From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 10 Jul 2015 05:12:32 +0000 (+0100)
Subject: JAL-1807 explicit imports (jalview.appletgui)
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a4677746324adeea9632d7306c83dfd94dff6181;p=jalview.git

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

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index f16da84..1d59202 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -24,6 +24,7 @@ import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentAnnotationUtils;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Conservation;
+import jalview.bin.JalviewLite;
 import jalview.commands.ChangeCaseCommand;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -48,6 +49,7 @@ import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TaylorColourScheme;
 import jalview.schemes.TurnColourScheme;
 import jalview.schemes.ZappoColourScheme;
+import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 
@@ -216,10 +218,10 @@ public class APopupMenu extends java.awt.PopupMenu implements
       e.printStackTrace();
     }
 
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (int i = 0; i < AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
       MenuItem item = new MenuItem(
-              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+AppletFormatAdapter.WRITEABLE_FORMATS[i]);
 
       item.addActionListener(this);
       outputmenu.add(item);
@@ -274,7 +276,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
         {
 
           // collect matching db-refs
-          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+          DBRefEntry[] dbr = DBRefUtils.selectRefs(
                   seq.getDBRef(), new String[]
                   { target });
           // collect id string too
@@ -348,16 +350,15 @@ public class APopupMenu extends java.awt.PopupMenu implements
          * 
          * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
          * // collect matching db-refs DBRefEntry[] dbr =
-         * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
-         * String[]{target}); // collect id string too String id =
-         * seq.getName(); if (id.indexOf("|") > -1) { id =
-         * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
-         * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
-         * suppress duplicate link creation for the bare sequence ID string with
-         * this link id = null; } addshowLink(linkMenu,
-         * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
-         * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
-         * create Bare ID link for this RUL addshowLink(linkMenu, target,
+         * DBRefUtils.selectRefs(seq.getDBRef(), new String[]{target}); //
+         * collect id string too String id = seq.getName(); if (id.indexOf("|")
+         * > -1) { id = id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null)
+         * { for (int r=0;r<dbr.length; r++) { if
+         * (dbr[r].getAccessionId().equals(id)) { // suppress duplicate link
+         * creation for the bare sequence ID string with this link id = null; }
+         * addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(),
+         * target, url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null)
+         * { // create Bare ID link for this RUL addshowLink(linkMenu, target,
          * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
          * link.substring(link.lastIndexOf("|")+1)); }
          */
@@ -824,14 +825,14 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+    JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.selection_output_command", new Object[]
             { e.getActionCommand() }), 600, 500);
     // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
     // now returns a full copy of sequence data
     // TODO consider using getSequenceSelection instead here
 
-    cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
+    cap.setText(new AppletFormatAdapter().formatSequences(
             e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));
 
   }
@@ -871,7 +872,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
     }
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
+    JalviewLite.addFrame(frame, "Sequence Details for "
             + (sequences.length == 1 ? sequences[0].getDisplayId(true)
                     : "Selection"), 600, 500);
     cap.setText(MessageManager.formatMessage("label.html_content",
@@ -902,7 +903,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
       if (ap.av.applet.jmolAvailable)
       {
-        new jalview.appletgui.AppletJmol(entry, new SequenceI[]
+        new AppletJmol(entry, new SequenceI[]
         { seq }, null, ap, AppletFormatAdapter.URL);
       }
       else
@@ -919,7 +920,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
       cap.setPDBImport(seq);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+      JalviewLite.addFrame(frame, MessageManager.formatMessage(
               "label.paste_pdb_file_for_sequence", new Object[]
               { seq.getName() }), 400, 300);
     }
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0225dc7..1fd4231 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -37,6 +37,7 @@ import jalview.commands.RemoveGapColCommand;
 import jalview.commands.RemoveGapsCommand;
 import jalview.commands.SlideSequencesCommand;
 import jalview.commands.TrimRegionCommand;
+import jalview.controller.AlignViewController;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -46,9 +47,11 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FeaturesFile;
+import jalview.io.NewickFile;
 import jalview.io.TCoffeeScoreFile;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
@@ -68,6 +71,7 @@ import jalview.schemes.TurnColourScheme;
 import jalview.schemes.ZappoColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.Comparison;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
@@ -219,7 +223,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
 
