLauncher
               .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide");
     } catch (Exception ex)
     {
diff --git a/src/jalview/gui/CutAndPasteHtmlTransfer.java b/src/jalview/gui/CutAndPasteHtmlTransfer.java
index ea5c75e..545460d 100644
--- a/src/jalview/gui/CutAndPasteHtmlTransfer.java
+++ b/src/jalview/gui/CutAndPasteHtmlTransfer.java
@@ -20,20 +20,29 @@
  */
 package jalview.gui;
 
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.event.*;
+import jalview.bin.Cache;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GCutAndPasteHtmlTransfer;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.StringSelection;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.MouseEvent;
 import java.io.StringWriter;
 
-import javax.swing.*;
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
 import javax.swing.event.HyperlinkEvent;
-import javax.swing.event.HyperlinkListener;
 import javax.swing.event.HyperlinkEvent.EventType;
-
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
+import javax.swing.event.HyperlinkListener;
 
 /**
  * Cut'n'paste files into the desktop See JAL-1105
@@ -138,7 +147,7 @@ public class CutAndPasteHtmlTransfer extends GCutAndPasteHtmlTransfer
   public void save_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index 979d1aa..2fc44a5 100644
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -24,6 +24,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeaturesDisplayedI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
@@ -123,7 +124,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
   public void save_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
 
     chooser.setAcceptAllFileFilterUsed(false);
     chooser.setFileView(new JalviewFileView());
@@ -269,7 +270,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
         try
         {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+          af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
                   false));
         } catch (Exception ex)
         {
diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java
index fab4cb3..f781473 100644
--- a/src/jalview/gui/DasSourceBrowser.java
+++ b/src/jalview/gui/DasSourceBrowser.java
@@ -20,6 +20,13 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
+import jalview.jbgui.GDasSourceBrowser;
+import jalview.util.MessageManager;
+import jalview.util.TableSorter;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+
 import java.awt.BorderLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.MouseAdapter;
@@ -46,12 +53,6 @@ import org.biodas.jdas.schema.sources.COORDINATES;
 import org.biodas.jdas.schema.sources.PROP;
 import org.biodas.jdas.schema.sources.VERSION;
 
-import jalview.jbgui.GDasSourceBrowser;
-import jalview.util.MessageManager;
-import jalview.util.TableSorter;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-
 public class DasSourceBrowser extends GDasSourceBrowser implements
         Runnable, ListSelectionListener
 {
@@ -63,7 +64,7 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
   {
     fs = featureSettings;
     // TODO DasSourceRegistryProvider API
-    sourceRegistry = jalview.bin.Cache.getDasSourceRegistry();
+    sourceRegistry = Cache.getDasSourceRegistry();
     String registry = sourceRegistry.getDasRegistryURL();
 
     registryURL.setText(registry);
@@ -360,7 +361,7 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
 
   public void refresh_actionPerformed(ActionEvent e)
   {
-    saveProperties(jalview.bin.Cache.applicationProperties);
+    saveProperties(Cache.applicationProperties);
 
     Thread worker = new Thread(this);
     worker.start();
@@ -683,7 +684,7 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
 
   void setSelectedFromProperties()
   {
-    String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
+    String active = Cache.getDefault("DAS_ACTIVE_SOURCE",
             "uniprot");
     StringTokenizer st = new StringTokenizer(active, "\t");
     selectedSources = new Vector();
@@ -707,11 +708,11 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
   {
     if (registryURL.getText() == null || registryURL.getText().length() < 1)
     {
-      properties.remove(jalview.bin.Cache.DAS_REGISTRY_URL);
+      properties.remove(Cache.DAS_REGISTRY_URL);
     }
     else
     {
-      properties.setProperty(jalview.bin.Cache.DAS_REGISTRY_URL,
+      properties.setProperty(Cache.DAS_REGISTRY_URL,
               registryURL.getText());
     }
 
@@ -724,11 +725,11 @@ public class DasSourceBrowser extends GDasSourceBrowser implements
       }
     }
 
-    properties.setProperty(jalview.bin.Cache.DAS_ACTIVE_SOURCE,
+    properties.setProperty(Cache.DAS_ACTIVE_SOURCE,
             sb.toString());
 
     String sourceprop = sourceRegistry.getLocalSourceString();
-    properties.setProperty(jalview.bin.Cache.DAS_LOCAL_SOURCE, sourceprop);
+    properties.setProperty(Cache.DAS_LOCAL_SOURCE, sourceprop);
   }
 
   class DASTableModel extends AbstractTableModel
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 6a95363..2228725 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -22,15 +22,19 @@ package jalview.gui;
 
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.StructureSelectionManagerProvider;
 import jalview.bin.Cache;
+import jalview.io.AppletFormatAdapter;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
+import jalview.jbgui.GDesktop;
 import jalview.jbgui.GSplitFrame;
 import jalview.jbgui.GStructureViewer;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.BrowserLauncher;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
@@ -107,9 +111,10 @@ import javax.swing.event.MenuListener;
  * @author $author$
  * @version $Revision: 1.155 $
  */
-public class Desktop extends jalview.jbgui.GDesktop implements
-        DropTargetListener, ClipboardOwner, IProgressIndicator,
-        jalview.api.StructureSelectionManagerProvider
+public class Desktop extends GDesktop implements
+ DropTargetListener,
+        ClipboardOwner, IProgressIndicator,
+        StructureSelectionManagerProvider
 {
 
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
@@ -300,11 +305,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     doVamsasClientCheck();
     doGroovyCheck();
     doConfigureStructurePrefs();
-    setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
+    setTitle("Jalview " + Cache.getProperty("VERSION"));
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
-    boolean selmemusage = jalview.bin.Cache.getDefault("SHOW_MEMUSAGE",
+    boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE",
             false);
-    boolean showjconsole = jalview.bin.Cache.getDefault(
+    boolean showjconsole = Cache.getDefault(
             "SHOW_JAVA_CONSOLE", false);
     desktop = new MyDesktopPane(selmemusage);
     showMemusage.setSelected(selmemusage);
@@ -336,11 +341,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     jconsole = new Console(this, showjconsole);
     // add essential build information
     jconsole.setHeader("Jalview Version: "
-            + jalview.bin.Cache.getProperty("VERSION") + "\n"
+            + Cache.getProperty("VERSION") + "\n"
             + "Jalview Installation: "
-            + jalview.bin.Cache.getDefault("INSTALLATION", "unknown")
+            + Cache.getDefault("INSTALLATION", "unknown")
             + "\n" + "Build Date: "
-            + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown") + "\n"
+            + Cache.getDefault("BUILD_DATE", "unknown") + "\n"
             + "Java version: " + System.getProperty("java.version") + "\n"
             + System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
@@ -408,10 +413,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         Cache.log.debug("Filechooser init thread started.");
         JalviewFileChooser chooser = new JalviewFileChooser(
-                jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-                jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
-                jalview.io.AppletFormatAdapter.READABLE_FNAMES,
-                jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+                Cache.getProperty("LAST_DIRECTORY"),
+                AppletFormatAdapter.READABLE_EXTENSIONS,
+                AppletFormatAdapter.READABLE_FNAMES,
+                Cache.getProperty("DEFAULT_FILE_FORMAT"));
         Cache.log.debug("Filechooser init thread finished.");
       }
     }).start();
@@ -436,13 +441,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     // configure services
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(this);
-    if (jalview.bin.Cache.getDefault(Preferences.ADD_SS_ANN, true))
+    if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
     {
-      ssm.setAddTempFacAnnot(jalview.bin.Cache.getDefault(
+      ssm.setAddTempFacAnnot(Cache.getDefault(
               Preferences.ADD_TEMPFACT_ANN, true));
-      ssm.setProcessSecondaryStructure(jalview.bin.Cache.getDefault(
+      ssm.setProcessSecondaryStructure(Cache.getDefault(
               Preferences.STRUCT_FROM_PDB, true));
-      ssm.setSecStructServices(jalview.bin.Cache.getDefault(
+      ssm.setSecStructServices(Cache.getDefault(
               Preferences.USE_RNAVIEW, true));
     }
     else
@@ -513,26 +518,26 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     // TODO: lock aspect ratio for scaling desktop Bug #0058199
     Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
-    String x = jalview.bin.Cache.getProperty(windowName + "SCREEN_X");
-    String y = jalview.bin.Cache.getProperty(windowName + "SCREEN_Y");
-    String width = jalview.bin.Cache.getProperty(windowName
+    String x = Cache.getProperty(windowName + "SCREEN_X");
+    String y = Cache.getProperty(windowName + "SCREEN_Y");
+    String width = Cache.getProperty(windowName
             + "SCREEN_WIDTH");
-    String height = jalview.bin.Cache.getProperty(windowName
+    String height = Cache.getProperty(windowName
             + "SCREEN_HEIGHT");
     if ((x != null) && (y != null) && (width != null) && (height != null))
     {
       int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer
               .parseInt(width), ih = Integer.parseInt(height);
-      if (jalview.bin.Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
+      if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
       {
         // attempt #1 - try to cope with change in screen geometry - this
         // version doesn't preserve original jv aspect ratio.
         // take ratio of current screen size vs original screen size.
         double sw = ((1f * screenSize.width) / (1f * Integer
-                .parseInt(jalview.bin.Cache
+                .parseInt(Cache
                         .getProperty("SCREENGEOMETRY_WIDTH"))));
         double sh = ((1f * screenSize.height) / (1f * Integer
-                .parseInt(jalview.bin.Cache
+                .parseInt(Cache
                         .getProperty("SCREENGEOMETRY_HEIGHT"))));
         // rescale the bounds depending upon the current screen geometry.
         ix = (int) (ix * sw);
@@ -541,17 +546,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         ih = (int) (ih * sh);
         while (ix >= screenSize.width)
         {
-          jalview.bin.Cache.log
+          Cache.log
                   .debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
           ix -= screenSize.width;
         }
         while (iy >= screenSize.height)
         {
-          jalview.bin.Cache.log
+          Cache.log
                   .debug("Window geometry location recall error: shifting vertical to within screenbounds.");
           iy -= screenSize.height;
         }
-        jalview.bin.Cache.log.debug("Got last known dimensions for "
+        Cache.log.debug("Got last known dimensions for "
                 + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
                 + " height:" + ih);
       }
@@ -563,7 +568,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   private void doVamsasClientCheck()
   {
-    if (jalview.bin.Cache.vamsasJarsPresent())
+    if (Cache.vamsasJarsPresent())
     {
       setupVamsasDisconnectedGui();
       VamsasMenu.setVisible(true);
@@ -991,10 +996,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-            jalview.io.AppletFormatAdapter.READABLE_EXTENSIONS,
-            jalview.io.AppletFormatAdapter.READABLE_FNAMES,
-            jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+            Cache.getProperty("LAST_DIRECTORY"),
+            AppletFormatAdapter.READABLE_EXTENSIONS,
+            AppletFormatAdapter.READABLE_FNAMES,
+            Cache.getProperty("DEFAULT_FILE_FORMAT"));
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
@@ -1006,7 +1011,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+      Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
       String format = null;
@@ -1060,7 +1065,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     history.setEditable(true);
     history.addItem("http://www.");
 
