From: BobHanson <hansonr@stolaf.edu>
Date: Tue, 9 Jun 2020 06:42:17 +0000 (-0500)
Subject: JAL-3446 from applet; JAL-3374
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=be8b1d254f658181eec3c29dc696114e3ffdd4df;p=jalview.git

JAL-3446 from applet; JAL-3374

- JalviewJSApp interface updated
- Jalview "noannotations" fixed
- AlignFrame show annotations menu item when started with noannations
fixed
- reorganization of timing of setting range start/end and scrollbar
values solves (many) timing issues in SeqCanvasTest and
AlignmentPanelTest, which were due to asynchronous delayed repaints
setting range values in paintComponent(g) way too late.
- correction of font checking in AlignmentPanelTest - "VERY LONG LABEL"
not long enough after adding "MMMM" in a prior test
- corrections for "isMac()" (now "!isWin()") in tests
- addition of Jalview.isInteractive for SeqCanvasTest -- still an
occasional conflict with previous test when in batch mode
- addition of Jalview.allowServices for simple tests (using -jabaws
"none"), allowing them to not run unnecessary service look-up threads
- centralization of AlignmentViewport firing of "alignment" property
change for sanity only
- adding of "sequence" property change for notification of need to
refresh the horizontal scrollbar after changes in range and scrollbar
update timing

- still a minor issue with noannotation starting up ok, but the first
annotation spilling over into scrollbar space (is that a filler?)
---

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index e1bfbde..311f1e7 100644
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -773,8 +773,7 @@ public class APopupMenu extends java.awt.PopupMenu
 
           ap.alignFrame.addHistoryItem(editCommand);
 
-          ap.av.firePropertyChange("alignment", null,
-                  ap.av.getAlignment().getSequences());
+          ap.av.notifyAlignment();
         }
       }
     }
@@ -811,8 +810,7 @@ public class APopupMenu extends java.awt.PopupMenu
 
         ap.alignFrame.addHistoryItem(caseCommand);
 
-        ap.av.firePropertyChange("alignment", null,
-                ap.av.getAlignment().getSequences());
+        ap.av.notifyAlignment();
 
       }
     }
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1a46585..fc1f26d 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -882,7 +882,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else if (source == autoCalculate)
     {
-      viewport.autoCalculateConsensus = autoCalculate.getState();
+      viewport.setAutoCalculateConsensusAndConservation(autoCalculate.getState());
     }
     else if (source == sortByTree)
     {
@@ -1701,8 +1701,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                                           // viewport.getColumnSelection().getHiddenColumns()
                                           // != null;
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.getAlignment().getSequences());
+    originalSource.notifyAlignment();
   }
 
   /**
@@ -1734,8 +1733,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                                           // != null;
 
     updateEditMenuBar();
-    originalSource.firePropertyChange("alignment", null,
-            originalSource.getAlignment().getSequences());
+    originalSource.notifyAlignment();
   }
 
   AlignmentViewport getOriginatingSource(CommandI command)
@@ -2084,8 +2082,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
                                                                              // 2019.04.18
     viewport.getAlignment().getWidth();
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
 
   }
 
@@ -2159,8 +2156,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     viewport.setSelectionGroup(null);
     viewport.getAlignment().deleteGroup(sg);
 
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
 
     if (viewport.getAlignment().getHeight() < 1)
     {
@@ -2372,7 +2368,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         }
       }
 
-      viewport.firePropertyChange("alignment", null, al.getSequences());
+      viewport.notifyAlignment();
     }
   }
 
@@ -2416,7 +2412,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
     ranges.setStartRes(seq.findIndex(startRes) - 1);
-    viewport.firePropertyChange("alignment", null, al.getSequences());
+    viewport.notifyAlignment();
 
   }
 
@@ -2450,7 +2446,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     ranges.setStartRes(seq.findIndex(startRes) - 1);
 
-    viewport.firePropertyChange("alignment", null, al.getSequences());
+    viewport.notifyAlignment();
 
   }
 
diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 0324d8c..b379c2d 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -352,7 +352,7 @@ public class AlignViewport extends AlignmentViewport
     if (mappedCommand != null)
     {
       mappedCommand.doCommand(null);
-      firePropertyChange("alignment", null, getAlignment().getSequences());
+      notifyAlignment();
 
       // ap.scalePanelHolder.repaint();
       // ap.repaint();
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index bd36b0d..6488c61 100644
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -227,8 +227,7 @@ public class RedundancyPanel extends SliderPanel
       ap.alignFrame.addHistoryItem(cut);
 
       PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
-      ap.av.firePropertyChange("alignment", null,
-              ap.av.getAlignment().getSequences());
+      ap.av.notifyAlignment();
     }
 
   }
@@ -243,8 +242,7 @@ public class RedundancyPanel extends SliderPanel
     {
       ap.av.getHistoryList().remove(command);
       ap.alignFrame.updateEditMenuBar();
-      ap.av.firePropertyChange("alignment", null,
-              ap.av.getAlignment().getSequences());
+      ap.av.notifyAlignment();
     }
 
     ap.paintAlignment(true, true);
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 776e9ad..a1e2340 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -132,8 +132,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     if (editCommand != null && editCommand.getSize() > 0)
     {
       ap.alignFrame.addHistoryItem(editCommand);
-      av.firePropertyChange("alignment", null,
-              av.getAlignment().getSequences());
+      av.notifyAlignment();
     }
 
     startseq = -1;
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index cb26fb5..46d6c11 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -715,8 +715,10 @@ public class TreeCanvas extends Panel
     ap.updateAnnotation();
     if (av.getCodingComplement() != null)
     {
-      ((AlignmentViewport) av.getCodingComplement()).firePropertyChange(
-              "alignment", null, ap.av.getAlignment().getSequences());
+      ((AlignmentViewport) av.getCodingComplement()).notifyAlignment();
+      // Technically, the property change is not the same because av is not necessarily getCodingComplement(), 
+      // but this is the appletgui, so I am not going to worry about it. BH
+      //.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
     }
   }
 
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 81193e6..4a5c733 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -297,6 +297,8 @@ public class Jalview implements ApplicationSingletonI
 
     Cache.loadProperties(usrPropsFile); // must do this before
 
+    boolean allowServices = true;
+    
     if (isJS)
     {
       j2sAppletID = Platform.getAppID(null);
@@ -336,7 +338,8 @@ public class Jalview implements ApplicationSingletonI
       // anything else!
 
       final String jabawsUrl = aparser.getValue(ArgsParser.JABAWS);
-      if (jabawsUrl != null)
+      allowServices = !("none".equals(jabawsUrl));
+      if (allowServices && jabawsUrl != null)
       {
         try
         {
@@ -469,7 +472,8 @@ public class Jalview implements ApplicationSingletonI
        * @j2sIgnore
        */
       {
-        desktop.startServiceDiscovery();
+        if (allowServices)
+          desktop.startServiceDiscovery();
         if (!aparser.contains("nousagestats"))
         {
           startUsageStats(desktop);
@@ -525,9 +529,11 @@ public class Jalview implements ApplicationSingletonI
   }
 
   /**
-   * Parse all command-line String[] arguments as well as all JavaScript-derived parameters from Info.
+   * Parse all command-line String[] arguments as well as all JavaScript-derived
+   * parameters from Info.
    * 
-   * We allow for this method to be run from JavaScript. Basically allowing simple scripting.
+   * We allow for this method to be run from JavaScript. Basically allowing
+   * simple scripting.
    * 
    * @param aparser
    * @param isStartup
@@ -573,6 +579,8 @@ public class Jalview implements ApplicationSingletonI
       System.exit(1);
     }
 