     alignPanel = new AlignmentPanel(this, viewport);
-    avc = new jalview.controller.AlignViewController(this, viewport,
+    avc = new AlignViewController(this, viewport,
             alignPanel);
     viewport.updateConservation(alignPanel);
     viewport.updateConsensus(alignPanel);
@@ -366,7 +370,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     boolean featuresFile = false;
     try
     {
-      featuresFile = new jalview.io.FeaturesFile(file, type)
+      featuresFile = new FeaturesFile(file, type)
               .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
                       .getFeatureRenderer().getFeatureColours(), featureLinks,
                       true, viewport.applet.getDefaultParameter(
@@ -1171,13 +1175,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == alProperties)
     {
-      StringBuffer contents = new jalview.io.AlignmentProperties(
+      StringBuffer contents = new AlignmentProperties(
               viewport.getAlignment()).formatAsString();
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       cap.setText(contents.toString());
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+      JalviewLite.addFrame(frame, MessageManager.formatMessage(
               "label.alignment_properties", new String[]
               { getTitle() }), 400, 250);
     }
@@ -1330,7 +1334,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("label.input_cut_paste"), 500, 500);
   }
 
@@ -1339,7 +1343,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+    JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.alignment_output_command", new Object[]
             { e.getActionCommand() }), 600, 500);
 
@@ -1357,7 +1361,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     cap.setAnnotationImport();
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("action.paste_annotations"), 400, 300);
 
   }
@@ -1372,7 +1376,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
+      JalviewLite.addFrame(frame,
               MessageManager.getString("label.annotations"), 600, 500);
       cap.setText(annotation);
     }
@@ -1422,7 +1426,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame,
+      JalviewLite.addFrame(frame,
               MessageManager.getString("label.features"), 600, 500);
       cap.setText(features);
     }
@@ -1918,7 +1922,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
       {
         ch = seq.getCharAt(j);
-        if (!jalview.util.Comparison.isGap((ch)))
+        if (!Comparison.isGap((ch)))
         {
           endRes++;
         }
@@ -1998,7 +2002,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           }
         }
 
-        jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+        JalviewLite.addFrame(af, newtitle, frameWidth,
                 frameHeight);
       }
       else
@@ -2550,7 +2554,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     OverviewPanel overview = new OverviewPanel(alignPanel);
     frame.add(overview);
     // +50 must allow for applet frame window
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+    JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.overview_params", new String[]
             { this.getTitle() }), overview.getPreferredSize().width,
             overview.getPreferredSize().height + 50);
@@ -2603,8 +2607,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       alignPanel.getOverviewPanel().updateOverviewImage();
     }
 
-    jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(viewport.applet)
+    StructureSelectionManager.getStructureSelectionManager(viewport.applet)
             .sequenceColoursChanged(alignPanel);
 
     alignPanel.paintAlignment(true);
@@ -2707,7 +2710,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       Frame frame = new Frame();
       frame.add(new PairwiseAlignPanel(alignPanel));
-      jalview.bin.JalviewLite.addFrame(frame,
+      JalviewLite.addFrame(frame,
               MessageManager.getString("action.pairwise_alignment"), 600,
               500);
     }
@@ -2799,7 +2802,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
       addTreeMenuItem(tp, title);
 
-      jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
+      JalviewLite.addFrame(tp, title, 600, 500);
     }
   }
 
@@ -2810,15 +2813,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     cap.setTreeImport();
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("label.paste_newick_file"), 400, 300);
   }
 
-  public void loadTree(jalview.io.NewickFile tree, String treeFile)
+  public void loadTree(NewickFile tree, String treeFile)
   {
     TreePanel tp = new TreePanel(alignPanel, treeFile,
             MessageManager.getString("label.load_tree_from_file"), tree);
-    jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
+    JalviewLite.addFrame(tp, treeFile, 600, 500);
     addTreeMenuItem(tp, treeFile);
   }
 
@@ -2968,7 +2971,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     Frame frame = new Frame();
     frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
             .getBuildDate()));
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("label.jalview"), 580, 220);
 