-    String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");
+    String historyItems = Cache.getProperty("RECENT_URL");
 
     StringTokenizer st;
 
@@ -1146,9 +1151,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void quit()
   {
     Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
-    jalview.bin.Cache
+    Cache
             .setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
-    jalview.bin.Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height
+    Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height
             + "");
     storeLastKnownDimensions("", new Rectangle(getBounds().x,
             getBounds().y, getWidth(), getHeight()));
@@ -1173,14 +1178,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   private void storeLastKnownDimensions(String string, Rectangle jc)
   {
-    jalview.bin.Cache.log.debug("Storing last known dimensions for "
+    Cache.log.debug("Storing last known dimensions for "
             + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
             + " height:" + jc.height);
 
-    jalview.bin.Cache.setProperty(string + "SCREEN_X", jc.x + "");
-    jalview.bin.Cache.setProperty(string + "SCREEN_Y", jc.y + "");
-    jalview.bin.Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
-    jalview.bin.Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
+    Cache.setProperty(string + "SCREEN_X", jc.x + "");
+    Cache.setProperty(string + "SCREEN_Y", jc.y + "");
+    Cache.setProperty(string + "SCREEN_WIDTH", jc.width + "");
+    Cache.setProperty(string + "SCREEN_HEIGHT", jc.height + "");
   }
 
   /**
@@ -1211,9 +1216,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (shortv)
     {
       message.append("<h1><strong>Version: "
-              + jalview.bin.Cache.getProperty("VERSION") + "</strong></h1>");
+              + Cache.getProperty("VERSION") + "</strong></h1>");
       message.append("<strong>Last Updated: <em>"
-              + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown")
+              + Cache.getDefault("BUILD_DATE", "unknown")
               + "</em></strong>");
 
     }
@@ -1221,21 +1226,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
 
       message.append("<strong>Version "
-              + jalview.bin.Cache.getProperty("VERSION")
+              + Cache.getProperty("VERSION")
               + "; last updated: "
-              + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+              + Cache.getDefault("BUILD_DATE", "unknown"));
     }
 
-    if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals(
+    if (Cache.getDefault("LATEST_VERSION", "Checking").equals(
             "Checking"))
     {
       message.append("<br>...Checking latest version...</br>");
     }
-    else if (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
-            .equals(jalview.bin.Cache.getProperty("VERSION")))
+    else if (!Cache.getDefault("LATEST_VERSION", "Checking")
+            .equals(Cache.getProperty("VERSION")))
     {
       boolean red = false;
-      if (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
+      if (Cache.getProperty("VERSION").toLowerCase()
               .indexOf("automated build") == -1)
       {
         red = true;
@@ -1245,10 +1250,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
 
       message.append("<br>!! Version "
-              + jalview.bin.Cache.getDefault("LATEST_VERSION",
+              + Cache.getDefault("LATEST_VERSION",
                       "..Checking..")
               + " is available for download from "
-              + jalview.bin.Cache.getDefault("www.jalview.org",
+              + Cache.getDefault("www.jalview.org",
                       "http://www.jalview.org") + " !!");
       if (red)
       {
@@ -1256,7 +1261,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     }
     message.append("<br>Authors:  "
-            + jalview.bin.Cache
+            + Cache
                     .getDefault("AUTHORFNAMES",
                             "The Jalview Authors (See AUTHORS file for current list)")
             + "<br><br>Development managed by The Barton Group, University of Dundee, Scotland, UK.<br>"
@@ -1329,9 +1334,9 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   protected void garbageCollect_actionPerformed(ActionEvent e)
   {
     // We simply collect the garbage
-    jalview.bin.Cache.log.debug("Collecting garbage...");
+    Cache.log.debug("Collecting garbage...");
     System.gc();
-    jalview.bin.Cache.log.debug("Finished garbage collection.");
+    Cache.log.debug("Finished garbage collection.");
   }
 
   /*
@@ -1471,7 +1476,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void saveState_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "jvp" }, new String[]
             { "Jalview Project" }, "Jalview Project");
 
@@ -1494,7 +1499,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           setProgressBar(MessageManager.formatMessage(
                   "label.saving_jalview_project", new Object[]
                   { choice.getName() }), choice.hashCode());
-          jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+          Cache.setProperty("LAST_DIRECTORY",
                   choice.getParent());
           // TODO catch and handle errors for savestate
           // TODO prevent user from messing with the Desktop whilst we're saving
@@ -1542,7 +1547,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void loadState_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "jvp", "jar" }, new String[]
             { "Jalview Project", "Jalview Project (old)" },
             "Jalview Project");
@@ -1556,7 +1561,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       final File selectedFile = chooser.getSelectedFile();
       setProjectFile(selectedFile);
       final String choice = selectedFile.getAbsolutePath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY",
+      Cache.setProperty("LAST_DIRECTORY",
               selectedFile.getParent());
       new Thread(new Runnable()
       {
@@ -1839,7 +1844,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   }
 
-  jalview.gui.VamsasApplication v_client = null;
+  VamsasApplication v_client = null;
 
   public void vamsasImport_actionPerformed(ActionEvent e)
   {
@@ -1847,7 +1852,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     {
       // Load and try to start a session.
       JalviewFileChooser chooser = new JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+              Cache.getProperty("LAST_DIRECTORY"));
 
       chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(MessageManager
@@ -1877,13 +1882,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     }
     else
     {
-      jalview.bin.Cache.log
+      Cache.log
               .error("Implementation error - load session from a running session is not supported.");
     }
   }
 
   /**
-   * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+   * import file into a new vamsas session (uses VamsasApplication)
    * 
    * @param file
    * @return true if import was a success and a session was started.
@@ -1894,7 +1899,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (v_client != null)
     {
 
-      jalview.bin.Cache.log
+      Cache.log
               .error("Implementation error - load session from a running session is not supported.");
       return false;
     }
@@ -1914,11 +1919,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
       bis.close();
       fos.close();
-      v_client = new jalview.gui.VamsasApplication(this, file,
+      v_client = new VamsasApplication(this, file,
               url.toExternalForm());
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log.error(
+      Cache.log.error(
               "Failed to create new vamsas session from contents of URL "
                       + url, ex);
       return false;
@@ -1929,7 +1934,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   }
 
   /**
-   * import file into a new vamsas session (uses jalview.gui.VamsasApplication)
+   * import file into a new vamsas session (uses VamsasApplication)
    * 
    * @param file
    * @return true if import was a success and a session was started.
@@ -1939,7 +1944,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (v_client != null)
     {
 
-      jalview.bin.Cache.log
+      Cache.log
               .error("Implementation error - load session from a running session is not supported.");
       return false;
     }
@@ -1949,13 +1954,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             { file.getName() }), file.hashCode());
     try
     {
-      v_client = new jalview.gui.VamsasApplication(this, file, null);
+      v_client = new VamsasApplication(this, file, null);
     } catch (Exception ex)
     {
       setProgressBar(MessageManager.formatMessage(
               "status.importing_vamsas_session_from", new Object[]
               { file.getName() }), file.hashCode());
-      jalview.bin.Cache.log.error(
+      Cache.log.error(
               "New vamsas session from existing session file failed:", ex);
       return false;
     }
@@ -1993,7 +1998,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       // Start a session.
       // we just start a default session for moment.
       /*
-       * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+       * JalviewFileChooser chooser = new JalviewFileChooser(Cache.
        * getProperty("LAST_DIRECTORY"));
        * 
        * chooser.setFileView(new JalviewFileView());
@@ -2003,7 +2008,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
        * int value = chooser.showOpenDialog(this);
        * 
        * if (value == JalviewFileChooser.APPROVE_OPTION) { v_client = new
-       * jalview.gui.VamsasApplication(this, chooser.getSelectedFile());
+       * VamsasApplication(this, chooser.getSelectedFile());
        */
       v_client = new VamsasApplication(this);
       setupVamsasConnectedGui();
@@ -2054,13 +2059,13 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         sess = VamsasApplication.getSessionList();
       } catch (Exception e)
       {
-        jalview.bin.Cache.log.warn(
+        Cache.log.warn(
                 "Problem getting current sessions list.", e);
         sess = null;
       }
       if (sess != null)
       {
-        jalview.bin.Cache.log.debug("Got current sessions list: "
+        Cache.log.debug("Got current sessions list: "
                 + sess.length + " entries.");
         VamsasStMenu.removeAll();
         for (int i = 0; i < sess.length; i++)
@@ -2102,7 +2107,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
       else
       {
-        jalview.bin.Cache.log.debug("No current vamsas sessions.");
+        Cache.log.debug("No current vamsas sessions.");
         VamsasStMenu.removeAll();
         VamsasStMenu.setVisible(false);
       }
@@ -2119,7 +2124,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (v_client != null)
     {
       JalviewFileChooser chooser = new JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+              Cache.getProperty("LAST_DIRECTORY"), new String[]
               { "vdj" }, // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
               new String[]
               { "Vamsas Document" }, "Vamsas Document");
@@ -2136,7 +2141,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         JPanel progpanel = addProgressPanel(MessageManager.formatMessage(
                 "label.saving_vamsas_doc", new Object[]
                 { choice.getName() }));
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+        Cache.setProperty("LAST_DIRECTORY", choice.getParent());
         String warnmsg = null;
         String warnttl = null;
         try
@@ -2146,14 +2151,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           warnttl = "Serious Problem saving Vamsas Document";
           warnmsg = ex.toString();
-          jalview.bin.Cache.log.error("Error Whilst saving document to "
+          Cache.log.error("Error Whilst saving document to "
                   + choice, ex);
 
         } catch (Exception ex)
         {
           warnttl = "Problem saving Vamsas Document.";
           warnmsg = ex.toString();
-          jalview.bin.Cache.log.warn("Exception Whilst saving document to "
+          Cache.log.warn("Exception Whilst saving document to "
                   + choice, ex);
 
         }
@@ -2178,7 +2183,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
    */
   public void setVamsasUpdate(boolean b)
   {
-    jalview.bin.Cache.log.debug("Setting gui for Vamsas update "
+    Cache.log.debug("Setting gui for Vamsas update "
             + (b ? "in progress" : "finished"));
 
     if (vamUpdate != null)
@@ -2322,7 +2327,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   public void doGroovyCheck()
   {
-    if (jalview.bin.Cache.groovyJarsPresent())
+    if (Cache.groovyJarsPresent())
     {
       groovyShell = new JMenuItem();
       groovyShell.setText(MessageManager.getString("label.groovy_console"));
@@ -2420,7 +2425,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   public void groovyShell_actionPerformed(ActionEvent e)
   {
     // use reflection to avoid creating compilation dependency.
-    if (!jalview.bin.Cache.groovyJarsPresent())
+    if (!Cache.groovyJarsPresent())
     {
       throw new Error(
               MessageManager
@@ -2441,7 +2446,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       run.invoke(gc);
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log.error("Groovy Shell Creation failed.", ex);
+      Cache.log.error("Groovy Shell Creation failed.", ex);
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
 