+    setDisplayParameters(aparser);
+    
     // time to open a file.
 
     long progress = -1;
@@ -582,7 +590,65 @@ public class Jalview implements ApplicationSingletonI
     // Finally, deal with the remaining input data.
     AlignFrame af = null;
 
-    if (file != null)
+    JalviewJSApp jsApp = (isJS ? new JalviewJSApp(this, aparser) : null);
+
+    if (file == null)
+    {
+      if (isJS)
+      {
+        // JalviewJS allows sequence1 sequence2 ....
+        
+      }
+      else if (!headless && Cache.getDefault("SHOW_STARTUP_FILE", true))
+      /**
+       * Java only
+       * 
+       * @j2sIgnore
+       */
+      {
+
+        // We'll only open the default file if the desktop is visible.
+        // And the user
+        // ////////////////////
+
+        file = Cache.getDefault("STARTUP_FILE",
+                Cache.getDefault("www.jalview.org",
+                        "http://www.jalview.org")
+                        + "/examples/exampleFile_2_7.jar");
+        if (file.equals(
+                "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+        {
+          // hardwire upgrade of the startup file
+          file.replace("_2_3.jar", "_2_7.jar");
+          // and remove the stale setting
+          Cache.removeProperty("STARTUP_FILE");
+        }
+
+        protocol = DataSourceType.FILE;
+
+        if (file.indexOf("http:") > -1)
+        {
+          protocol = DataSourceType.URL;
+        }
+
+        if (file.endsWith(".jar"))
+        {
+          format = FileFormat.Jalview;
+        }
+        else
+        {
+          try
+          {
+            format = new IdentifyFile().identify(file, protocol);
+          } catch (FileFormatException e)
+          {
+            // TODO what?
+          }
+        }
+        af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
+      }
+    }
+    else
     {
       if (!headless)
       {
@@ -613,6 +679,7 @@ public class Jalview implements ApplicationSingletonI
           }
         }
       }
+      
       String fileFormat = (isJS
               ? (String) aparser.getAppletValue("format", null, true)
               : null);
@@ -631,35 +698,11 @@ public class Jalview implements ApplicationSingletonI
         // TODO ?
       }
 
-      if (aparser.contains(ArgsParser.NOMENUBAR))
-      {
-        noMenuBar = true;
-        System.out.println("CMD [nomenu] executed successfully!");
-      }
-
-      if (aparser.contains(ArgsParser.NOSTATUS))
-      {
-        noStatus = true;
-        System.out.println("CMD [nostatus] executed successfully!");
-      }
-
-      if (aparser.contains(ArgsParser.NOANNOTATION)
-              || aparser.contains(ArgsParser.NOANNOTATION2))
-      {
-        noAnnotation = true;
-        System.out.println("CMD no-annotation executed successfully!");
-      }
-      if (aparser.contains(ArgsParser.NOCALCULATION))
-      {
-        noCalculation = true;
-        System.out.println("CMD [nocalculation] executed successfully!");
-      }
-
       af = new FileLoader(!headless).LoadFileWaitTillLoaded(file, protocol,
               format);
       if (af == null)
       {
-        System.out.println("error");
+        System.out.println("jalview error - AlignFrame was not created");
       }
       else
       {
@@ -694,133 +737,11 @@ public class Jalview implements ApplicationSingletonI
         }
         setCurrentAlignFrame(af);
 
-        String data = aparser.getValue(ArgsParser.COLOUR, true);
-        if (data != null)
-        {
-          data.replaceAll("%20", " ");
-
-          ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
-                  af.getViewport(), af.getViewport().getAlignment(), data);
-
-          if (cs != null)
-          {
-            System.out.println(
-                    "CMD [-color " + data + "] executed successfully!");
-          }
-          af.changeColour(cs);
-        }
-
-        // Must maintain ability to use the groups flag
-        data = aparser.getValue(ArgsParser.GROUPS, true);
-        if (data != null)
-        {
-          af.parseFeaturesFile(data,
-                  AppletFormatAdapter.checkProtocol(data));
-          // System.out.println("Added " + data);
-          System.out.println(
-                  "CMD groups[-" + data + "]  executed successfully!");
-        }
-        data = aparser.getValue(ArgsParser.FEATURES, true);
-        if (data != null)
-        {
-          af.parseFeaturesFile(data,
-                  AppletFormatAdapter.checkProtocol(data));
-          // System.out.println("Added " + data);
-          System.out.println(
-                  "CMD [-features " + data + "]  executed successfully!");
-        }
-        data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
-        if (data != null)
-        {
-          af.loadJalviewDataFile(data, null, null, null);
-          // System.out.println("Added " + data);
-          System.out.println(
-                  "CMD [-annotations " + data + "] executed successfully!");
-        }
-
-        // JavaScript feature
-
-        if (aparser.contains(ArgsParser.SHOWOVERVIEW))
-        {
-          af.overviewMenuItem_actionPerformed(null);
-          System.out.println("CMD [showoverview] executed successfully!");
-        }
-
-        // set or clear the sortbytree flag.
-        if (aparser.contains(ArgsParser.SORTBYTREE))
-        {
-          af.getViewport().setSortByTree(true);
-          if (af.getViewport().getSortByTree())
-          {
-            System.out.println("CMD [-sortbytree] executed successfully!");
-          }
-        }
-
-        boolean doUpdateAnnotation = false;
-        /**
-         * we do this earlier in JalviewJS because of a complication with
-         * SHOWOVERVIEW
-         * 
-         * For now, just fixing this in JalviewJS.
-         *
-         * 
-         * @j2sIgnore
-         * 
-         */
-        {
-          if (aparser.contains(ArgsParser.NOANNOTATION)
-                  || aparser.contains(ArgsParser.NOANNOTATION2))
-          {
-            af.getViewport().setShowAnnotation(false);
-            if (!af.getViewport().isShowAnnotation())
-            {
-              doUpdateAnnotation = true;
-              System.out
-                      .println("CMD no-annotation executed successfully!");
-            }
-          }
-        }
-
-        if (aparser.contains(ArgsParser.NOSORTBYTREE))
-        {
-          af.getViewport().setSortByTree(false);
-          if (!af.getViewport().getSortByTree())
-          {
-            doUpdateAnnotation = true;
-            System.out
-                    .println("CMD [-nosortbytree] executed successfully!");
-          }
-        }
-        if (doUpdateAnnotation)
-        { // BH 2019.07.24
-          af.setMenusForViewport();
-          af.alignPanel.updateLayout();
-        }
-
-        data = aparser.getValue(ArgsParser.TREE, true);
-        if (data != null)
-        {
-          try
-          {
-            NewickFile nf = new NewickFile(data,
-                    AppletFormatAdapter.checkProtocol(data));
-            af.getViewport()
-                    .setCurrentTree(af.showNewickTree(nf, data).getTree());
-            System.out.println(
-                    "CMD [-tree " + data + "] executed successfully!");
-          } catch (IOException ex)
-          {
-            System.err.println("Couldn't add tree " + data);
-            ex.printStackTrace(System.err);
-          }
-        }
-        // TODO - load PDB structure(s) to alignment JAL-629
-        // (associate with identical sequence in alignment, or a specified
-        // sequence)
-
+        setFrameDependentProperties(aparser, af);
+        
         if (isJS)
         {
-          new JalviewJSApp(this, aparser, af);
+          jsApp.initFromParams(af);
         }
         else
         /**
@@ -840,61 +761,10 @@ public class Jalview implements ApplicationSingletonI
                     + "] executed successfully!");
             groovyscript = null;
           }
-          createOutputFiles(aparser, af, format);
-        }
-      }
-    }
-    else
-    {
-      if (!isJS && !headless && Cache.getDefault("SHOW_STARTUP_FILE", true))
-      /**
-       * Java only
-       * 
-       * @j2sIgnore
-       */
-      {
-
-        // We'll only open the default file if the desktop is visible.
-        // And the user
-        // ////////////////////
-
-        file = Cache.getDefault("STARTUP_FILE",
-                Cache.getDefault("www.jalview.org",
-                        "http://www.jalview.org")
-                        + "/examples/exampleFile_2_7.jar");
-        if (file.equals(
-                "http://www.jalview.org/examples/exampleFile_2_3.jar"))
-        {
-          // hardwire upgrade of the startup file
-          file.replace("_2_3.jar", "_2_7.jar");
-          // and remove the stale setting
-          Cache.removeProperty("STARTUP_FILE");
-        }
-
-        protocol = DataSourceType.FILE;
-
-        if (file.indexOf("http:") > -1)
-        {
-          protocol = DataSourceType.URL;
         }
-
-        if (file.endsWith(".jar"))
-        {
-          format = FileFormat.Jalview;
+        if (!isJS || !isStartup) {
+          createOutputFiles(aparser, format);
         }
-        else
-        {
-          try
-          {
-            format = new IdentifyFile().identify(file, protocol);
-          } catch (FileFormatException e)
-          {
-            // TODO what?
-          }
-        }
-
-        af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);
-
       }
     }
     // extract groovy arguments before anything else.
@@ -923,9 +793,170 @@ public class Jalview implements ApplicationSingletonI
       }
       desktop.setInBatchMode(false);
     }
-
+    
+    if (jsApp != null) {
+      jsApp.callInitCallback();
+    }
   }
   