   }
@@ -3198,11 +3201,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     inputText.addActionListener(this);
     Menu outputTextboxMenu = new Menu(
             MessageManager.getString("label.out_to_textbox"));
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (int i = 0; i < AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
     {
 
-      MenuItem item = new MenuItem(
-              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+      MenuItem item = new MenuItem(AppletFormatAdapter.WRITEABLE_FORMATS[i]);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
@@ -3806,7 +3808,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       add(statusBar, BorderLayout.SOUTH);
       add(alignPanel, BorderLayout.CENTER);
       // and register with the applet so it can pass external API calls to us
-      jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
+      JalviewLite.addFrame(this, this.getTitle(),
               frameWidth,
               frameHeight);
     }
@@ -4064,12 +4066,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       // can only do alignments with Jmol
       // find the last jmol window assigned to this alignment
-      jalview.appletgui.AppletJmol ajm = null, tajm;
+      AppletJmol ajm = null, tajm;
       Vector jmols = applet
-              .getAppletWindow(jalview.appletgui.AppletJmol.class);
+.getAppletWindow(AppletJmol.class);
       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
       {
-        tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+        tajm = (AppletJmol) jmols.elementAt(i);
         if (tajm.ap.alignFrame == this)
         {
           ajm = tajm;
@@ -4088,8 +4090,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // otherwise, create a new window
     if (applet.jmolAvailable)
     {
-      new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
-              protocol);
+      new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
       applet.lastFrameX += 40;
       applet.lastFrameY += 40;
     }
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index e4e3e17..68d6c90 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -36,7 +36,9 @@ import jalview.structure.CommandListener;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
+import jalview.util.Platform;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.workers.AlignCalcManager;
 
 import java.awt.Font;
 
@@ -51,7 +53,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   NJTree currentTree = null;
 
-  public jalview.bin.JalviewLite applet;
+  public JalviewLite applet;
 
   boolean MAC = false;
 
@@ -68,7 +70,7 @@ public class AlignViewport extends AlignmentViewport implements
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     super();
-    calculator = new jalview.workers.AlignCalcManager();
+    calculator = new AlignCalcManager();
     this.applet = applet;
     alignment = al;
     // we always pad gaps
@@ -129,7 +131,7 @@ public class AlignViewport extends AlignmentViewport implements
     }
     setFont(font);
 
-    MAC = new jalview.util.Platform().isAMac();
+    MAC = Platform.isAMac();
 
     if (applet != null)
     {
@@ -338,8 +340,7 @@ public class AlignViewport extends AlignmentViewport implements
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {
-    return jalview.structure.StructureSelectionManager
-            .getStructureSelectionManager(applet);
+    return StructureSelectionManager.getStructureSelectionManager(applet);
   }
 
   /**
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 463c6c3..d82b3c3 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -953,8 +953,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
 
     if (updateOverview)
     {
-      jalview.structure.StructureSelectionManager
-              .getStructureSelectionManager(av.applet)
+      StructureSelectionManager.getStructureSelectionManager(av.applet)
               .sequenceColoursChanged(this);
 
       if (overviewPanel != null)
diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 5fa7d6e..3d79588 100644
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -20,6 +20,9 @@
  */
 package jalview.appletgui;
 
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
@@ -61,7 +64,7 @@ public class AnnotationColourChooser extends Panel implements
 
   Hashtable oldgroupColours;
 
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  AlignmentAnnotation currentAnnotation;
 
   boolean adjusting = false;
 
@@ -174,7 +177,7 @@ public class AnnotationColourChooser extends Panel implements
 
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("label.colour_by_annotation"), 560,
             175);
     validate();
@@ -458,7 +461,7 @@ public class AnnotationColourChooser extends Panel implements
             && currentAnnotation.threshold == null)
     {
       currentAnnotation
-              .setThreshold(new jalview.datamodel.GraphLine(
+              .setThreshold(new GraphLine(
                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
                       "Threshold", Color.black));
     }
diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index 0375de2..07eef12 100644
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -1,7 +1,9 @@
 package jalview.appletgui;
 
+import jalview.bin.JalviewLite;
 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;
@@ -108,7 +110,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     super(av, ap);
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("label.select_by_annotation"), 520,
             215);
 