       MessageManager.getString("label.couldnt_create_groovy_shell"),
@@ -2762,7 +2767,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
                     "status.opening_params", new Object[]
                     { url }), this.hashCode());
           }
-          jalview.util.BrowserLauncher.openURL(url);
+          BrowserLauncher.openURL(url);
         } catch (Exception ex)
         {
           JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -2890,7 +2895,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     invalidate();
     File of;
-    ImageMaker im = new jalview.util.ImageMaker(this, ImageMaker.TYPE.EPS,
+    ImageMaker im = new ImageMaker(this, ImageMaker.TYPE.EPS,
             "View of Desktop", getWidth(), getHeight(), of = new File(
                     "Jalview_snapshot" + System.currentTimeMillis()
                             + ".eps"), "View of desktop");
diff --git a/src/jalview/gui/EPSOptions.java b/src/jalview/gui/EPSOptions.java
index b5c3762..518cd4a 100644
--- a/src/jalview/gui/EPSOptions.java
+++ b/src/jalview/gui/EPSOptions.java
@@ -20,11 +20,22 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.util.MessageManager;
 
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
+import java.awt.BorderLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.ButtonGroup;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JRadioButton;
 
 public class EPSOptions extends JPanel
 {
@@ -131,11 +142,11 @@ public class EPSOptions extends JPanel
 
     if (!askAgain.isSelected())
     {
-      jalview.bin.Cache.applicationProperties.remove("EPS_RENDERING");
+      Cache.applicationProperties.remove("EPS_RENDERING");
     }
     else
     {
-      jalview.bin.Cache.setProperty("EPS_RENDERING", value);
+      Cache.setProperty("EPS_RENDERING", value);
     }
 
     dialog.setVisible(false);
diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java
index 7f76760..d204f11 100644
--- a/src/jalview/gui/FeatureColourChooser.java
+++ b/src/jalview/gui/FeatureColourChooser.java
@@ -20,19 +20,32 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.border.LineBorder;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.GraphLine;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
 import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
+
+import javax.swing.BorderFactory;
+import javax.swing.JCheckBox;
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JSlider;
+import javax.swing.JTextField;
+import javax.swing.border.LineBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
 
 public class FeatureColourChooser extends JalviewDialog
 {
@@ -92,7 +105,7 @@ public class FeatureColourChooser extends JalviewDialog
       {
         if (!adjusting)
         {
-          thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+          thresholdValue.setText((slider.getValue() / 1000f) + "");
           valueChanged();
         }
       }
@@ -158,7 +171,7 @@ public class FeatureColourChooser extends JalviewDialog
                       : 2);
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
-      threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
+      threshline = new GraphLine((max - min) / 2f,
               "Threshold", Color.black);
 
     }
@@ -410,7 +423,7 @@ public class FeatureColourChooser extends JalviewDialog
             && threshline == null)
     {
       // todo visual indication of feature threshold
-      threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
+      threshline = new GraphLine((max - min) / 2f,
               "Threshold", Color.black);
     }
 
@@ -529,7 +542,7 @@ public class FeatureColourChooser extends JalviewDialog
 
   public void valueChanged()
   {
-    threshline.value = (float) slider.getValue() / 1000f;
+    threshline.value = slider.getValue() / 1000f;
     cs.setThresh(threshline.value);
     changeColour();
     ap.paintAlignment(false);
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 9e09bfb..6e03dd7 100644
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -23,7 +23,9 @@ package jalview.gui;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
 import jalview.schemes.GraduatedColor;
+import jalview.schemes.UserColourScheme;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -200,7 +202,7 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
           Object col = getFeatureStyle(name.getText());
           if (col == null)
           {
-            col = new jalview.schemes.UserColourScheme()
+            col = new UserColourScheme()
                     .createColourFromName(name.getText());
           }
           oldcol = fcol = col;
@@ -322,7 +324,7 @@ public class FeatureRenderer extends jalview.renderer.seqfeatures.FeatureRendere
             bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
             JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok"));
 
-    jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+    FeaturesFile ffile = new FeaturesFile();
 
     if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
     {
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 2818fb9..30794df 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -26,10 +26,15 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.Help.HelpId;
 import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.GraduatedColor;
+import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.QuickSort;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.DasSequenceFeatureFetcher;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
 
 import java.awt.BorderLayout;
@@ -94,7 +99,7 @@ public class FeatureSettings extends JPanel implements
 {
   DasSourceBrowser dassourceBrowser;
 
-  jalview.ws.DasSequenceFeatureFetcher dasFeatureFetcher;
+  DasSequenceFeatureFetcher dasFeatureFetcher;
 
   JPanel settingsPane = new JPanel();
 
@@ -249,7 +254,7 @@ public class FeatureSettings extends JPanel implements
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    if (new jalview.util.Platform().isAMac())
+    if (Platform.isAMac())
     {
       Desktop.addInternalFrame(frame,
               MessageManager.getString("label.sequence_feature_settings"),
@@ -698,17 +703,17 @@ public class FeatureSettings extends JPanel implements
     }
     if (sort)
     {
-      jalview.util.QuickSort.sortFloat(order, data);
+      QuickSort.sortFloat(order, data);
     }
   }
 
   void load()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "fc" }, new String[]
             { "Sequence Feature Colours" }, "Sequence Feature Colours");
-    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.load_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.load"));
 
@@ -803,10 +808,10 @@ public class FeatureSettings extends JPanel implements
   void save()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "fc" }, new String[]
             { "Sequence Feature Colours" }, "Sequence Feature Colours");
-    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_feature_colours"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
@@ -833,7 +838,7 @@ public class FeatureSettings extends JPanel implements
           sortOrder[i] = fr.getOrder(sortTypes[i]);
           i++;
         }
-        jalview.util.QuickSort.sortFloat(sortOrder, sortTypes);
+        QuickSort.sortFloat(sortOrder, sortTypes);
         sortOrder = null;
         Object fcol;
         GraduatedColor gcol;
@@ -841,7 +846,7 @@ public class FeatureSettings extends JPanel implements
         {
           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
           col.setName(sortTypes[i]);
-          col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
+          col.setRGB(Format.getHexString(fr.getColour(col
                   .getName())));
           fcol = fr.getFeatureStyle(sortTypes[i]);
           if (fcol instanceof GraduatedColor)
@@ -849,7 +854,7 @@ public class FeatureSettings extends JPanel implements
             gcol = (GraduatedColor) fcol;
             col.setMin(gcol.getMin());
             col.setMax(gcol.getMax());
-            col.setMinRGB(jalview.util.Format.getHexString(gcol
+            col.setMinRGB(Format.getHexString(gcol
                     .getMinColor()));
             col.setAutoScale(gcol.isAutoScale());
             col.setThreshold(gcol.getThresh());
@@ -943,7 +948,7 @@ public class FeatureSettings extends JPanel implements
     }
     if (sort)
      {
-      jalview.util.QuickSort.sortFloat(width, data);
+      QuickSort.sortFloat(width, data);
     // update global priority order
     }
 
@@ -1236,7 +1241,7 @@ public class FeatureSettings extends JPanel implements
     }
 
     cancelDAS.setEnabled(true);
-    dasFeatureFetcher = new jalview.ws.DasSequenceFeatureFetcher(dataset,
+    dasFeatureFetcher = new DasSequenceFeatureFetcher(dataset,
             this, selectedSources, checkDbRefs, promptFetchDbRefs);
     af.getViewport().setShowSequenceFeatures(true);
     af.showSeqFeatures.setSelected(true);
@@ -1320,7 +1325,7 @@ public class FeatureSettings extends JPanel implements
   public void saveDAS_actionPerformed(ActionEvent e)
   {
     dassourceBrowser
-            .saveProperties(jalview.bin.Cache.applicationProperties);
+            .saveProperties(Cache.applicationProperties);
   }
 
   public void complete()
diff --git a/src/jalview/gui/HTMLOptions.java b/src/jalview/gui/HTMLOptions.java
index 0ef4710..7e826a8 100644
--- a/src/jalview/gui/HTMLOptions.java
+++ b/src/jalview/gui/HTMLOptions.java
@@ -1,5 +1,6 @@
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -120,11 +121,11 @@ public class HTMLOptions extends JPanel
 
     if (!askAgain.isSelected())
     {
-      jalview.bin.Cache.applicationProperties.remove("HTML_RENDERING");
+      Cache.applicationProperties.remove("HTML_RENDERING");
     }
     else
     {
-      jalview.bin.Cache.setProperty("HTML_RENDERING", value);
+      Cache.setProperty("HTML_RENDERING", value);
     }
 
     dialog.setVisible(false);
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 88d0c69..fe05c4d 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -20,11 +20,13 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.SequenceAnnotationReport;
+import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 import jalview.viewmodel.AlignmentViewport;
@@ -212,13 +214,13 @@ public class IdPanel extends JPanel implements MouseListener,
       // DEFAULT LINK IS FIRST IN THE LINK LIST
       // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
       url = links.elementAt(i++).toString();
-      jalview.util.UrlLink urlLink = null;
+      UrlLink urlLink = null;
       try
       {
         urlLink = new UrlLink(url);
       } catch (Exception foo)
       {
-        jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'",
+        Cache.log.error("Exception for URLLink '" + url + "'",
                 foo);
         url = null;
         continue;
@@ -226,7 +228,7 @@ public class IdPanel extends JPanel implements MouseListener,
       ;
       if (!urlLink.isValid())
       {
-        jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+        Cache.log.error(urlLink.getInvalidMessage());
         url = null;
         continue;
       }
@@ -242,7 +244,7 @@ public class IdPanel extends JPanel implements MouseListener,
     }
     try
     {
-      jalview.util.BrowserLauncher.openURL(url);
+      BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
       JOptionPane
@@ -339,7 +341,7 @@ public class IdPanel extends JPanel implements MouseListener,
         }
       }
 
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq,
+      PopupMenu pop = new PopupMenu(alignPanel, sq,
               nlinks, new Vector(Preferences.getGroupURLLinks()));
       pop.show(this, e.getX(), e.getY());
 
diff --git a/src/jalview/gui/JDatabaseTree.java b/src/jalview/gui/JDatabaseTree.java
index 94ac141..ac76ba4 100644
--- a/src/jalview/gui/JDatabaseTree.java
+++ b/src/jalview/gui/JDatabaseTree.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import jalview.bin.Cache;
 import jalview.util.MessageManager;
+import jalview.util.QuickSort;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
@@ -222,7 +223,7 @@ public class JDatabaseTree extends JalviewDialog implements KeyListener
         throw new Error(MessageManager.getString("error.implementation_error_cant_reorder_tree"));
       }
     }
-    jalview.util.QuickSort.sort(names, nodes);
+    QuickSort.sort(names, nodes);
     root.removeAllChildren();
     for (int i = count - 1; i >= 0; i--)
     {
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 7caea29..5318889 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AlignSeq;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
@@ -34,6 +35,7 @@ import jalview.datamodel.StructureViewerModel;
 import jalview.datamodel.StructureViewerModel.StructureData;
 import jalview.ext.varna.RnaModel;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.AppletFormatAdapter;
 import jalview.schemabinding.version2.AlcodMap;
 import jalview.schemabinding.version2.AlcodonFrame;
 import jalview.schemabinding.version2.Annotation;
@@ -76,6 +78,8 @@ import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.Comparison;
+import jalview.util.MapList;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.jarInputStreamProvider;
@@ -629,10 +633,10 @@ public class Jalview2XML
     object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 
     object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
-    object.setVersion(jalview.bin.Cache.getDefault("VERSION",
+    object.setVersion(Cache.getDefault("VERSION",
             "Development Build"));
 