+  /**
+   * Set general display parameters irrespective of file loading or headlessness.
+   * 
+   * @param aparser
+   */
+  private void setDisplayParameters(ArgsParser aparser)
+  {
+    if (aparser.contains(ArgsParser.NOMENUBAR))
+    {
+      noMenuBar = true;
+      System.out.println("CMD [nomenu] executed successfully!");
+    }
+
+    if (aparser.contains(ArgsParser.NOSTATUS))
+    {
+      noStatus = true;
+      System.out.println("CMD [nostatus] executed successfully!");
+    }
+
+    if (aparser.contains(ArgsParser.NOANNOTATION)
+            || aparser.contains(ArgsParser.NOANNOTATION2))
+    {
+      noAnnotation = true;
+      System.out.println("CMD no-annotation executed successfully!");
+    }
+    if (aparser.contains(ArgsParser.NOCALCULATION))
+    {
+      noCalculation = true;
+      System.out.println("CMD [nocalculation] executed successfully!");
+    }
+  }
+
+
+  private void setFrameDependentProperties(ArgsParser aparser,
+          AlignFrame af)
+  {
+    String data = aparser.getValue(ArgsParser.COLOUR, true);
+    if (data != null)
+    {
+      data.replaceAll("%20", " ");
+
+      ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+              af.getViewport(), af.getViewport().getAlignment(), data);
+
+      if (cs != null)
+      {
+        System.out.println(
+                "CMD [-color " + data + "] executed successfully!");
+      }
+      af.changeColour(cs);
+    }
+
+    // Must maintain ability to use the groups flag
+    data = aparser.getValue(ArgsParser.GROUPS, true);
+    if (data != null)
+    {
+      af.parseFeaturesFile(data,
+              AppletFormatAdapter.checkProtocol(data));
+      // System.out.println("Added " + data);
+      System.out.println(
+              "CMD groups[-" + data + "]  executed successfully!");
+    }
+    data = aparser.getValue(ArgsParser.FEATURES, true);
+    if (data != null)
+    {
+      af.parseFeaturesFile(data,
+              AppletFormatAdapter.checkProtocol(data));
+      // System.out.println("Added " + data);
+      System.out.println(
+              "CMD [-features " + data + "]  executed successfully!");
+    }
+    data = aparser.getValue(ArgsParser.ANNOTATIONS, true);
+    if (data != null)
+    {
+      af.loadJalviewDataFile(data, null, null, null);
+      // System.out.println("Added " + data);
+      System.out.println(
+              "CMD [-annotations " + data + "] executed successfully!");
+    }
+
+    // JavaScript feature
+
+    if (aparser.contains(ArgsParser.SHOWOVERVIEW))
+    {
+      af.overviewMenuItem_actionPerformed(null);
+      System.out.println("CMD [showoverview] executed successfully!");
+    }
+
+    // set or clear the sortbytree flag.
+    if (aparser.contains(ArgsParser.SORTBYTREE))
+    {
+      af.getViewport().setSortByTree(true);
+      if (af.getViewport().getSortByTree())
+      {
+        System.out.println("CMD [-sortbytree] executed successfully!");
+      }
+    }
+
+    boolean doUpdateAnnotation = false;
+    /**
+     * we do this earlier in JalviewJS because of a complication with
+     * SHOWOVERVIEW
+     * 
+     * For now, just fixing this in JalviewJS.
+     *
+     * 
+     * @j2sIgnore
+     * 
+     */
+    {
+      if (noAnnotation)
+      {
+        af.getViewport().setShowAnnotation(false);
+        if (!af.getViewport().isShowAnnotation())
+        {
+          doUpdateAnnotation = true;
+        }
+      }
+    }
+
+    if (aparser.contains(ArgsParser.NOSORTBYTREE))
+    {
+      af.getViewport().setSortByTree(false);
+      if (!af.getViewport().getSortByTree())
+      {
+        doUpdateAnnotation = true;
+        System.out
+                .println("CMD [-nosortbytree] executed successfully!");
+      }
+    }
+    if (doUpdateAnnotation)
+    { // BH 2019.07.24
+      af.setMenusForViewport();
+      af.alignPanel.updateLayout();
+    }
+
+    data = aparser.getValue(ArgsParser.TREE, true);
+    if (data != null)
+    {
+      try
+      {
+        NewickFile nf = new NewickFile(data,
+                AppletFormatAdapter.checkProtocol(data));
+        af.getViewport()
+                .setCurrentTree(af.showNewickTree(nf, data).getTree());
+        System.out.println(
+                "CMD [-tree " + data + "] executed successfully!");
+      } catch (IOException ex)
+      {
+        System.err.println("Couldn't add tree " + data);
+        ex.printStackTrace(System.err);
+      }
+    }
+    // TODO - load PDB structure(s) to alignment JAL-629
+    // (associate with identical sequence in alignment, or a specified
+    // sequence)
+
+  }
 