@@ -385,7 +387,7 @@ 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/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 67faf11..c490fba 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -20,6 +20,15 @@
  */
 package jalview.appletgui;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.util.ParseHtmlBodyAndLinks;
+
 import java.awt.Checkbox;
 import java.awt.CheckboxMenuItem;
 import java.awt.Color;
@@ -44,14 +53,6 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.Vector;
 
-import jalview.analysis.AlignmentUtils;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-import jalview.util.ParseHtmlBodyAndLinks;
-
 public class AnnotationLabels extends Panel implements ActionListener,
         MouseListener, MouseMotionListener
 {
@@ -200,7 +201,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
               ap.alignFrame);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
+      JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
               + " - " + aa[selectedRow].label, 500, 100);
       cap.setText(aa[selectedRow].toString());
     }
@@ -766,16 +767,16 @@ public class AnnotationLabels extends Panel implements ActionListener,
     {
       return;
     }
-    jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
-    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
+    AlignFrame.copiedSequences = new StringBuffer();
+    AlignFrame.copiedSequences.append(sq.getName() + "\t"
             + sq.getStart() + "\t" + sq.getEnd() + "\t"
             + sq.getSequenceAsString() + "\n");
     if (av.hasHiddenColumns())
     {
-      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
+      AlignFrame.copiedHiddenColumns = new Vector();
       for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
-        jalview.appletgui.AlignFrame.copiedHiddenColumns
+        AlignFrame.copiedHiddenColumns
                 .addElement(new int[]
                 { region[0], region[1] });
       }
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 32d528c..6f406a4 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -25,6 +25,7 @@ import jalview.datamodel.Annotation;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -98,7 +99,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
 
   public AnnotationPanel(AlignmentPanel ap)
   {
-    MAC = new jalview.util.Platform().isAMac();
+    MAC = Platform.isAMac();
     this.ap = ap;
     av = ap.av;
     setLayout(null);
diff --git a/src/jalview/appletgui/AnnotationRowFilter.java b/src/jalview/appletgui/AnnotationRowFilter.java
index 8a0a44a..1345503 100644
--- a/src/jalview/appletgui/AnnotationRowFilter.java
+++ b/src/jalview/appletgui/AnnotationRowFilter.java
@@ -1,5 +1,6 @@
 package jalview.appletgui;
 
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
 
@@ -26,7 +27,7 @@ public abstract class AnnotationRowFilter extends Panel
 
   protected boolean enableSeqAss = false;
 
-  private jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  private AlignmentAnnotation currentAnnotation;
 
   protected boolean adjusting = false;
 
@@ -179,13 +180,12 @@ public abstract class AnnotationRowFilter extends Panel
   }
 
 
-  public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
+  public AlignmentAnnotation getCurrentAnnotation()
   {
     return currentAnnotation;
   }
 
-  public void setCurrentAnnotation(
-          jalview.datamodel.AlignmentAnnotation currentAnnotation)
+  public void setCurrentAnnotation(AlignmentAnnotation currentAnnotation)
   {
     this.currentAnnotation = currentAnnotation;
   }
diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index e889467..c981104 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -20,6 +20,7 @@
  */
 package jalview.appletgui;
 
+import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -197,7 +198,7 @@ public class AppletJmol extends EmbmenuFrame implements
       }
     }
 
-    if (jalview.bin.JalviewLite.debug)
+    if (JalviewLite.debug)
     {
       System.err
               .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'");
@@ -318,7 +319,7 @@ public class AppletJmol extends EmbmenuFrame implements
           java.io.Reader freader = null;
           if (reader != null)
           {
-            if (jalview.bin.JalviewLite.debug)
+            if (JalviewLite.debug)
             {
               System.err
                       .println("AppletJmol:Trying to reuse existing PDBfile IO parser.");
@@ -328,7 +329,7 @@ public class AppletJmol extends EmbmenuFrame implements
           }
           if (freader == null)
           {
-            if (jalview.bin.JalviewLite.debug)
+            if (JalviewLite.debug)
             {
               System.err
                       .println("AppletJmol:Creating new PDBfile IO parser.");
@@ -362,7 +363,7 @@ public class AppletJmol extends EmbmenuFrame implements
       }
     }
 