-    jalview.datamodel.AlignmentI jal = av.getAlignment();
+    AlignmentI jal = av.getAlignment();
 
     if (av.hasHiddenRows())
     {
@@ -1974,7 +1978,7 @@ public class Jalview2XML
     {
       mp = new Mapping();
 
-      jalview.util.MapList mlst = jmp.getMap();
+      MapList mlst = jmp.getMap();
       List<int[]> r = mlst.getFromRanges();
       for (int[] range : r)
       {
@@ -2020,12 +2024,12 @@ public class Jalview2XML
           mpc.setDseqFor(jmpid);
           if (!seqRefIds.containsKey(mpc.getDseqFor()))
           {
-            jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+            Cache.log.debug("creatign new DseqFor ID");
             seqRefIds.put(mpc.getDseqFor(), ps);
           }
           else
           {
-            jalview.bin.Cache.log.debug("reusing DseqFor ID");
+            Cache.log.debug("reusing DseqFor ID");
           }
         }
         mp.setMappingChoice(mpc);
@@ -2618,7 +2622,7 @@ public class Jalview2XML
     /**
      * persisted version of annotation row from which to take vis properties
      */
-    public jalview.datamodel.AlignmentAnnotation template;
+    public AlignmentAnnotation template;
 
     /**
      * original position of the annotation row in the alignment
@@ -2943,7 +2947,7 @@ public class Jalview2XML
             }
           }
         }
-        jalview.datamodel.AlignmentAnnotation jaa = null;
+        AlignmentAnnotation jaa = null;
 
         if (annotation.getGraph())
         {
@@ -2951,7 +2955,7 @@ public class Jalview2XML
           // if (autoForView || an[i].isAutoCalculated()) {
           // hlim=11f;
           // }
-          jaa = new jalview.datamodel.AlignmentAnnotation(
+          jaa = new AlignmentAnnotation(
                   annotation.getLabel(), annotation.getDescription(), anot,
                   llim, hlim, annotation.getGraphType());
 
@@ -2974,7 +2978,7 @@ public class Jalview2XML
         }
         else
         {
-          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+          jaa = new AlignmentAnnotation(an[i].getLabel(),
                   an[i].getDescription(), anot);
           jaa._linecolour = firstColour;
         }
@@ -3004,11 +3008,11 @@ public class Jalview2XML
         // and make a note of any group association
         if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
         {
-          List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
+          List<AlignmentAnnotation> aal = groupAnnotRefs
                   .get(an[i].getGroupRef());
           if (aal == null)
           {
-            aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
+            aal = new ArrayList<AlignmentAnnotation>();
             groupAnnotRefs.put(an[i].getGroupRef(), aal);
           }
           aal.add(jaa);
@@ -3968,7 +3972,7 @@ public class Jalview2XML
       String pdbFile = filedat.getFilePath();
       SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
       binding.getSsm().setMapping(seq, null, pdbFile,
-              jalview.io.AppletFormatAdapter.FILE);
+              AppletFormatAdapter.FILE);
       binding.addSequenceForStructFile(pdbFile, seq);
     }
     // and add the AlignmentPanel's reference to the view panel
@@ -4593,7 +4597,7 @@ public class Jalview2XML
       List<String> remains = new ArrayList<String>(visan.keySet());
       for (int h = 0; h < hSize; h++)
       {
-        jalview.datamodel.AlignmentAnnotation jalan = al
+        AlignmentAnnotation jalan = al
                 .getAlignmentAnnotation()[h];
         if (jalan.autoCalculated)
         {
@@ -4839,8 +4843,8 @@ public class Jalview2XML
     if (sq != dsq)
     {
       // StringBuffer sb = new StringBuffer();
-      String newres = jalview.analysis.AlignSeq.extractGaps(
-              jalview.util.Comparison.GapChars, sq.getSequenceAsString());
+      String newres = AlignSeq.extractGaps(
+              Comparison.GapChars, sq.getSequenceAsString());
       if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
               && newres.length() > dsq.getLength())
       {
@@ -5024,7 +5028,7 @@ public class Jalview2XML
           seqRefIds.put(sqid, djs);
 
         }
-        jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+        Cache.log.debug("about to recurse on addDBRefs.");
         addDBRefs(djs, ms);
 
       }
@@ -5202,7 +5206,7 @@ public class Jalview2XML
         seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
         seqsToIds.put((SequenceI) jvobj, id);
       }
-      else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
+      else if (jvobj instanceof AlignmentAnnotation)
       {
         String anid;
         AlignmentAnnotation jvann = (AlignmentAnnotation) jvobj;
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index cb572cd..51db9df 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.analysis.Conservation;
 import jalview.binding.Annotation;
 import jalview.binding.AnnotationElement;
 import jalview.binding.Features;
@@ -34,10 +35,12 @@ import jalview.binding.Setting;
 import jalview.binding.Tree;
 import jalview.binding.UserColours;
 import jalview.binding.Viewport;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.PDBEntry;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.util.jarInputStreamProvider;
@@ -73,8 +76,7 @@ public class Jalview2XML_V1
     this.raiseGUI = raiseGUI;
   };
 
-  jalview.schemes.UserColourScheme GetUserColourScheme(
-          JalviewModelSequence jms, String id)
+  UserColourScheme GetUserColourScheme(JalviewModelSequence jms, String id)
   {
     UserColours[] uc = jms.getUserColours();
     UserColours colours = null;
@@ -98,7 +100,7 @@ public class Jalview2XML_V1
               .getUserColourScheme().getColour(i).getRGB(), 16));
     }
 
-    return new jalview.schemes.UserColourScheme(newColours);
+    return new UserColourScheme(newColours);
   }
 
   /**
@@ -110,7 +112,7 @@ public class Jalview2XML_V1
   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
   {
     final String file = jprovider.getFilename();
-    jalview.gui.AlignFrame af = null;
+    AlignFrame af = null;
 
     try
     {
@@ -281,17 +283,17 @@ public class Jalview2XML_V1
                   ae[aa].getValue());
         }
 
-        jalview.datamodel.AlignmentAnnotation jaa = null;
+        AlignmentAnnotation jaa = null;
 
         if (an[i].getGraph())
         {
-          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+          jaa = new AlignmentAnnotation(an[i].getLabel(),
                   an[i].getDescription(), anot, 0, 0,
-                  jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
+                  AlignmentAnnotation.BAR_GRAPH);
         }
         else
         {
-          jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+          jaa = new AlignmentAnnotation(an[i].getLabel(),
                   an[i].getDescription(), anot);
         }
 
@@ -361,7 +363,7 @@ public class Jalview2XML_V1
 
         if (groups[i].getConsThreshold() != 0)
         {
-          jalview.analysis.Conservation c = new jalview.analysis.Conservation(
+          Conservation c = new Conservation(
                   "All", ResidueProperties.propHash, 3,
                   sg.getSequences(null), 0, sg.getWidth() - 1);
           c.calculate();
diff --git a/src/jalview/gui/OOMWarning.java b/src/jalview/gui/OOMWarning.java
index 319c283..c8b42c6 100644
--- a/src/jalview/gui/OOMWarning.java
+++ b/src/jalview/gui/OOMWarning.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.util.MessageManager;
 
 import java.awt.Component;
@@ -54,9 +55,9 @@ public class OOMWarning implements Runnable
       desktop = instance;
       if (oomex != null)
       {
-        if (jalview.bin.Cache.log != null)
+        if (Cache.log != null)
         {
-          jalview.bin.Cache.log
+          Cache.log
                   .error("Out of Memory when " + action, oomex);
         }
         else
diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 609e010..bd9e241 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 
 import java.awt.Color;
@@ -291,7 +292,7 @@ public class OverviewPanel extends JPanel implements Runnable
     int lastcol = -1, lastrow = -1;
     int color = Color.white.getRGB();
     int row, col;
-    jalview.datamodel.SequenceI seq;
+    SequenceI seq;
     final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
             .hasHiddenColumns();
     boolean hiddenRow = false;
diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index f4fd70b..f5f6332 100644
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -20,6 +20,19 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPCAPanel;
+import jalview.schemes.ResidueProperties;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.PCAModel;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Graphics;
@@ -37,17 +50,6 @@ import javax.swing.JMenuItem;
 import javax.swing.JOptionPane;
 import javax.swing.JRadioButtonMenuItem;
 
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SeqCigar;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GPCAPanel;
-import jalview.schemes.ResidueProperties;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-import jalview.viewmodel.PCAModel;
-
 /**
  * DOCUMENT ME!
  * 
@@ -347,7 +349,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
     // make this an abstract function of all jalview analysis windows
     if (pcaModel.getSeqtrings() == null)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
@@ -464,7 +466,7 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    */
   public void eps_actionPerformed(ActionEvent e)
   {
-    makePCAImage(jalview.util.ImageMaker.TYPE.EPS);
+    makePCAImage(ImageMaker.TYPE.EPS);
   }
 
   /**
@@ -475,33 +477,31 @@ public class PCAPanel extends GPCAPanel implements Runnable,
    */
   public void png_actionPerformed(ActionEvent e)
   {
-    makePCAImage(jalview.util.ImageMaker.TYPE.PNG);
+    makePCAImage(ImageMaker.TYPE.PNG);
   }
 
-  void makePCAImage(jalview.util.ImageMaker.TYPE type)
+  void makePCAImage(ImageMaker.TYPE type)
   {
     int width = rc.getWidth();
     int height = rc.getHeight();
 
-    jalview.util.ImageMaker im;
+    ImageMaker im;
 
-    if (type == jalview.util.ImageMaker.TYPE.PNG)
+    if (type == ImageMaker.TYPE.PNG)
     {
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.PNG,
+      im = new ImageMaker(this, ImageMaker.TYPE.PNG,
               "Make PNG image from PCA", width, height, null, null);
     }
-    else if (type == jalview.util.ImageMaker.TYPE.EPS)
+    else if (type == ImageMaker.TYPE.EPS)
     {
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.EPS,
+      im = new ImageMaker(this, ImageMaker.TYPE.EPS,
               "Make EPS file from PCA", width, height, null,
               this.getTitle());
     }
     else
     {
-      im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
+      im = new ImageMaker(this, ImageMaker.TYPE.SVG,
+              "Make SVG file from PCA",
               width, height, null, this.getTitle());
 
     }
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 2c65a49..292b970 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -25,6 +25,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPairwiseAlignPanel;
+import jalview.util.Format;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -112,8 +113,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
       for (int i = 0; i < count; i++)
       {
-        jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
-                + seqs[i].getName());
+        Format.print(System.out, "%s \n",
+                ("" + i) + " " + seqs[i].getName());
       }
 
       System.out.println("\n");
@@ -122,8 +123,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
       {
         for (int j = 0; j < i; j++)
         {
-          jalview.util.Format.printDouble(System.out, "%7.3f", scores[i][j]
-                  / totscore);
+          Format.printDouble(System.out, "%7.3f", scores[i][j] / totscore);
         }
       }
 