   /**
    * Writes an output file for each format (if any) specified in the
@@ -943,12 +974,12 @@ public class Jalview implements ApplicationSingletonI
    * corresponding alignment image output.
    * 
    * @param aparser
-   * @param af
    * @param format
    */
-  private void createOutputFiles(ArgsParser aparser, AlignFrame af,
+  private void createOutputFiles(ArgsParser aparser,
           FileFormatI format)
   {
+    AlignFrame af = currentAlignFrame;
     while (aparser.getSize() >= 2)
     {
       String outputFormat = aparser.nextValue();
@@ -1265,5 +1296,18 @@ public class Jalview implements ApplicationSingletonI
     // System.out.println("Jalview worker " + worker.getClass().getSimpleName()
     // + " " + status);
   }
-  
+
+
+  private static boolean isInteractive = true;
+
+  public static boolean isInteractive()
+  {
+    return isInteractive;
+  }
+
+  public static void setInteractive(boolean tf)
+  {
+    isInteractive = tf;
+  }
+
 }
diff --git a/src/jalview/bin/JalviewJSApp.java b/src/jalview/bin/JalviewJSApp.java
index 1ba7273..feab4ae 100644
--- a/src/jalview/bin/JalviewJSApp.java
+++ b/src/jalview/bin/JalviewJSApp.java
@@ -9,6 +9,8 @@ import java.util.List;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
+import javax.swing.SwingUtilities;
+
 import jalview.api.JalviewJSApi;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.Alignment;
@@ -153,13 +155,11 @@ public class JalviewJSApp implements JalviewJSApi
 
   }
 
-  public JalviewJSApp(Jalview jalview, ArgsParser aparser, AlignFrame alf)
+  public JalviewJSApp(Jalview jalview, ArgsParser aparser)
   {
     Platform.setAppClass(this);
     this.jalview = jalview;
     this.aparser = aparser;
-    initFromParams(alf);
-    callInitCallback();
   }
 
   @Override
@@ -1270,15 +1270,23 @@ public class JalviewJSApp implements JalviewJSApi
     Object initjscallback = getParameterAsObject("oninit");
     if (initjscallback != null)
     {
-      try
-      {
-        doSendCallback(initjscallback, new Object[0]);
-      } catch (Exception e)
-      {
-        System.err.println("Exception when executing _oninit callback '"
-                + initjscallback + "'.");
-        e.printStackTrace();
-      }
+      SwingUtilities.invokeLater(new Runnable() {
+
+        @Override
+        public void run()
+        {
+          try
+          {
+            doSendCallback(initjscallback, new Object[] {this});
+          } catch (Exception e)
+          {
+            System.err.println("Exception when executing _oninit callback '"
+                    + initjscallback + "'.");
+            e.printStackTrace();
+          }
+        }
+        
+      });
     }
   }
 
@@ -1328,7 +1336,7 @@ public class JalviewJSApp implements JalviewJSApi
    * 
    * @param alf
    */
-  private void initFromParams(AlignFrame alf)
+  void initFromParams(AlignFrame alf)
   {
     String sep = getParameter("separator");
     if (sep != null && sep.length() > 0)
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index f74eb32..b69ba88 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,59 +20,6 @@
  */
 package jalview.gui;
 
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusAdapter;
-import java.awt.event.FocusEvent;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.PrintWriter;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JComponent;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
-import ext.vamsas.ServiceHandle;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.CrossRef;
@@ -156,6 +103,60 @@ import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JComponent;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
+import ext.vamsas.ServiceHandle;
+
 /**
  * DOCUMENT ME!
  * 
@@ -168,7 +169,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 {
 
   public static int frameCount;
-  
+
   public static final int DEFAULT_WIDTH = 700;
 
   public static final int DEFAULT_HEIGHT = 500;
@@ -292,9 +293,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
           int height, String sequenceSetId, String viewId)
   {
-    
+
     id = (++frameCount);
-    
+
     setSize(width, height);
 
     if (al.getDataset() == null)
@@ -304,9 +305,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
 
-    alignPanel = new AlignmentPanel(this, viewport);
-
-    addAlignmentPanel(alignPanel, true);
+    // JalviewJS needs to distinguish a new panel from an old one in init()
+    // alignPanel = new AlignmentPanel(this, viewport);
+    // addAlignmentPanel(alignPanel, true);
     init();
   }
 
@@ -326,8 +327,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       viewport.hideSequence(hiddenSeqs);
     }
-    alignPanel = new AlignmentPanel(this, viewport);
-    addAlignmentPanel(alignPanel, true);
+    // alignPanel = new AlignmentPanel(this, viewport);
+    // addAlignmentPanel(alignPanel, true);
     init();
   }
 
@@ -343,7 +344,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     viewport = ap.av;
     alignPanel = ap;
-    addAlignmentPanel(ap, false);
+    // addAlignmentPanel(ap, false);
     init();
   }
 
@@ -351,13 +352,39 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * initalise the alignframe from the underlying viewport data and the
    * configurations
    */
+
   void init()
   {
+
+    boolean newPanel = (alignPanel == null);
+    viewport.setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+    if (newPanel)
+    {
+      if (Platform.isJS())
+      {
+        // need to set this up front if NOANNOTATION is
+        // used in conjunction with SHOWOVERVIEW.
+
+        // I have not determined if this is appropriate for
+        // Jalview/Java, as it means we are setting this flag
+        // for all subsequent AlignFrames. For now, at least,
+        // I am setting it to be JalviewJS-only.
+
+        boolean showAnnotation = Jalview.getInstance().getShowAnnotation();
+        viewport.setShowAnnotation(showAnnotation);
+      }
+      alignPanel = new AlignmentPanel(this, viewport);
+    }
+    addAlignmentPanel(alignPanel, newPanel);
+
     // setBackground(Color.white); // BH 2019
 
     if (!Jalview.isHeadlessMode())
     {
       progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+      // JalviewJS options
+      statusPanel.setVisible(Jalview.getInstance().getShowStatus());
+      alignFrameMenuBar.setVisible(Jalview.getInstance().getAllowMenuBar());
     }
 
     avc = new jalview.controller.AlignViewController(this, viewport,
@@ -372,7 +399,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // modifyPID.setEnabled(false);
     }
 
-    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
+    String sortby = jalview.bin.Cache.getDefault(Preferences.SORT_ALIGNMENT,
             "No sort");
 
     if (sortby.equals("Id"))
@@ -384,8 +411,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       sortPairwiseMenuItem_actionPerformed(null);
     }
 
-    this.alignPanel.av
-            .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+    // BH see above
+    //
+    // this.alignPanel.av
+    // .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
 
     setMenusFromViewport(viewport);
     buildSortByAnnotationScoresMenu();
@@ -415,7 +444,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       wrapMenuItem_actionPerformed(null);
     }
 
-    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+    if (jalview.bin.Cache.getDefault(Preferences.SHOW_OVERVIEW, false))
     {
       this.overviewMenuItem_actionPerformed(null);
     }
@@ -499,6 +528,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     addFocusListener(new FocusAdapter()
     {
+
       @Override
       public void focusGained(FocusEvent e)
       {
@@ -517,6 +547,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param format
    *          format of file
    */
+
   public void setFileName(String file, FileFormatI format)
   {
     fileName = file;
@@ -530,6 +561,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param file
    */
+
   public void setFileObject(File file)
   {
     this.fileObject = file;
@@ -539,10 +571,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Add a KeyListener with handlers for various KeyPressed and KeyReleased
    * events
    */
+
   void addKeyListener()
   {
     addKeyListener(new KeyAdapter()
     {
+
       @Override
       public void keyPressed(KeyEvent evt)
       {
@@ -559,7 +593,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         switch (evt.getKeyCode())
         {
 