-    jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
+    JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400);
   }
 
   public void loadInline(String string)
@@ -419,7 +420,7 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     if (evt.getSource() == mappingMenuItem)
     {
-      jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(
               false, null);
       Frame frame = new Frame();
       frame.add(cap);
@@ -435,7 +436,7 @@ public class AppletJmol extends EmbmenuFrame implements
                 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
         return;
       }
-      jalview.bin.JalviewLite.addFrame(frame,
+      JalviewLite.addFrame(frame,
               MessageManager.getString("label.pdb_sequence_mapping"), 550,
               600);
     }
diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 535dc62..20f61b5 100644
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -358,7 +358,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     try
     {
       tcf = new TCoffeeScoreFile(textarea.getText(),
-              jalview.io.AppletFormatAdapter.PASTE);
+              AppletFormatAdapter.PASTE);
       if (tcf.isValid())
       {
         if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(),
@@ -393,8 +393,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
     if (tcf == null)
     {
       if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport,
-              textarea.getText(),
-              jalview.io.AppletFormatAdapter.PASTE))
+              textarea.getText(), AppletFormatAdapter.PASTE))
       {
         alignFrame.alignPanel.fontChanged();
         alignFrame.alignPanel.setScrollValues(0, 0);
@@ -406,7 +405,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
       else
       {
         if (!alignFrame.parseFeaturesFile(textarea.getText(),
-                jalview.io.AppletFormatAdapter.PASTE))
+                AppletFormatAdapter.PASTE))
         {
           alignFrame.statusBar
                   .setText(MessageManager
@@ -429,7 +428,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
     if (alignFrame.alignPanel.av.applet.jmolAvailable)
     {
-      new jalview.appletgui.AppletJmol(pdb, new SequenceI[]
+      new AppletJmol(pdb, new SequenceI[]
       { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE);
     }
     else
diff --git a/src/jalview/appletgui/EmbmenuFrame.java b/src/jalview/appletgui/EmbmenuFrame.java
index be4eab6..a26202b 100644
--- a/src/jalview/appletgui/EmbmenuFrame.java
+++ b/src/jalview/appletgui/EmbmenuFrame.java
@@ -20,6 +20,8 @@
  */
 package jalview.appletgui;
 
+import jalview.util.Platform;
+
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.FlowLayout;
@@ -95,7 +97,7 @@ public class EmbmenuFrame extends Frame implements MouseListener
       return false;
     }
     // DEBUG Hint: can test embedded menus by inserting true here.
-    if (new jalview.util.Platform().isAMac())
+    if (Platform.isAMac())
     {
       // Build the embedded menu panel, allowing override with system font
       embeddedMenu = makeEmbeddedPopupMenu(topMenuBar, true, false);
diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index b4367bf..915d27f 100644
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -20,15 +20,33 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.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.Checkbox;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.Hashtable;
+
 public class FeatureColourChooser extends Panel implements ActionListener,
         AdjustmentListener, ItemListener, MouseListener
 {
@@ -279,14 +297,14 @@ public class FeatureColourChooser extends Panel implements ActionListener,
   {
     if (!adjusting)
     {
-      thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+      thresholdValue.setText((slider.getValue() / 1000f) + "");
       valueChanged();
     }
   }
 
   protected void valueChanged()
   {
-    threshline.value = (float) slider.getValue() / 1000f;
+    threshline.value = slider.getValue() / 1000f;
     cs.setThresh(threshline.value);
     changeColour();
     PaintRefresher.Refresh(this, fr.getViewport().getSequenceSetId());
@@ -368,7 +386,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
             && 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);
     }
 
diff --git a/src/jalview/appletgui/FeatureRenderer.java b/src/jalview/appletgui/FeatureRenderer.java
index 4536b1a..8a0e528 100644
--- a/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@ -20,6 +20,16 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
 import java.awt.BorderLayout;
 import java.awt.Button;
 import java.awt.Choice;
@@ -37,14 +47,6 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.Hashtable;
 