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ad3d6af..c9d9e50 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -20,31 +20,11 @@
  */
 package jalview.gui;
 
-import java.awt.Color;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Hashtable;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPopupMenu;
-import javax.swing.JRadioButtonMenuItem;
-
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
+import jalview.bin.Cache;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -58,7 +38,9 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
 import jalview.io.FormatAdapter;
+import jalview.io.JalviewFileChooser;
 import jalview.io.SequenceAnnotationReport;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.Blosum62ColourScheme;
@@ -75,10 +57,35 @@ import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
+import jalview.util.BrowserLauncher;
+import jalview.util.DBRefUtils;
 import jalview.util.GroupUrlLink;
 import jalview.util.GroupUrlLink.UrlStringTooLongException;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
+import jalview.ws.DBRefFetcher;
+
+import java.awt.Color;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JColorChooser;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPopupMenu;
+import javax.swing.JRadioButtonMenuItem;
 
 /**
  * DOCUMENT ME!
@@ -263,10 +270,10 @@ public class PopupMenu extends JPopupMenu
     colours.add(purinePyrimidineColour);
     colours.add(RNAInteractionColour);
 
-    for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (int i = 0; i < FormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
       JMenuItem item = new JMenuItem(
-              jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+              FormatAdapter.WRITEABLE_FORMATS[i]);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
@@ -618,14 +625,14 @@ public class PopupMenu extends JPopupMenu
           urlLink = new UrlLink(link);
         } catch (Exception foo)
         {
-          jalview.bin.Cache.log.error("Exception for URLLink '" + link
+          Cache.log.error("Exception for URLLink '" + link
                   + "'", foo);
           continue;
         }
         ;
         if (!urlLink.isValid())
         {
-          jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+          Cache.log.error(urlLink.getInvalidMessage());
           continue;
         }
         final String label = urlLink.getLabel();
@@ -633,7 +640,7 @@ public class PopupMenu extends JPopupMenu
         {
 
           // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+          DBRefEntry[] dbr = DBRefUtils.selectRefs(
                   seq.getDBRef(), new String[]
                   { urlLink.getTarget() });
           // collect id string too
@@ -896,7 +903,7 @@ public class PopupMenu extends JPopupMenu
       {
         for (int d = 0; d < dbr.length; d++)
         {
-          String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+          String src = dbr[d].getSource(); // DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
           Object[] sarray = (Object[]) commonDbrefs.get(src);
           if (sarray == null)
           {
@@ -932,20 +939,20 @@ public class PopupMenu extends JPopupMenu
         urlLink = new GroupUrlLink(link);
       } catch (Exception foo)
       {
-        jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
+        Cache.log.error("Exception for GroupURLLink '" + link
                 + "'", foo);
         continue;
       }
       ;
       if (!urlLink.isValid())
       {
-        jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+        Cache.log.error(urlLink.getInvalidMessage());
         continue;
       }
       final String label = urlLink.getLabel();
       boolean usingNames = false;
       // Now see which parts of the group apply for this URL
-      String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+      String ltarget = urlLink.getTarget(); // DBRefUtils.getCanonicalName(urlLink.getTarget());
       Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
       String[] seqstr, ids; // input to makeUrl
       if (idset != null)
@@ -1452,9 +1459,9 @@ public class PopupMenu extends JPopupMenu
     }
     colourMenu.add(userDefinedColour);
 
-    if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
+    if (UserDefinedColours.getUserColourSchemes() != null)
     {
-      java.util.Enumeration userColours = jalview.gui.UserDefinedColours
+      Enumeration userColours = UserDefinedColours
               .getUserColourSchemes().keys();
 
       while (userColours.hasMoreElements())
@@ -2292,7 +2299,7 @@ public class PopupMenu extends JPopupMenu
   {
     try
     {
-      jalview.util.BrowserLauncher.openURL(url);
+      BrowserLauncher.openURL(url);
     } catch (Exception ex)
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
@@ -2403,8 +2410,8 @@ public class PopupMenu extends JPopupMenu
 
   public void pdbFromFile_actionPerformed()
   {
-    jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle(MessageManager.formatMessage(
             "label.select_pdb_file_for", new Object[]
@@ -2415,12 +2422,12 @@ public class PopupMenu extends JPopupMenu
 
     int value = chooser.showOpenDialog(null);
 
-    if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
+      Cache.setProperty("LAST_DIRECTORY", choice);
       new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
-              jalview.io.AppletFormatAdapter.FILE, sequence, true,
+              AppletFormatAdapter.FILE, sequence, true,
               Desktop.instance);
     }
 
@@ -2454,7 +2461,7 @@ public class PopupMenu extends JPopupMenu
       public void run()
       {
 
-        new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
+        new DBRefFetcher(sequences, ap.alignFrame)
                 .fetchDBRefs(false);
       }
 
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 67e0f83..4c5e83f 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -20,6 +20,20 @@
  */
 package jalview.gui;
 
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.gui.Help.HelpId;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.io.PIRFile;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.BrowserLauncher;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -42,17 +56,6 @@ import javax.swing.JPanel;
 
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
 
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.bin.Cache;
-import jalview.gui.Help.HelpId;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GPreferences;
-import jalview.jbgui.GSequenceLink;
-import jalview.schemes.ColourSchemeProperty;
-import jalview.util.MessageManager;
-
 /**
  * DOCUMENT ME!
  * 
@@ -175,7 +178,7 @@ public class Preferences extends GPreferences
     wsPrefs = new WsPreferences();
     wsTab.add(wsPrefs, BorderLayout.CENTER);
     int width = 500, height = 450;
-    if (new jalview.util.Platform().isAMac())
+    if (Platform.isAMac())
     {
       width = 570;
       height = 480;
@@ -511,7 +514,7 @@ public class Preferences extends GPreferences
      */
     Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 
-    jalview.util.BrowserLauncher.resetBrowser();
+    BrowserLauncher.resetBrowser();
 
     if (nameLinks.size() > 0)
     {
@@ -589,7 +592,7 @@ public class Preferences extends GPreferences
             Boolean.toString(pirjv.isSelected()));
     Cache.applicationProperties.setProperty("PIR_MODELLER",
             Boolean.toString(modellerOutput.isSelected()));
-    jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+    PIRFile.useModellerOutput = modellerOutput.isSelected();
 
     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
             Boolean.toString(autoIdWidth.isSelected()));
@@ -647,12 +650,12 @@ public class Preferences extends GPreferences
   public void startupFileTextfield_mouseClicked()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            Cache.getProperty("LAST_DIRECTORY"),
             new String[]
             { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
             new String[]
             { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
-            jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+            Cache.getProperty("DEFAULT_FILE_FORMAT"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.select_startup_file"));
 
@@ -660,7 +663,7 @@ public class Preferences extends GPreferences
 
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-      jalview.bin.Cache.applicationProperties.setProperty(
+      Cache.applicationProperties.setProperty(
               "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
       startupFileTextfield.setText(chooser.getSelectedFile()
               .getAbsolutePath());
diff --git a/src/jalview/gui/PromptUserConfig.java b/src/jalview/gui/PromptUserConfig.java
index 7655251..41b082c 100644
--- a/src/jalview/gui/PromptUserConfig.java
+++ b/src/jalview/gui/PromptUserConfig.java
@@ -91,7 +91,7 @@ public class PromptUserConfig implements Runnable
    * @param desktop
    *          - where the dialog box will be shown
    * @param property
-   *          - boolean property in jalview.bin.Cache
+   *          - boolean property in Cache
    * @param dialogTitle
    *          - title of prompt box
    * @param dialogText
@@ -127,14 +127,14 @@ public class PromptUserConfig implements Runnable
       return;
     }
     // First - check to see if wee have an old questionnaire/response id pair.
-    String lastq = jalview.bin.Cache.getProperty(property);
+    String lastq = Cache.getProperty(property);
 
     if (lastq == null)
     {
       raiseDialog();
       Cache.log.debug("Got user response.");
     }
-    lastq = jalview.bin.Cache.getProperty(property);
+    lastq = Cache.getProperty(property);
     String extype = "";
     Exception e = null;
     if (lastq == null)
@@ -194,9 +194,9 @@ public class PromptUserConfig implements Runnable
    */
   private void raiseDialog()
   {
-    if (jalview.bin.Cache.log.isDebugEnabled())
+    if (Cache.log.isDebugEnabled())
     {
-      jalview.bin.Cache.log.debug("Prompting user for " + dialogTitle
+      Cache.log.debug("Prompting user for " + dialogTitle
               + " for Cache property " + property);
     }
     try
@@ -214,36 +214,36 @@ public class PromptUserConfig implements Runnable
         Desktop.instance.relayerWindows();
       }
       // and finish parsing the result
-      jalview.bin.Cache.log.debug("Got response : " + reply);
+      Cache.log.debug("Got response : " + reply);
       if (reply == JOptionPane.YES_OPTION)
       {
-        jalview.bin.Cache.setProperty(property, "true");
+        Cache.setProperty(property, "true");
       }
       else if (reply == JOptionPane.NO_OPTION)
       {
         if (removeifunset)
         {
-          jalview.bin.Cache.removeProperty(property);
+          Cache.removeProperty(property);
         }
         else
         {
-          jalview.bin.Cache.setProperty(property, "false");
+          Cache.setProperty(property, "false");
         }
       }
       else
       {
-        jalview.bin.Cache.log.debug("User cancelled setting " + property);
+        Cache.log.debug("User cancelled setting " + property);
         return;
       }
       // verify the property is set for debugging
-      if (jalview.bin.Cache.log.isDebugEnabled())
+      if (Cache.log.isDebugEnabled())
       {
-        jalview.bin.Cache.log.debug("User set property to "
-                + jalview.bin.Cache.getProperty(property));
+        Cache.log.debug("User set property to "
+                + Cache.getProperty(property));
       }
     } catch (Exception e)
     {
-      jalview.bin.Cache.log.warn(
+      Cache.log.warn(
               "Unexpected exception when prompting user for yes/no setting for property "
                       + property, e);
     }
diff --git a/src/jalview/gui/RestServiceEditorPane.java b/src/jalview/gui/RestServiceEditorPane.java
index 8a77329..cf01ab6 100644
--- a/src/jalview/gui/RestServiceEditorPane.java
+++ b/src/jalview/gui/RestServiceEditorPane.java
@@ -24,6 +24,7 @@ import jalview.io.packed.DataProvider.JvDataType;
 import jalview.jbgui.GRestServiceEditorPane;
 import jalview.util.MessageManager;
 import jalview.ws.rest.InputType;
+import jalview.ws.rest.RestClient;
 import jalview.ws.rest.RestServiceDescription;
 
 import java.awt.BorderLayout;
@@ -54,13 +55,13 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
   /**
    * the latest version of the service definition.
    */
-  jalview.ws.rest.RestServiceDescription currentservice = null;
+  RestServiceDescription currentservice = null;
 