-        case 27: // escape key
+        case KeyEvent.VK_ESCAPE: // escape key
+                                 // alignPanel.deselectAllSequences();
           alignPanel.deselectAllSequences();
 
           break;
@@ -743,16 +778,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         case KeyEvent.VK_LEFT:
           if (evt.isAltDown() || !viewport.cursorMode)
           {
-            viewport.firePropertyChange("alignment", null,
-                    viewport.getAlignment().getSequences());
+            viewport.notifyAlignment();
           }
           break;
 
         case KeyEvent.VK_RIGHT:
           if (evt.isAltDown() || !viewport.cursorMode)
           {
-            viewport.firePropertyChange("alignment", null,
-                    viewport.getAlignment().getSequences());
+            viewport.notifyAlignment();
           }
           break;
         }
@@ -798,9 +831,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         ap.av.getAlignment().padGaps();
       }
-      ap.av.updateConservation(ap);
-      ap.av.updateConsensus(ap);
-      ap.av.updateStrucConsensus(ap);
+      if (Jalview.getInstance().getStartCalculations())
+      {
+        ap.av.updateConservation(ap);
+        ap.av.updateConsensus(ap);
+        ap.av.updateStrucConsensus(ap);
+      }
     }
   }
 
@@ -826,6 +862,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     Desktop.getInstance().addJalviewPropertyChangeListener("services",
             thisListener = new java.beans.PropertyChangeListener()
             {
+
               @Override
               public void propertyChange(PropertyChangeEvent evt)
               {
@@ -849,6 +886,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             });
     addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
     {
+
       @Override
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
@@ -862,6 +900,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // Finally, build the menu once to get current service state
     new Thread(new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -874,6 +913,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Configure menu items that vary according to whether the alignment is
    * nucleotide or protein
    */
+
   public void setGUINucleotide()
   {
     AlignmentI al = getViewport().getAlignment();
@@ -898,6 +938,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * operation that affects the data in the current view (selection changed,
    * etc) to update the menus to reflect the new state.
    */
+
   @Override
   public void setMenusForViewport()
   {
@@ -911,6 +952,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param av
    *          AlignViewport
    */
+
   public void setMenusFromViewport(AlignViewport av)
   {
     padGapsMenuitem.setSelected(av.isPadGaps());
@@ -928,13 +970,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     scaleLeft.setVisible(av.getWrapAlignment());
     scaleRight.setVisible(av.getWrapAlignment());
     annotationPanelMenuItem.setState(av.isShowAnnotation());
-    /*
-     * Show/hide annotations only enabled if annotation panel is shown
-     */
-    showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
-    hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
+    // Show/hide annotations only enabled if annotation panel is shown
+    syncAnnotationMenuItems(av.isShowAnnotation());
     viewBoxesMenuItem.setSelected(av.getShowBoxes());
     viewTextMenuItem.setSelected(av.getShowText());
     showNonconservedMenuItem.setSelected(av.getShowUnconserved());
@@ -952,7 +989,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     applyToAllGroups.setState(av.getColourAppliesToAllGroups());
     showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
     showDbRefsMenuitem.setSelected(av.isShowDBRefs());
-    autoCalculate.setSelected(av.autoCalculateConsensus);
+    autoCalculate
+            .setSelected(av.getAutoCalculateConsensusAndConservation());
     sortByTree.setSelected(av.sortByTree);
     listenToViewSelections.setSelected(av.followSelection);
 
@@ -967,6 +1005,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param b
    */
+
   public void setGroovyEnabled(boolean b)
   {
     runGroovy.setEnabled(b);
@@ -979,6 +1018,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
    */
+
   @Override
   public void setProgressBar(String message, long id)
   {
@@ -996,6 +1036,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return true if any progress bars are still active
    */
+
   @Override
   public boolean operationInProgress()
   {
@@ -1007,6 +1048,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * will cause the status bar to be hidden, with possibly undesirable flicker
    * of the screen layout.
    */
+
   @Override
   public void setStatus(String text)
   {
@@ -1016,6 +1058,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /*
    * Added so Castor Mapping file can obtain Jalview Version
    */
+
   public String getVersion()
   {
     return jalview.bin.Cache.getProperty("VERSION");
@@ -1041,84 +1084,87 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void reload_actionPerformed(ActionEvent e)
   {
-    if (fileName != null)
+    if (fileName == null)
+    {
+      return;
+    }
+    // TODO: JAL-1108 - ensure all associated frames are closed regardless of
+    // originating file's format
+    // TODO: work out how to recover feature settings for correct view(s) when
+    // file is reloaded.
+    if (FileFormat.Jalview.equals(currentFileFormat))
     {
-      // TODO: JAL-1108 - ensure all associated frames are closed regardless of
-      // originating file's format
-      // TODO: work out how to recover feature settings for correct view(s) when
-      // file is reloaded.
-      if (FileFormat.Jalview.equals(currentFileFormat))
+      JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+      for (int i = 0; i < frames.length; i++)
       {
-        JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
-        for (int i = 0; i < frames.length; i++)
+        if (frames[i] instanceof AlignFrame && frames[i] != this
+                && ((AlignFrame) frames[i]).fileName != null
+                && ((AlignFrame) frames[i]).fileName.equals(fileName))
         {
-          if (frames[i] instanceof AlignFrame && frames[i] != this
-                  && ((AlignFrame) frames[i]).fileName != null
-                  && ((AlignFrame) frames[i]).fileName.equals(fileName))
+          try
+          {
+            frames[i].setSelected(true);
+            Desktop.getInstance().closeAssociatedWindows();
+          } catch (java.beans.PropertyVetoException ex)
           {
-            try
-            {
-              frames[i].setSelected(true);
-              Desktop.getInstance().closeAssociatedWindows();
-            } catch (java.beans.PropertyVetoException ex)
-            {
-            }
           }
-
         }
-        Desktop.getInstance().closeAssociatedWindows();
 
-        FileLoader loader = new FileLoader();
-        DataSourceType protocol = fileName.startsWith("http:")
-                ? DataSourceType.URL
-                : DataSourceType.FILE;
-        loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
       }
-      else
-      {
-        Rectangle bounds = this.getBounds();
+      Desktop.getInstance().closeAssociatedWindows();
 
-        FileLoader loader = new FileLoader();
+      FileLoader loader = new FileLoader();
+      DataSourceType protocol = fileName.startsWith("http:")
+              ? DataSourceType.URL
+              : DataSourceType.FILE;
+      loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
+    }
+    else
+    {
+      Rectangle bounds = this.getBounds();
 
-        AlignFrame newframe = null;
+      FileLoader loader = new FileLoader();
 
-        if (fileObject == null)
-        {
+      AlignFrame newframe = null;
 
-          DataSourceType protocol = (fileName.startsWith("http:")
-                  ? DataSourceType.URL
-                  : DataSourceType.FILE);
-          newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
-                  currentFileFormat);
-        }
-        else
-        {
-          newframe = loader.LoadFileWaitTillLoaded(fileObject,
-                  DataSourceType.FILE, currentFileFormat);
-        }
+      if (fileObject == null)
+      {
 