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.GraduatedColor;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-
 /**
  * DOCUMENT ME!
  * 
@@ -249,8 +251,8 @@ public class FeatureRenderer extends
           Object col = getFeatureStyle(name.getText());
           if (col == null)
           {
-            col = new jalview.schemes.UserColourScheme()
-                    .createColourFromName(name.getText());
+            col = new UserColourScheme().createColourFromName(name
+                    .getText());
           }
 
           colourPanel.updateColor(col);
@@ -361,7 +363,7 @@ public class FeatureRenderer extends
     Color col = getColour(name.getText());
     if (col == null)
     {
-      col = new jalview.schemes.UserColourScheme()
+      col = new UserColourScheme()
               .createColourFromName(name.getText());
     }
     Object fcol = getFeatureStyle(name.getText());
@@ -387,7 +389,7 @@ public class FeatureRenderer extends
     });
     dialog.setVisible(true);
 
-    jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
+    FeaturesFile ffile = new FeaturesFile();
 
     if (dialog.accept)
     {
@@ -468,9 +470,9 @@ public class FeatureRenderer extends
       }
     }
     // refresh the alignment and the feature settings dialog
-    if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
+    if (((AlignViewport) av).featureSettings != null)
     {
-      ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
+      ((AlignViewport) av).featureSettings.refreshTable();
     }
     // findAllFeatures();
 
diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 2b79256..8984390 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -21,6 +21,7 @@
 package jalview.appletgui;
 
 import jalview.api.FeatureSettingsControllerI;
+import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 import jalview.schemes.AnnotationColourGradient;
@@ -178,7 +179,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     height = Math.max(200, height);
     height = Math.min(400, height);
     int width = 300;
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("label.feature_settings"), width,
             height);
   }
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 5412472..7315eea 100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -20,6 +20,7 @@
  */
 package jalview.appletgui;
 
+import jalview.bin.JalviewLite;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -71,7 +72,7 @@ public class Finder extends Panel implements ActionListener
     this.ap = ap;
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("action.find"), 340, 120);
     frame.repaint();
     frame.addWindowListener(new WindowAdapter()
diff --git a/src/jalview/appletgui/FontChooser.java b/src/jalview/appletgui/FontChooser.java
index 6456878..739eeb2 100644
--- a/src/jalview/appletgui/FontChooser.java
+++ b/src/jalview/appletgui/FontChooser.java
@@ -20,6 +20,10 @@
  */
 package jalview.appletgui;
 
+import jalview.api.ViewStyleI;
+import jalview.bin.JalviewLite;
+import jalview.util.MessageManager;
+
 import java.awt.BorderLayout;
 import java.awt.Button;
 import java.awt.Checkbox;
@@ -37,9 +41,6 @@ import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 
-import jalview.api.ViewStyleI;
-import jalview.util.MessageManager;
-
 /**
  * This dialog allows the user to try different font settings and related
  * options. Changes are immediately visible on the alignment or tree. The user
@@ -151,7 +152,7 @@ public class FontChooser extends Panel implements ItemListener
 
     this.frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("action.change_font"), 440, 115);
 
     init = false;
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 258b8b6..c4b9651 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -20,6 +20,13 @@
  */
 package jalview.appletgui;
 
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.UrlLink;
+import jalview.viewmodel.AlignmentViewport;
+
 import java.awt.BorderLayout;
 import java.awt.Panel;
 import java.awt.event.InputEvent;
@@ -29,13 +36,6 @@ import java.awt.event.MouseMotionListener;
 import java.util.List;
 import java.util.Vector;
 
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.UrlLink;
-import jalview.viewmodel.AlignmentViewport;
-
 public class IdPanel extends Panel implements MouseListener,
         MouseMotionListener
 {
@@ -231,7 +231,7 @@ public class IdPanel extends Panel 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);
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index f09bda5..5c5ae84 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -21,6 +21,7 @@
 package jalview.appletgui;
 
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -297,7 +298,7 @@ public class OverviewPanel extends Panel implements Runnable,
     int xstart = 0, ystart = 0;
     Color color = Color.yellow;
     int row, col, sameRow = 0, sameCol = 0;
-    jalview.datamodel.SequenceI seq;
+    SequenceI seq;
     final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
             .hasHiddenColumns();
     boolean hiddenRow = false;
diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 10969b9..1746736 100644
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -20,13 +20,32 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 import jalview.viewmodel.PCAModel;
 