   /**
    * original service passed to editor if we are modifying an existing service
    * definition
    */
-  jalview.ws.rest.RestServiceDescription oldservice = null;
+  RestServiceDescription oldservice = null;
 
   public RestServiceEditorPane()
   {
@@ -474,8 +475,7 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
             df.getContentPane().setLayout(new BorderLayout());
             df.getContentPane().add(
                     (nulserv = !nulserv) ? new RestServiceEditorPane(
-                            jalview.ws.rest.RestClient
-                                    .makeShmmrRestClient()
+                            RestClient.makeShmmrRestClient()
                                     .getRestDescription())
                             : new RestServiceEditorPane(),
                     BorderLayout.CENTER);
diff --git a/src/jalview/gui/SVGOptions.java b/src/jalview/gui/SVGOptions.java
index c3bdc70..fb4287c 100644
--- a/src/jalview/gui/SVGOptions.java
+++ b/src/jalview/gui/SVGOptions.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -140,11 +141,11 @@ public class SVGOptions extends JPanel
 
     if (!askAgain.isSelected())
     {
-      jalview.bin.Cache.applicationProperties.remove("SVG_RENDERING");
+      Cache.applicationProperties.remove("SVG_RENDERING");
     }
     else
     {
-      jalview.bin.Cache.setProperty("SVG_RENDERING", value);
+      Cache.setProperty("SVG_RENDERING", value);
     }
 
     dialog.setVisible(false);
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 4c04ad3..2feba14 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -24,6 +24,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
 
 import java.awt.BasicStroke;
 import java.awt.BorderLayout;
@@ -181,7 +182,7 @@ public class SeqCanvas extends JComponent
 
       while (index < endx)
       {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        if (Comparison.isGap(seq.getCharAt(index)))
         {
           index++;
 
@@ -234,7 +235,7 @@ public class SeqCanvas extends JComponent
 
       while (index > startx)
       {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        if (Comparison.isGap(seq.getCharAt(index)))
         {
           index--;
 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index e34a864..875b3a7 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -20,24 +20,8 @@
  */
 package jalview.gui;
 
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Point;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.awt.event.MouseWheelEvent;
-import java.awt.event.MouseWheelListener;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.ToolTipManager;
-
 import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
@@ -60,6 +44,23 @@ import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
+
 /**
  * DOCUMENT ME!
  * 
@@ -1141,7 +1142,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           {
             for (int j = 0; j < startres - lastres; j++)
             {
-              if (!jalview.util.Comparison.isGap(groupSeqs[g]
+              if (!Comparison.isGap(groupSeqs[g]
                       .getCharAt(fixedRight - j)))
               {
                 blank = false;
@@ -1204,7 +1205,7 @@ public class SeqPanel extends JPanel implements MouseListener,
               continue;
             }
 
-            if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+            if (!Comparison.isGap(groupSeqs[g].getCharAt(j)))
             {
               // Not a gap, block edit not valid
               endEditing();
@@ -1339,7 +1340,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
       {
-        if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+        if (Comparison.isGap(seq[s].getCharAt(blankColumn)))
         {
           // Theres a space, so break and insert the gap
           break;
@@ -1585,7 +1586,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
       }
 
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
+      PopupMenu pop = new PopupMenu(ap, null, links);
       pop.show(this, evt.getX(), evt.getY());
       return;
     }
@@ -1927,7 +1928,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       if (av.getAlignment() == null)
       {
-        jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
+        Cache.log.warn("alignviewport av SeqSetId="
                 + av.getSequenceSetId() + " ViewId=" + av.getViewId()
                 + " 's alignment is NULL! returning immediately.");
         return;
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index c330a92..1561ecc 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -29,7 +30,9 @@ import jalview.io.FormatAdapter;
 import jalview.io.IdentifyFile;
 import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.awt.BorderLayout;
@@ -155,9 +158,9 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
     }
     if (sfetch == null
-            || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
-            || lastDasSourceRegistry != (jalview.bin.Cache
-                    .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
+            || dasRegistry != Cache.getDasSourceRegistry()
+            || lastDasSourceRegistry != (Cache
+                    .getDasSourceRegistry().getDasRegistryURL() + Cache
                     .getDasSourceRegistry().getLocalSourceString())
                     .hashCode())
     {
@@ -171,7 +174,7 @@ public class SequenceFetcher extends JPanel implements Runnable
         guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
                 Thread.currentThread().hashCode());
       }
-      dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+      dasRegistry = Cache.getDasSourceRegistry();
       dasRegistry.refreshSources();
 
       jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
@@ -260,7 +263,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    if (new jalview.util.Platform().isAMac())
+    if (Platform.isAMac())
     {
       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
     }
@@ -408,7 +411,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
       for (DbSourceProxy dbs : database.getSelectedSources())
       {
-        if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+        if (dbs instanceof DasSequenceSource)
         {
           enablePunct = false;
           break;
@@ -484,21 +487,21 @@ public class SequenceFetcher extends JPanel implements Runnable
       error += "Please select the source database\n";
     }
     // TODO: make this transformation more configurable
-    com.stevesoft.pat.Regex empty;
+    Regex empty;
     if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
     {
-      empty = new com.stevesoft.pat.Regex(
+      empty = new Regex(
       // replace commas and spaces with a semicolon
               "(\\s|[,; ])+", ";");
     }
     else
     {
       // just turn spaces and semicolons into single semicolons
-      empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
+      empty = new Regex("(\\s|[; ])+", ";");
     }
     textArea.setText(empty.replaceAll(textArea.getText()));
     // see if there's anthing to search with
-    if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
+    if (!new Regex("[A-Za-z0-9_.]").search(textArea
             .getText()))
     {
       error += "Please enter a (semi-colon separated list of) database id(s)";
@@ -579,7 +582,7 @@ public class SequenceFetcher extends JPanel implements Runnable
               }
             } catch (Exception e)
             {
-              jalview.bin.Cache.log.info("Error retrieving " + item
+              Cache.log.info("Error retrieving " + item
                       + " from " + proxy.getDbName(), e);
               nextfetch.add(item);
             }
@@ -856,7 +859,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
         try
         {
-          af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+          af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN",
                   false));
         } catch (Exception ex)
         {
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 21286ad..aca07b7 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -24,6 +24,7 @@ import jalview.api.FeatureRenderer;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
+import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.awt.FontMetrics;
@@ -150,7 +151,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
     }
     else if (forOverview
-            && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+            && !Comparison.isGap(seq.getCharAt(i)))
     {
       resBoxColour = Color.lightGray;
     }
@@ -334,7 +335,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         getboxColour = false;
         s = seq.getCharAt(i);
 
-        if (!renderGaps && jalview.util.Comparison.isGap(s))
+        if (!renderGaps && Comparison.isGap(s))
         {
           continue;
         }
diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index 16ec9d9..21fbd41 100755
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -283,26 +283,26 @@ public class SplashScreen extends JPanel implements Runnable,
     /*
      * int y = yoffset;
      * 
-     * g.drawString("Jalview " + jalview.bin.Cache.getProperty("VERSION"), 50,
+     * g.drawString("Jalview " + Cache.getProperty("VERSION"), 50,
      * y);
      * 
      * FontMetrics fm = g.getFontMetrics(); int vwidth =
-     * fm.stringWidth("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
+     * fm.stringWidth("Jalview " + Cache.getProperty("VERSION"));
      * g.setFont(new Font("Verdana", Font.BOLD, fontSize + 2)); g.drawString(
-     * "Last updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"),
-     * 50 + vwidth + 5, y); if (jalview.bin.Cache.getDefault("LATEST_VERSION",
+     * "Last updated: " + Cache.getDefault("BUILD_DATE", "unknown"),
+     * 50 + vwidth + 5, y); if (Cache.getDefault("LATEST_VERSION",
      * "Checking").equals( "Checking")) { // Displayed when code version and
      * jnlp version do not match g.drawString("...Checking latest version...",
      * 50, y += fontSize + 10); y += 5; g.setColor(Color.black); } else if
-     * (!jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking")
-     * .equals(jalview.bin.Cache.getProperty("VERSION"))) { if
-     * (jalview.bin.Cache.getProperty("VERSION").toLowerCase()
+     * (!Cache.getDefault("LATEST_VERSION", "Checking")
+     * .equals(Cache.getProperty("VERSION"))) { if
+     * (Cache.getProperty("VERSION").toLowerCase()
      * .indexOf("automated build") == -1) { // Displayed when code version and
      * jnlp version do not match and code // version is not a development build
      * g.setColor(Color.red); } g.drawString( "!! Jalview version " +
-     * jalview.bin.Cache.getDefault("LATEST_VERSION", "..Checking..") +
+     * Cache.getDefault("LATEST_VERSION", "..Checking..") +
      * " is available for download from "
-     * +jalview.bin.Cache.getDefault("www.jalview.org"
+     * +Cache.getDefault("www.jalview.org"
      * ,"http://www.jalview.org")+" !!", 50, y += fontSize + 10); y += 5;
      * g.setColor(Color.black); }
      * 
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 2e3b37a..afadbea 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -22,6 +22,23 @@
 
 package jalview.gui;
 
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureChooser;
+import jalview.jbgui.PDBDocFieldPreferences;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.PDBRestClient;
+import jalview.ws.dbsources.PDBRestClient.PDBDocField;
+import jalview.ws.uimodel.PDBRestRequest;
+import jalview.ws.uimodel.PDBRestResponse;
+import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+
 import java.awt.event.ItemEvent;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -36,19 +53,6 @@ import javax.swing.JLabel;
 import javax.swing.JOptionPane;
 import javax.swing.table.DefaultTableModel;
 
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GStructureChooser;
-import jalview.jbgui.PDBDocFieldPreferences;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
-import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
-
 
 /**
  * Provides the behaviors for the Structure chooser Panel
@@ -446,9 +450,9 @@ public class StructureChooser extends GStructureChooser
    */
   public void pdbFromFile_actionPerformed()
   {
-    jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-    chooser.setFileView(new jalview.io.JalviewFileView());
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            Cache.getProperty("LAST_DIRECTORY"));
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.formatMessage(
             "label.select_pdb_file_for", new String[]
             { selectedSequence.getDisplayId(false) }));
@@ -457,10 +461,10 @@ public class StructureChooser extends GStructureChooser
             { selectedSequence.getDisplayId(false) }));
 
     int value = chooser.showOpenDialog(null);
-    if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       selectedPdbFileName = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
+      Cache.setProperty("LAST_DIRECTORY", selectedPdbFileName);
       validateSelections();
     }
   }
@@ -733,7 +737,7 @@ public class StructureChooser extends GStructureChooser
       }
       PDBEntry fileEntry = new AssociatePdbFileWithSeq()
               .associatePdbWithSeq(
-              selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
+              selectedPdbFileName, AppletFormatAdapter.FILE,
               selectedSequence, true, Desktop.instance);
 
       launchStructureViewer(ap.getStructureSelectionManager(),
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 7177e43..cbcea76 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -42,6 +42,7 @@ import jalview.io.JalviewFileView;
 import jalview.io.NewickFile;
 import jalview.jbgui.GTreePanel;
 import jalview.schemes.ResidueProperties;
+import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -262,7 +263,7 @@ public class TreePanel extends GTreePanel
   {
     NewickFile newtree;
 
-    jalview.datamodel.AlignmentView odata = null;
+    AlignmentView odata = null;
 
     public TreeLoader(NewickFile newtree)
     {
@@ -413,8 +414,7 @@ public class TreePanel extends GTreePanel
       buffer.append("PID");
     }
 