-        newframe.setBounds(bounds);
-        if (featureSettings != null && featureSettings.isShowing())
+        DataSourceType protocol = (fileName.startsWith("http:")
+                ? DataSourceType.URL
+                : DataSourceType.FILE);
+        newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
+                currentFileFormat);
+      }
+      else
+      {
+        newframe = loader.LoadFileWaitTillLoaded(fileObject,
+                DataSourceType.FILE, currentFileFormat);
+      }
+
+      newframe.setBounds(bounds);
+      if (featureSettings != null && featureSettings.isShowing())
+      {
+        final Rectangle fspos = featureSettings.frame.getBounds();
+        // TODO: need a 'show feature settings' function that takes bounds -
+        // need to refactor Desktop.addFrame
+        newframe.featureSettings_actionPerformed(null);
+        final FeatureSettings nfs = newframe.featureSettings;
+        SwingUtilities.invokeLater(new Runnable()
         {
-          final Rectangle fspos = featureSettings.frame.getBounds();
-          // TODO: need a 'show feature settings' function that takes bounds -
-          // need to refactor Desktop.addFrame
-          newframe.featureSettings_actionPerformed(null);
-          final FeatureSettings nfs = newframe.featureSettings;
-          SwingUtilities.invokeLater(new Runnable()
+
+          @Override
+          public void run()
           {
-            @Override
-            public void run()
-            {
-              nfs.frame.setBounds(fspos);
-            }
-          });
-          this.featureSettings.close();
-          this.featureSettings = null;
-        }
-        this.closeMenuItem_actionPerformed(true);
+            nfs.frame.setBounds(fspos);
+          }
+        });
+        this.featureSettings.close();
+        this.featureSettings = null;
       }
+      this.closeMenuItem_actionPerformed(true);
     }
+
   }
 
   @Override
@@ -1152,6 +1198,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Saves the alignment to a file with a name chosen by the user, if necessary
    * warning if a file would be overwritten
    */
+
   @Override
   public void saveAs_actionPerformed()
   {
@@ -1206,6 +1253,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *
    * @return true if last call to saveAlignment(file, format) was successful.
    */
+
   public boolean isSaveAlignmentSuccessful()
   {
 
@@ -1238,6 +1286,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param file
    * @param format
    */
+
   public void saveAlignment(String file, FileFormatI format)
   {
     lastSaveSuccessful = true;
@@ -1265,6 +1314,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
     Runnable cancelAction = new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -1273,6 +1323,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     };
     Runnable outputAction = new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -1347,6 +1398,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param fileFormatName
    */
+
   @Override
   protected void outputText_actionPerformed(String fileFormatName)
   {
@@ -1355,6 +1407,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
     Runnable outputAction = new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -1405,6 +1458,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1419,12 +1473,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     bjs.exportHTML(null);
   }
 
+  // ??
+
+  public void createImageMap(File file, String image)
+  {
+    alignPanel.makePNGImageMap(file, image);
+  }
+
   /**
    * Creates a PNG image of the alignment and writes it to the given file. If
    * the file is null, the user is prompted to choose a file.
    * 
    * @param f
    */
+
   @Override
   public void createPNG(File f)
   {
@@ -1437,6 +1499,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
+
   @Override
   public void createEPS(File f)
   {
@@ -1449,6 +1512,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param f
    */
+
   @Override
   public void createSVG(File f)
   {
@@ -1468,6 +1532,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void printMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1500,6 +1565,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     chooser.setToolTipText(tooltip);
     chooser.setResponseHandler(0, new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -1518,6 +1584,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param closeAllTabs
    */
+
   @Override
   public void closeMenuItem_actionPerformed(boolean closeAllTabs)
   {
@@ -1572,6 +1639,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param panelToClose
    */
+
   public void closeView(AlignmentPanel panelToClose)
   {
     int index = tabbedPane.getSelectedIndex();
@@ -1595,6 +1663,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * DOCUMENT ME!
    */
+
   void updateEditMenuBar()
   {
 
@@ -1648,6 +1717,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return alignment objects for all views
    */
+
   AlignmentI[] getViewAlignments()
   {
     if (alignPanels != null)
@@ -1673,6 +1743,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1700,8 +1771,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // && viewport.getColumnSelection().getHiddenColumns() != null &&
       // viewport.getColumnSelection()
       // .getHiddenColumns().size() > 0);
-      originalSource.firePropertyChange("alignment", null,
-              originalSource.getAlignment().getSequences());
+      originalSource.notifyAlignment();
+
     }
   }
 
@@ -1711,6 +1782,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1740,8 +1812,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // && viewport.getColumnSelection().getHiddenColumns() != null &&
       // viewport.getColumnSelection()
       // .getHiddenColumns().size() > 0);
-      originalSource.firePropertyChange("alignment", null,
-              originalSource.getAlignment().getSequences());
+      originalSource.notifyAlignment();
+
     }
   }
 
@@ -1793,6 +1865,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param up
    *          DOCUMENT ME!
    */
+
   public void moveSelectedSequences(boolean up)
   {
     SequenceGroup sg = viewport.getSelectionGroup();
@@ -1917,6 +1990,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void copy_actionPerformed()
   {
@@ -1939,9 +2013,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     StringSelection ss = new StringSelection(output);
 
+    Desktop d = Desktop.getInstance();
     try
     {
-      Desktop.getInstance().internalCopy = true;
+      d.internalCopy = true;
       // Its really worth setting the clipboard contents
       // to empty before setting the large StringSelection!!
       Toolkit.getDefaultToolkit().getSystemClipboard()
@@ -1968,7 +2043,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               hiddenCutoff, hiddenOffset);
     }
 
-    Desktop.getInstance().jalviewClipboard = new Object[] { seqs,
+    d.jalviewClipboard = new Object[] { seqs,
         viewport.getAlignment().getDataset(), hiddenColumns };
     setStatus(MessageManager.formatMessage(
             "label.copied_sequences_to_clipboard", new Object[]
@@ -1981,6 +2056,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void pasteNew_actionPerformed(ActionEvent e)
   {
@@ -1993,6 +2069,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void pasteThis_actionPerformed(ActionEvent e)
   {
@@ -2005,10 +2082,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param newAlignment
    *          true to paste to a new alignment, otherwise add to this.
    */
+
   void paste(boolean newAlignment)
   {
     boolean externalPaste = true;
-    Desktop d = Desktop.getInstance();
     try
     {
       Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
@@ -2041,6 +2118,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       boolean annotationAdded = false;
       AlignmentI alignment = null;
 
+      Desktop d = Desktop.getInstance();
+
       if (d.jalviewClipboard != null)
       {
         // The clipboard was filled from within Jalview, we must use the
@@ -2272,8 +2351,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           buildSortByAnnotationScoresMenu();
         }
-        viewport.firePropertyChange("alignment", null,
-                alignment.getSequences());
+        viewport.notifyAlignment();
         if (alignPanels != null)
         {
           for (AlignmentPanel ap : alignPanels)
@@ -2389,6 +2467,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Action Cut (delete and copy) the selected region
    */
+
   @Override
   protected void cut_actionPerformed()
   {
@@ -2399,6 +2478,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Performs menu option to Delete the currently selected region
    */
+
   @Override
   protected void delete_actionPerformed()
   {
@@ -2411,6 +2491,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     Runnable okAction = new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -2427,8 +2508,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         viewport.sendSelection();
         viewport.getAlignment().deleteGroup(sg);
 
-        viewport.firePropertyChange("alignment", null,
-                viewport.getAlignment().getSequences());
+        viewport.notifyAlignment();
+
         if (viewport.getAlignment().getHeight() < 1)
         {
           try
@@ -2473,6 +2554,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
@@ -2490,6 +2572,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2502,6 +2585,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2514,6 +2598,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2553,6 +2638,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2565,6 +2651,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void remove2RightMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2626,8 +2713,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         }
       }
 
-      viewport.firePropertyChange("alignment", null,
-              viewport.getAlignment().getSequences());
+      viewport.notifyAlignment();
+
     }
   }
 