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.CheckboxMenuItem;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+
 public class PCAPanel extends EmbmenuFrame implements Runnable,
         ActionListener, ItemListener
 {
@@ -87,7 +106,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     embedMenuIfNeeded(rc);
     add(rc, BorderLayout.CENTER);
 
-    jalview.bin.JalviewLite.addFrame(this,
+    JalviewLite.addFrame(this,
             MessageManager.getString("label.principal_component_analysis"),
             475, 400);
 
@@ -222,7 +241,7 @@ public class PCAPanel extends EmbmenuFrame implements Runnable,
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("label.pca_details"), 500, 500);
 
     cap.setText(pcaModel.getDetails());
diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 27470f0..5548795 100644
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -24,6 +24,7 @@ import jalview.analysis.AlignSeq;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.util.Format;
 import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
@@ -107,7 +108,8 @@ public class PairwiseAlignPanel extends Panel implements ActionListener
 
       for (int i = 0; i < count; i++)
       {
-        jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
+        Format.print(System.out, "%s \n",
+                ("" + i) + " "
                 + seqs[i].getName());
       }
 
@@ -117,7 +119,7 @@ public class PairwiseAlignPanel extends Panel implements ActionListener
       {
         for (int j = 0; j < i; j++)
         {
-          jalview.util.Format.printDouble(System.out, "%7.3f", scores[i][j]
+          Format.printDouble(System.out, "%7.3f", scores[i][j]
                   / totscore);
         }
       }
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index c4a6989..9ce4f26 100644
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -21,6 +21,7 @@
 package jalview.appletgui;
 
 import jalview.analysis.AlignSeq;
+import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -83,7 +84,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable,
 
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager
+    JalviewLite.addFrame(frame, MessageManager
             .getString("label.redundancy_threshold_selection"), 400, 100);
 
     frame.addWindowListener(this);
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 522151c..0057194 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/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 jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
@@ -138,7 +139,7 @@ public class SeqCanvas extends Panel
 
       while (index < endx)
       {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        if (Comparison.isGap(seq.getCharAt(index)))
         {
           index++;
 
@@ -179,7 +180,7 @@ public class SeqCanvas extends Panel
 
       while (index > startx)
       {
-        if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
+        if (Comparison.isGap(seq.getCharAt(index)))
         {
           index--;
 
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 86dedfc..348a921 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -20,18 +20,6 @@
  */
 package jalview.appletgui;
 
-import java.awt.BorderLayout;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Panel;
-import java.awt.Point;
-import java.awt.event.InputEvent;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.api.AlignViewportI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
@@ -48,10 +36,23 @@ import jalview.structure.SelectionSource;
 import jalview.structure.SequenceListener;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.List;
+import java.util.Vector;
+
 public class SeqPanel extends Panel implements MouseMotionListener,
         MouseListener, SequenceListener, SelectionListener
 {
@@ -1178,7 +1179,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           {
             for (int j = 0; j < startres - lastres; j++)
             {
-              if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
+              if (!Comparison.isGap(gs.getCharAt(fixedRight
                       - j)))
               {
                 blank = false;
@@ -1241,7 +1242,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
               continue;
             }
 
-            if (!jalview.util.Comparison.isGap(gs.getCharAt(j)))
+            if (!Comparison.isGap(gs.getCharAt(j)))
             {
               // Not a gap, block edit not valid
               endEditing();
@@ -1312,7 +1313,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           for (int j = lastres; j > startres; j--)
           {
-            if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+            if (!Comparison.isGap(seq.getCharAt(startres)))
             {
               endEditing();
               break;
@@ -1327,7 +1328,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           int max = 0;
           for (int m = startres; m < lastres; m++)
           {
-            if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+            if (!Comparison.isGap(seq.getCharAt(m)))
             {
               break;
             }
@@ -1357,7 +1358,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       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;
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index feb2705..e2e98cb 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/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.Font;
@@ -117,8 +118,7 @@ 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)))
+    else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
     {
       resBoxColour = Color.lightGray;
     }
@@ -237,7 +237,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
       graphics.setColor(Color.black);
 
       s = seq.getCharAt(i);
-      if (!renderGaps && jalview.util.Comparison.isGap(s))
+      if (!renderGaps && Comparison.isGap(s))
       {
         continue;
       }
diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
index 65622aa..b267678 100644
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -20,6 +20,7 @@
  */
 package jalview.appletgui;
 