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(
-            tree.getTopNode());
+    NewickFile fout = new NewickFile(tree.getTopNode());
     try
     {
       cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
@@ -437,7 +437,7 @@ public class TreePanel extends GTreePanel
   public void saveAsNewick_actionPerformed(ActionEvent e)
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
@@ -447,13 +447,12 @@ public class TreePanel extends GTreePanel
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+      Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
       try
       {
-        jalview.io.NewickFile fout = new jalview.io.NewickFile(
-                tree.getTopNode());
+        NewickFile fout = new NewickFile(tree.getTopNode());
         String output = fout.print(tree.isHasBootstrap(),
                 tree.isHasDistances(), tree.isHasRootDistance());
         java.io.PrintWriter out = new java.io.PrintWriter(
@@ -483,7 +482,7 @@ public class TreePanel extends GTreePanel
   {
     if (!tree.hasOriginalSequenceData())
     {
-      jalview.bin.Cache.log
+      Cache.log
               .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
       return;
     }
@@ -702,7 +701,7 @@ public class TreePanel extends GTreePanel
   {
     boolean accurateText = true;
 
-    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+    String renderStyle = Cache.getDefault("EPS_RENDERING",
             "Prompt each time");
 
     // If we need to prompt, and if the GUI is visible then
@@ -731,8 +730,8 @@ public class TreePanel extends GTreePanel
 
     try
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+      JalviewFileChooser chooser = new JalviewFileChooser(
+              Cache.getProperty("LAST_DIRECTORY"), new String[]
               { "eps" }, new String[]
               { "Encapsulated Postscript" }, "Encapsulated Postscript");
       chooser.setFileView(new jalview.io.JalviewFileView());
@@ -741,12 +740,12 @@ public class TreePanel extends GTreePanel
 
       int value = chooser.showSaveDialog(this);
 
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      if (value != JalviewFileChooser.APPROVE_OPTION)
       {
         return;
       }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+      Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
@@ -777,23 +776,23 @@ public class TreePanel extends GTreePanel
 
     try
     {
-      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+      JalviewFileChooser chooser = new JalviewFileChooser(
+              Cache.getProperty("LAST_DIRECTORY"), new String[]
               { "png" }, new String[]
               { "Portable network graphics" }, "Portable network graphics");
 
-      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(MessageManager.getString("label.create_png_from_tree"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
 
       int value = chooser.showSaveDialog(this);
 
-      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+      if (value != JalviewFileChooser.APPROVE_OPTION)
       {
         return;
       }
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+      Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
       FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
@@ -836,7 +835,7 @@ public class TreePanel extends GTreePanel
           if (sq != null)
           {
             // search dbrefs, features and annotation
-            DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
+            DBRefEntry[] refs = DBRefUtils.selectRefs(
                     sq.getDBRef(), new String[]
                     { labelClass.toUpperCase() });
             if (refs != null)
diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index a907187..b4a513e 100755
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -20,6 +20,19 @@
  */
 package jalview.gui;
 
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceGroup;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GUserDefinedColours;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
+import jalview.util.Format;
+import jalview.util.MessageManager;
+
 import java.awt.Color;
 import java.awt.Font;
 import java.awt.event.ActionEvent;
@@ -40,16 +53,6 @@ import javax.swing.JOptionPane;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.datamodel.SequenceGroup;
-import jalview.io.JalviewFileChooser;
-import jalview.jbgui.GUserDefinedColours;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
-import jalview.util.ColorUtils;
-import jalview.util.MessageManager;
-
 /**
  * This panel allows the user to assign colours to Amino Acid residue codes, and
  * save the colour scheme.
@@ -585,10 +588,10 @@ public class UserDefinedColours extends GUserDefinedColours implements
     lowerCaseButtons = new ArrayList<JButton>();
 
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "jc" }, new String[]
             { "Jalview User Colours" }, "Jalview User Colours");
-    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager
             .getString("label.load_colour_scheme"));
     chooser.setToolTipText(MessageManager.getString("action.load"));
@@ -598,8 +601,8 @@ public class UserDefinedColours extends GUserDefinedColours implements
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       File choice = chooser.getSelectedFile();
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
-      String defaultColours = jalview.bin.Cache.getDefault(
+      Cache.setProperty("LAST_DIRECTORY", choice.getParent());
+      String defaultColours = Cache.getDefault(
               "USER_DEFINED_COLOURS", choice.getPath());
       if (defaultColours.indexOf(choice.getPath()) == -1)
       {
@@ -607,7 +610,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
                 .concat(choice.getPath());
       }
 
-      jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
+      Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 
       UserColourScheme ucs = loadColours(choice.getAbsolutePath());
       Color[] colors = ucs.getColours();
@@ -650,7 +653,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
   {
     UserColourScheme ret = null;
 
-    String colours = jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS");
+    String colours = Cache.getProperty("USER_DEFINED_COLOURS");
     if (colours != null)
     {
       if (colours.indexOf("|") > -1)
@@ -822,11 +825,11 @@ public class UserDefinedColours extends GUserDefinedColours implements
       userColourSchemes.remove(schemeName.getText());
     }
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            Cache.getProperty("LAST_DIRECTORY"), new String[]
             { "jc" }, new String[]
             { "Jalview User Colours" }, "Jalview User Colours");
 
-    chooser.setFileView(new jalview.io.JalviewFileView());
+    chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_colour_scheme"));
     chooser.setToolTipText(MessageManager.getString("action.save"));
 
@@ -835,7 +838,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      String defaultColours = jalview.bin.Cache.getDefault(
+      String defaultColours = Cache.getDefault(
               "USER_DEFINED_COLOURS", choice);
       if (defaultColours.indexOf(choice) == -1)
       {
@@ -850,7 +853,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
       ap.alignFrame.updateUserColourMenu();
 
-      jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
+      Cache.setProperty("USER_DEFINED_COLOURS", defaultColours);
 
       jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
 
@@ -865,8 +868,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
           JButton button = (JButton) buttonPanel.getComponent(i);
           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
           col.setName(button.getText());
-          col.setRGB(jalview.util.Format.getHexString(button
-                  .getBackground()));
+          col.setRGB(Format.getHexString(button.getBackground()));
           ucs.addColour(col);
         }
 
@@ -958,12 +960,12 @@ public class UserDefinedColours extends GUserDefinedColours implements
     {
       if (coloursFound.toString().length() > 1)
       {
-        jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
+        Cache.setProperty("USER_DEFINED_COLOURS",
                 coloursFound.toString());
       }
       else
       {
-        jalview.bin.Cache.applicationProperties
+        Cache.applicationProperties
                 .remove("USER_DEFINED_COLOURS");
       }
     }
@@ -979,7 +981,7 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     StringBuffer coloursFound = new StringBuffer();
     StringTokenizer st = new StringTokenizer(
-            jalview.bin.Cache.getProperty("USER_DEFINED_COLOURS"), "|");
+            Cache.getProperty("USER_DEFINED_COLOURS"), "|");
 
     while (st.hasMoreElements())
     {
@@ -1004,12 +1006,12 @@ public class UserDefinedColours extends GUserDefinedColours implements
 
     if (coloursFound.toString().length() > 1)
     {
-      jalview.bin.Cache.setProperty("USER_DEFINED_COLOURS",
+      Cache.setProperty("USER_DEFINED_COLOURS",
               coloursFound.toString());
     }
     else
     {
-      jalview.bin.Cache.applicationProperties
+      Cache.applicationProperties
               .remove("USER_DEFINED_COLOURS");
     }
 
diff --git a/src/jalview/gui/UserQuestionnaireCheck.java b/src/jalview/gui/UserQuestionnaireCheck.java
index 02f6054..068e7cc 100644
--- a/src/jalview/gui/UserQuestionnaireCheck.java
+++ b/src/jalview/gui/UserQuestionnaireCheck.java
@@ -20,12 +20,15 @@
  */
 package jalview.gui;
 
+import jalview.bin.Cache;
+import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 
-import java.io.*;
-import java.net.*;
+import java.io.BufferedReader;
+import java.io.InputStreamReader;
+import java.net.URL;
 
-import javax.swing.*;
+import javax.swing.JOptionPane;
 
 public class UserQuestionnaireCheck implements Runnable
 {
@@ -41,7 +44,7 @@ public class UserQuestionnaireCheck implements Runnable
   {
     if (url.indexOf("questionnaire.pl") == -1)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .error("'"
                       + url
                       + "' is an Invalid URL for the checkForQuestionnaire() method.\n"
@@ -57,7 +60,7 @@ public class UserQuestionnaireCheck implements Runnable
 
   private boolean checkresponse(URL qurl) throws Exception
   {
-    jalview.bin.Cache.log.debug("Checking Response for : " + qurl);
+    Cache.log.debug("Checking Response for : " + qurl);
     boolean prompt = false;
     // see if we have already responsed to this questionnaire or get a new
     // qid/rid pair
@@ -102,7 +105,7 @@ public class UserQuestionnaireCheck implements Runnable
     try
     {
       // First - check to see if wee have an old questionnaire/response id pair.
-      String lastq = jalview.bin.Cache.getProperty("QUESTIONNAIRE");
+      String lastq = Cache.getProperty("QUESTIONNAIRE");
       if (lastq == null)
       {
         prompt = checkresponse(new URL(url
@@ -133,13 +136,13 @@ public class UserQuestionnaireCheck implements Runnable
       if (qid != null && rid != null)
       {
         // Update our local property cache with latest qid and rid
-        jalview.bin.Cache.setProperty("QUESTIONNAIRE", qid + ":" + rid);
+        Cache.setProperty("QUESTIONNAIRE", qid + ":" + rid);
       }
       if (prompt)
       {
         String qurl = url + (url.indexOf('?') > -1 ? "&" : "?") + "qid="
                 + qid + "&rid=" + rid;
-        jalview.bin.Cache.log.info("Prompting user for questionnaire at "
+        Cache.log.info("Prompting user for questionnaire at "
                 + qurl);
         int reply = JOptionPane
                 .showInternalConfirmDialog(Desktop.desktop, MessageManager
@@ -151,13 +154,13 @@ public class UserQuestionnaireCheck implements Runnable
 
         if (reply == JOptionPane.YES_OPTION)
         {
-          jalview.bin.Cache.log.debug("Opening " + qurl);
-          jalview.util.BrowserLauncher.openURL(qurl);
+          Cache.log.debug("Opening " + qurl);
+          BrowserLauncher.openURL(qurl);
         }
       }
     } catch (Exception e)
     {
-      jalview.bin.Cache.log.warn("When trying to access questionnaire URL "
+      Cache.log.warn("When trying to access questionnaire URL "
               + url, e);
     }
   }
diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 6444667..38f1571 100644
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -200,7 +200,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
 
     } catch (Exception e)
     {
-      jalview.bin.Cache.log
+      Cache.log
               .error("Couldn't instantiate vamsas client !", e);
       return false;
     }
@@ -243,7 +243,7 @@ public class VamsasApplication implements SelectionSource, VamsasSource
   private ClientHandle getJalviewHandle()
   {
     return new ClientHandle("jalview.bin.Jalview",
-            jalview.bin.Cache.getProperty("VERSION"));
+            Cache.getProperty("VERSION"));
   }
 