@@ -2637,6 +2724,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2676,8 +2764,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // if (viewport.hasHiddenColumns)
     // viewport.getColumnSelection().compensateForEdits(shifts);
     ranges.setStartRes(seq.findIndex(startRes) - 1);
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
+
 
   }
 
@@ -2687,6 +2775,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2714,9 +2803,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             viewport.getAlignment()));
 
     viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
-
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
 
   }
 
@@ -2726,12 +2813,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void padGapsMenuitem_actionPerformed(ActionEvent e)
   {
     viewport.setPadGaps(padGapsMenuitem.isSelected());
-    viewport.firePropertyChange("alignment", null,
-            viewport.getAlignment().getSequences());
+    viewport.notifyAlignment();
+
   }
 
   /**
@@ -2740,6 +2828,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2749,6 +2838,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Create a new view of the current alignment.
    */
+
   @Override
   public void newView_actionPerformed(ActionEvent e)
   {
@@ -2764,6 +2854,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          if true then duplicate all annnotation, groups and settings
    * @return new alignment panel, already displayed.
    */
+
   public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
   {
     /*
@@ -2836,6 +2927,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param viewTitle
    * @return
    */
+
   protected String getNewViewName(String viewTitle)
   {
     int index = Desktop.getViewCount(viewport.getSequenceSetId());
@@ -2870,6 +2962,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param comps
    * @return
    */
+
   protected List<String> getExistingViewNames(List<Component> comps)
   {
     List<String> existingNames = new ArrayList<>();
@@ -2890,6 +2983,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Explode tabbed views into separate windows.
    */
+
   @Override
   public void expandViews_actionPerformed(ActionEvent e)
   {
@@ -2899,6 +2993,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Gather views in separate windows back into a tabbed presentation.
    */
+
   @Override
   public void gatherViews_actionPerformed(ActionEvent e)
   {
@@ -2911,6 +3006,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void font_actionPerformed(ActionEvent e)
   {
@@ -2923,6 +3019,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void seqLimit_actionPerformed(ActionEvent e)
   {
@@ -2952,6 +3049,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
    */
+
   @Override
   protected void followHighlight_actionPerformed()
   {
@@ -2973,6 +3071,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void colourTextMenuItem_actionPerformed(ActionEvent e)
   {
@@ -2986,6 +3085,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void wrapMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3022,6 +3122,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param toggleSeqs
    * @param toggleCols
    */
+
   protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
   {
 
@@ -3089,6 +3190,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
    * event.ActionEvent)
    */
+
   @Override
   public void hideAllButSelection_actionPerformed(ActionEvent e)
   {
@@ -3103,6 +3205,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+
   @Override
   public void hideAllSelection_actionPerformed(ActionEvent e)
   {
@@ -3122,6 +3225,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
    * ActionEvent)
    */
+
   @Override
   public void showAllhidden_actionPerformed(ActionEvent e)
   {
@@ -3153,6 +3257,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void scaleAbove_actionPerformed(ActionEvent e)
   {
@@ -3167,6 +3272,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void scaleLeft_actionPerformed(ActionEvent e)
   {
@@ -3181,6 +3287,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void scaleRight_actionPerformed(ActionEvent e)
   {
@@ -3195,6 +3302,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3208,6 +3316,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void viewTextMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3221,6 +3330,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3266,6 +3376,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param evt
    *          DOCUMENT ME!
    */
+
   @Override
   public void showSeqFeatures_actionPerformed(ActionEvent evt)
   {
@@ -3282,16 +3393,32 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param e
    */
+
   @Override
   public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
   {
     final boolean setVisible = annotationPanelMenuItem.isSelected();
     viewport.setShowAnnotation(setVisible);
-    this.showAllSeqAnnotations.setEnabled(setVisible);
-    this.hideAllSeqAnnotations.setEnabled(setVisible);
-    this.showAllAlAnnotations.setEnabled(setVisible);
-    this.hideAllAlAnnotations.setEnabled(setVisible);
+    syncAnnotationMenuItems(setVisible);
     alignPanel.updateLayout();
+    repaint();
+    SwingUtilities.invokeLater(new Runnable() {
+
+      @Override
+      public void run()
+      {
+        alignPanel.updateScrollBarsFromRanges();
+      }
+      
+    });
+  }
+
+  private void syncAnnotationMenuItems(boolean setVisible)
+  {
+    showAllSeqAnnotations.setEnabled(setVisible);
+    hideAllSeqAnnotations.setEnabled(setVisible);
+    showAllAlAnnotations.setEnabled(setVisible);
+    hideAllAlAnnotations.setEnabled(setVisible);
   }
 
   @Override
@@ -3345,6 +3472,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void overviewMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3382,13 +3510,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             "resize") != "none");
     Desktop.addInternalFrame(frame, MessageManager
             .formatMessage("label.overview_params", new Object[]
-            { this.getTitle() }), Desktop.FRAME_MAKE_VISIBLE, dim.width, dim.height, resizable,
-            Desktop.FRAME_ALLOW_ANY_SIZE);
+            { this.getTitle() }), Desktop.FRAME_MAKE_VISIBLE, dim.width,
+            dim.height, resizable, Desktop.FRAME_ALLOW_ANY_SIZE);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(
             new javax.swing.event.InternalFrameAdapter()
             {
+
               @Override
               public void internalFrameClosed(
                       javax.swing.event.InternalFrameEvent evt)
@@ -3417,6 +3546,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
    * ()[0])); }
    */
+
   @Override
   public void annotationColour_actionPerformed()
   {
@@ -3436,6 +3566,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param selected
    */
+
   @Override
   public void applyToAllGroups_actionPerformed(boolean selected)
   {
@@ -3448,6 +3579,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param name
    *          the name (not the menu item label!) of the colour scheme
    */
+
   @Override
   public void changeColour_actionPerformed(String name)
   {
@@ -3475,6 +3607,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param cs
    */
+
   @Override
   public void changeColour(ColourSchemeI cs)
   {
@@ -3489,6 +3622,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Show the PID threshold slider panel
    */
+
   @Override
   protected void modifyPID_actionPerformed()
   {
@@ -3500,6 +3634,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Show the Conservation slider panel
    */
+
   @Override
   protected void modifyConservation_actionPerformed()
   {
@@ -3511,6 +3646,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Action on selecting or deselecting (Colour) By Conservation
    */
+
   @Override
   public void conservationMenuItem_actionPerformed(boolean selected)
   {
@@ -3532,6 +3668,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Action on selecting or deselecting (Colour) Above PID Threshold
    */
+
   @Override
   public void abovePIDThreshold_actionPerformed(boolean selected)
   {
@@ -3560,6 +3697,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3577,6 +3715,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void sortIDMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3593,6 +3732,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void sortLengthMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3609,6 +3749,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void sortGroupMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3626,6 +3767,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3638,6 +3780,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
@@ -3663,11 +3806,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void autoCalculate_actionPerformed(ActionEvent e)
   {
-    viewport.autoCalculateConsensus = autoCalculate.isSelected();
-    if (viewport.autoCalculateConsensus)
+    viewport.setAutoCalculateConsensusAndConservation(
+            autoCalculate.isSelected());
+    if (viewport.getAutoCalculateConsensusAndConservation())
+    // ??
+    // viewport.autoCalculateConsensus = autoCalculate.isSelected();
+    // if (viewport.autoCalculateConsensus)
     {
-      viewport.firePropertyChange("alignment", null,
-              viewport.getAlignment().getSequences());
+      viewport.notifyAlignment();
     }
   }
 