+import jalview.bin.JalviewLite;
 import jalview.datamodel.SequenceGroup;
 import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
@@ -99,7 +100,7 @@ public class SliderPanel extends Panel implements ActionListener,
 
     if (!conservationSlider.isVisible())
     {
-      jalview.bin.JalviewLite.addFrame(conservationSlider,
+      JalviewLite.addFrame(conservationSlider,
               conservationSlider.getTitle(), 420, 100);
       conservationSlider.addWindowListener(new WindowAdapter()
       {
@@ -155,7 +156,7 @@ public class SliderPanel extends Panel implements ActionListener,
 
     if (!PIDSlider.isVisible())
     {
-      jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(),
+      JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(),
               420, 100);
       PIDSlider.addWindowListener(new WindowAdapter()
       {
diff --git a/src/jalview/appletgui/SplitFrame.java b/src/jalview/appletgui/SplitFrame.java
index 836d70c..3d30800 100644
--- a/src/jalview/appletgui/SplitFrame.java
+++ b/src/jalview/appletgui/SplitFrame.java
@@ -1,10 +1,5 @@
 package jalview.appletgui;
 
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.GridLayout;
-import java.awt.Panel;
-
 import jalview.analysis.AlignmentUtils;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ViewStyleI;
@@ -13,6 +8,11 @@ import jalview.datamodel.AlignmentI;
 import jalview.structure.StructureSelectionManager;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.Panel;
+
 public class SplitFrame extends EmbmenuFrame
 {
   private static final long serialVersionUID = 1L;
@@ -193,8 +193,7 @@ public class SplitFrame extends EmbmenuFrame
       this.add(outermost);
       int width = Math.max(topFrame.frameWidth, bottomFrame.frameWidth);
       int height = topFrame.frameHeight + bottomFrame.frameHeight;
-      jalview.bin.JalviewLite
-              .addFrame(this, this.getTitle(), width, height);
+      JalviewLite.addFrame(this, this.getTitle(), width, height);
     }
   }
 
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index b4b8ec2..e5971e5 100644
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -23,6 +23,7 @@ package jalview.appletgui;
 import jalview.analysis.NJTree;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.bin.JalviewLite;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.ColumnSelection;
@@ -193,7 +194,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
   {
     NewickFile newtree;
 
-    jalview.datamodel.AlignmentView odata = null;
+    AlignmentView odata = null;
 
     public TreeLoader(NewickFile newtree)
     {
@@ -329,14 +330,13 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
 
   public void newickOutput_actionPerformed()
   {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(
-            tree.getTopNode());
+    NewickFile fout = new NewickFile(tree.getTopNode());
     String output = fout.print(false, true);
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
     cap.setText(output);
     java.awt.Frame frame = new java.awt.Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
+    JalviewLite.addFrame(frame, type + " " + pwtype, 500, 100);
   }
 
   public java.awt.Font getTreeFont()
diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 277bd55..afea10d 100644
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -20,6 +20,14 @@
  */
 package jalview.appletgui;
 
+import jalview.bin.JalviewLite;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.MessageManager;
+
 import java.awt.Button;
 import java.awt.Color;
 import java.awt.Component;
@@ -42,13 +50,6 @@ import java.awt.event.FocusListener;
 import java.awt.event.MouseEvent;
 import java.util.Vector;
 
-import jalview.datamodel.SequenceGroup;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.GraduatedColor;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
-import jalview.util.MessageManager;
-
 public class UserDefinedColours extends Panel implements ActionListener,
         AdjustmentListener, FocusListener
 {
@@ -281,7 +282,7 @@ public class UserDefinedColours extends Panel implements ActionListener,
     }
     frame = new Frame();
     frame.add(this);
-    jalview.bin.JalviewLite.addFrame(frame,
+    JalviewLite.addFrame(frame,
             MessageManager.getString("label.user_defined_colours"), 420,
             345);