   /**
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 8e78b93..3cafaf4 100644
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -20,6 +20,10 @@
  */
 package jalview.gui;
 
+import jalview.jbgui.GWebserviceInfo;
+import jalview.util.MessageManager;
+import jalview.ws.WSClientI;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Font;
@@ -45,10 +49,6 @@ import javax.swing.event.HyperlinkListener;
 import javax.swing.text.html.HTMLEditorKit;
 import javax.swing.text.html.StyleSheet;
 
-import jalview.jbgui.GWebserviceInfo;
-import jalview.util.MessageManager;
-import jalview.ws.WSClientI;
-
 /**
  * Base class for web service client thread and gui TODO: create StAX parser to
  * extract html body content reliably when preparing html formatted job statuses
@@ -86,7 +86,7 @@ public class WebserviceInfo extends GWebserviceInfo implements
 
   String title = "";
 
-  jalview.ws.WSClientI thisService;
+  WSClientI thisService;
 
   boolean serviceIsCancellable;
 
@@ -265,7 +265,7 @@ public class WebserviceInfo extends GWebserviceInfo implements
    * 
    * @return DOCUMENT ME!
    */
-  public jalview.ws.WSClientI getthisService()
+  public WSClientI getthisService()
   {
     return thisService;
   }
@@ -277,7 +277,7 @@ public class WebserviceInfo extends GWebserviceInfo implements
    * @param newservice
    *          service client to query for capabilities
    */
-  public void setthisService(jalview.ws.WSClientI newservice)
+  public void setthisService(WSClientI newservice)
   {
     thisService = newservice;
     serviceIsCancellable = newservice.isCancellable();
diff --git a/src/jalview/gui/WsJobParameters.java b/src/jalview/gui/WsJobParameters.java
index a3a61b7..c1b09b7 100644
--- a/src/jalview/gui/WsJobParameters.java
+++ b/src/jalview/gui/WsJobParameters.java
@@ -20,6 +20,20 @@
  */
 package jalview.gui;
 
+import jalview.gui.OptsAndParamsPage.OptionBox;
+import jalview.gui.OptsAndParamsPage.ParamBox;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.JabaParamStore;
+import jalview.ws.jws2.JabaPreset;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.ParameterUtils;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.OptionI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.ParameterI;
+import jalview.ws.params.WsParamSetI;
+
 import java.awt.BorderLayout;
 import java.awt.Component;
 import java.awt.Dimension;
@@ -66,19 +80,6 @@ import compbio.metadata.Preset;
 import compbio.metadata.PresetManager;
 import compbio.metadata.RunnerConfig;
 
-import jalview.gui.OptsAndParamsPage.OptionBox;
-import jalview.gui.OptsAndParamsPage.ParamBox;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.JabaParamStore;
-import jalview.ws.jws2.JabaPreset;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.jws2.jabaws2.Jws2Instance;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.OptionI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.ParameterI;
-import jalview.ws.params.WsParamSetI;
-
 /**
  * job parameter editing/browsing dialog box. User can browse existing settings
  * (user + presets + Defaults), and any changes to parameters creates a modified
@@ -952,8 +953,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
    */
   public static void main(String[] args)
   {
-    jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer
-            .getDiscoverer();
+    Jws2Discoverer disc = Jws2Discoverer.getDiscoverer();
     int p = 0;
     if (args.length > 0)
     {
@@ -1021,7 +1021,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
               {
                 try
                 {
-                  Option cpy = jalview.ws.jws2.ParameterUtils.copyOption(o);
+                  Option cpy = ParameterUtils.copyOption(o);
                 } catch (Exception e)
                 {
                   System.err.println("Failed to copy " + o.getName());
@@ -1041,7 +1041,7 @@ public class WsJobParameters extends JPanel implements ItemListener,
               {
                 try
                 {
-                  Parameter cpy = jalview.ws.jws2.ParameterUtils
+                  Parameter cpy = ParameterUtils
                           .copyParameter(o);
                 } catch (Exception e)
                 {
@@ -1059,15 +1059,15 @@ public class WsJobParameters extends JPanel implements ItemListener,
               List<String> writeparam = null, readparam = null;
               try
               {
-                writeparam = jalview.ws.jws2.ParameterUtils
+                writeparam = ParameterUtils
                         .writeParameterSet(
                                 pr.getArguments(lastserv.getRunnerConfig()),
                                 " ");
                 System.out.println("Testing param read :");
-                List<Option> pset = jalview.ws.jws2.ParameterUtils
+                List<Option> pset = ParameterUtils
                         .processParameters(writeparam,
                                 lastserv.getRunnerConfig(), " ");
-                readparam = jalview.ws.jws2.ParameterUtils
+                readparam = ParameterUtils
                         .writeParameterSet(pset, " ");
                 Iterator<String> o = pr.getOptions().iterator(), s = writeparam
                         .iterator(), t = readparam.iterator();
diff --git a/src/jalview/gui/WsParamSetManager.java b/src/jalview/gui/WsParamSetManager.java
index f00f50c..a9817a0 100644
--- a/src/jalview/gui/WsParamSetManager.java
+++ b/src/jalview/gui/WsParamSetManager.java
@@ -22,6 +22,8 @@ package jalview.gui;
 
 import jalview.bin.Cache;
 import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.schemabinding.version2.WebServiceParameterSet;
 import jalview.util.MessageManager;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.ParamManager;
@@ -114,15 +116,14 @@ public class WsParamSetManager implements ParamManager
     InputStreamReader is = new InputStreamReader(
             new java.io.FileInputStream(new File(filename)), "UTF-8");
 
-    jalview.schemabinding.version2.WebServiceParameterSet wspset = new jalview.schemabinding.version2.WebServiceParameterSet();
+    WebServiceParameterSet wspset = new WebServiceParameterSet();
 
     org.exolab.castor.xml.Unmarshaller unmar = new org.exolab.castor.xml.Unmarshaller(
             wspset);
     unmar.setWhitespacePreserve(true);
     try
     {
-      wspset = (jalview.schemabinding.version2.WebServiceParameterSet) unmar
-              .unmarshal(is);
+      wspset = (WebServiceParameterSet) unmar.unmarshal(is);
     } catch (Exception ex)
     {
       throw new IOException(ex);
@@ -183,18 +184,18 @@ public class WsParamSetManager implements ParamManager
     if (filename == null)
     {
       JalviewFileChooser chooser = new JalviewFileChooser(
-              jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+              Cache.getProperty("LAST_DIRECTORY"), new String[]
               { "wsparams" }, new String[]
               { "Web Service Parameter File" },
               "Web Service Parameter File");
-      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setFileView(new JalviewFileView());
       chooser.setDialogTitle(MessageManager.getString("label.choose_filename_for_param_file"));
       chooser.setToolTipText(MessageManager.getString("action.save"));
       int value = chooser.showSaveDialog(Desktop.instance);
       if (value == JalviewFileChooser.APPROVE_OPTION)
       {
         outfile = chooser.getSelectedFile();
-        jalview.bin.Cache
+        Cache
                 .setProperty("LAST_DIRECTORY", outfile.getParent());
         filename = outfile.getAbsolutePath();
         if (!filename.endsWith(".wsparams"))
@@ -206,7 +207,7 @@ public class WsParamSetManager implements ParamManager
     }
     if (outfile != null)
     {
-      String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES",
+      String paramFiles = Cache.getDefault("WS_PARAM_FILES",
               filename);
       if (paramFiles.indexOf(filename) == -1)
       {
@@ -216,9 +217,9 @@ public class WsParamSetManager implements ParamManager
         }
         paramFiles = paramFiles.concat(filename);
       }
-      jalview.bin.Cache.setProperty("WS_PARAM_FILES", paramFiles);
+      Cache.setProperty("WS_PARAM_FILES", paramFiles);
 
-      jalview.schemabinding.version2.WebServiceParameterSet paramxml = new jalview.schemabinding.version2.WebServiceParameterSet();
+      WebServiceParameterSet paramxml = new WebServiceParameterSet();
 
       paramxml.setName(parameterSet.getName());
       paramxml.setDescription(parameterSet.getDescription());
@@ -242,7 +243,7 @@ public class WsParamSetManager implements ParamManager
 
   /*
    * 
-   * JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
+   * JalviewFileChooser chooser = new JalviewFileChooser(Cache
    * .getProperty("LAST_DIRECTORY"), new String[] { "jc" }, new String[] {
    * "Jalview User Colours" }, "Jalview User Colours"); chooser.setFileView(new
    * jalview.io.JalviewFileView());
@@ -252,8 +253,8 @@ public class WsParamSetManager implements ParamManager
    * int value = chooser.showOpenDialog(this);
    * 
    * if (value == JalviewFileChooser.APPROVE_OPTION) { File choice =
-   * chooser.getSelectedFile(); jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-   * choice.getParent()); String defaultColours = jalview.bin.Cache.getDefault(
+   * chooser.getSelectedFile(); Cache.setProperty("LAST_DIRECTORY",
+   * choice.getParent()); String defaultColours = Cache.getDefault(
    * "USER_DEFINED_COLOURS", choice.getPath()); if
    * (defaultColours.indexOf(choice.getPath()) == -1) { defaultColours =
    * defaultColours.concat("|") .concat(choice.getPath()); } (non-Javadoc)
@@ -270,7 +271,7 @@ public class WsParamSetManager implements ParamManager
     {
       return;
     }
-    String paramFiles = jalview.bin.Cache.getDefault("WS_PARAM_FILES", "");
+    String paramFiles = Cache.getDefault("WS_PARAM_FILES", "");
     if (paramFiles.indexOf(filename) > -1)
     {
       String nparamFiles = new String();
@@ -283,7 +284,7 @@ public class WsParamSetManager implements ParamManager
           nparamFiles = nparamFiles.concat("|").concat(fl);
         }
       }
-      jalview.bin.Cache.setProperty("WS_PARAM_FILES", nparamFiles);
+      Cache.setProperty("WS_PARAM_FILES", nparamFiles);
     }
 
     try
diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index 25ada33..39117d0 100644
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -24,6 +24,7 @@ import jalview.bin.Cache;
 import jalview.jbgui.GWsPreferences;
 import jalview.util.MessageManager;
 import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.rest.RestClient;
 import jalview.ws.rest.RestServiceDescription;
 
 import java.awt.BorderLayout;
@@ -78,7 +79,7 @@ public class WsPreferences extends GWsPreferences
     wsList.setDefaultRenderer(Integer.class, new JabaWSStatusRenderer());
     wsList.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
     updateList();
-    rsbsUrls = jalview.ws.rest.RestClient.getRsbsDescriptions();
+    rsbsUrls = RestClient.getRsbsDescriptions();
     if (rsbsUrls != null)
     {
       oldRsbsUrls = new Vector<String>(rsbsUrls);
@@ -243,7 +244,7 @@ public class WsPreferences extends GWsPreferences
 
   private void updateRsbsServiceList()
   {
-    jalview.ws.rest.RestClient.setRsbsServices(rsbsUrls);
+    RestClient.setRsbsServices(rsbsUrls);
   }
 
   /*