@@ -3693,6 +3839,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param options
    *          parameters for the distance or similarity calculation
    */
+
   void newTreePanel(String type, String modelName,
           SimilarityParamsI options)
   {
@@ -3754,6 +3901,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param order
    *          DOCUMENT ME!
    */
+
   public void addSortByOrderMenuItem(String title,
           final AlignmentOrder order)
   {
@@ -3763,6 +3911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
+
       @Override
       public void actionPerformed(ActionEvent e)
       {
@@ -3789,6 +3938,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          the label used to retrieve scores for each sequence on the
    *          alignment
    */
+
   public void addSortByAnnotScoreMenuItem(JMenu sort,
           final String scoreLabel)
   {
@@ -3796,6 +3946,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     sort.add(item);
     item.addActionListener(new java.awt.event.ActionListener()
     {
+
       @Override
       public void actionPerformed(ActionEvent e)
       {
@@ -3821,6 +3972,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * rebuilding in subsequence calls.
    * 
    */
+
   @Override
   public void buildSortByAnnotationScoresMenu()
   {
@@ -3867,6 +4019,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * closed, and adjust the tree leaf to sequence mapping when the alignment is
    * modified.
    */
+
   @Override
   public void buildTreeSortMenu()
   {
@@ -3896,6 +4049,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       final JMenuItem item = new JMenuItem(tp.getTitle());
       item.addActionListener(new java.awt.event.ActionListener()
       {
+
         @Override
         public void actionPerformed(ActionEvent e)
         {
@@ -3927,6 +4081,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * be submitted for multiple alignment.
    * 
    */
+
   public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
   {
     // Now, check we have enough sequences
@@ -3972,6 +4127,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * region or the whole alignment. (where the first sequence in the set is the
    * one that the prediction will be for).
    */
+
   public AlignmentView gatherSeqOrMsaForSecStrPrediction()
   {
     AlignmentView seqs = null;
@@ -4005,6 +4161,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param e
    *          DOCUMENT ME!
    */
+
   @Override
   protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
   {
@@ -4019,6 +4176,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     chooser.setResponseHandler(0, new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -4083,6 +4241,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          position
    * @return TreePanel handle
    */
+
   public TreePanel showNewickTree(NewickFile nf, String treeTitle,
           AlignmentView input, int w, int h, int x, int y)
   {
@@ -4128,6 +4287,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Generates menu items and listener event actions for web service clients
    * 
    */
+
   public void BuildWebServiceMenu()
   {
     while (buildingMenu)
@@ -4144,6 +4304,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     buildingMenu = true;
     new Thread(new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -4179,8 +4340,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           // JAL-940 - only show secondary structure prediction services from
           // the legacy server
           Hashtable<String, Vector<ServiceHandle>> ds = Discoverer
-                  .getServices();
-
+                  .getInstance().getServices();
           if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
               // &&
           ds != null && (ds.size() > 0))
@@ -4222,6 +4382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
           javax.swing.SwingUtilities.invokeLater(new Runnable()
           {
+
             @Override
             public void run()
             {
@@ -4241,7 +4402,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   webService.add(me.webServiceNoServices);
                 }
                 // TODO: move into separate menu builder class.
-                boolean new_sspred = false;
+                // boolean new_sspred = false;
                 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
                 {
                   Jws2Discoverer jws2servs = Jws2Discoverer.getInstance();
@@ -4306,6 +4467,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param webService
    */
+
   protected void build_urlServiceMenu(JMenu webService)
   {
     // TODO: remove this code when 2.7 is released
@@ -4314,7 +4476,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
      * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
      * 
-     * @Override public void actionPerformed(ActionEvent e) {
+     *  public void actionPerformed(ActionEvent e) {
      * jalview.datamodel.AlignmentView
      * .testSelectionViews(af.viewport.getAlignment(),
      * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
@@ -4343,6 +4505,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return true if Show Cross-references menu should be enabled
    */
+
   public boolean canShowProducts()
   {
     SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
@@ -4370,6 +4533,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         JMenuItem xtype = new JMenuItem(source);
         xtype.addActionListener(new ActionListener()
         {
+
           @Override
           public void actionPerformed(ActionEvent e)
           {
@@ -4402,6 +4566,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param source
    *          the database to show cross-references for
    */
+
   protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
           final String source)
   {
@@ -4413,6 +4578,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Construct and display a new frame containing the translation of this
    * frame's DNA sequences to their aligned protein (amino acid) equivalents.
    */
+
   @Override
   public void showTranslation_actionPerformed(GeneticCodeI codeTable)
   {
@@ -4470,6 +4636,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param format
    */
+
   public void setFileFormat(FileFormatI format)
   {
     this.currentFileFormat = format;
@@ -4484,11 +4651,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          access mode of file (see jalview.io.AlignFile)
    * @return true if features file was parsed correctly.
    */
+
   public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
   {
     // BH 2018
     return avc.parseFeaturesFile(file, sourceType,
-            Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+            Cache.getDefault(Preferences.RELAXEDSEQIDMATCHING, false));
 
   }
 
@@ -4544,6 +4712,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         new Thread(new Runnable()
         {
+
           @Override
           public void run()
           {
@@ -4642,8 +4811,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       int assocfiles = 0;
       if (filesmatched.size() > 0)
       {
-        boolean autoAssociate = Cache.getDefault("AUTOASSOCIATE_PDBANDSEQS",
-                false);
+        boolean autoAssociate = Cache
+                .getDefault(Preferences.AUTOASSOCIATE_PDBANDSEQS, false);
         if (!autoAssociate)
         {
           String msg = MessageManager.formatMessage(
@@ -4665,10 +4834,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // associating PDB files which have no IDs.
             for (SequenceI toassoc : (SequenceI[]) fm[2])
             {
-              PDBEntry pe = new AssociatePdbFileWithSeq()
-                      .associatePdbWithSeq(fm[0].toString(),
-                              (DataSourceType) fm[1], toassoc, false,
-                              Desktop.getInstance());
+              PDBEntry pe = AssociatePdbFileWithSeq.associatePdbWithSeq(
+                      fm[0].toString(), (DataSourceType) fm[1], toassoc,
+                      false);
               if (pe != null)
               {
                 System.err.println("Associated file : " + (fm[0].toString())
@@ -4733,6 +4901,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param file
    *          either a filename or a URL string.
    */
+
   public void loadJalviewDataFile(Object file, DataSourceType sourceType,
           FileFormatI format, SequenceI assocSeq)
   {
@@ -4897,6 +5066,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param state
    *          visible or invisible
    */
+
   public void setFeatureGroupState(String[] groups, boolean state)
   {
     jalview.api.FeatureRenderer fr = null;
@@ -4918,6 +5088,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Method invoked by the ChangeListener on the tabbed pane, in other words
    * when a different tabbed pane is selected by the user or programmatically.
    */
+
   @Override
   public void tabSelectionChanged(int index)
   {
@@ -4988,6 +5159,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * On right mouse click on view tab, prompt for and set new view name.
    */
+
   @Override
   public void tabbedPane_mousePressed(MouseEvent e)
   {
@@ -5014,6 +5186,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Open the dialog for regex description parsing.
    */
+
   @Override
   protected void extractScores_actionPerformed(ActionEvent e)
   {
@@ -5037,6 +5210,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
    * )
    */
+
   @Override
   protected void showDbRefs_actionPerformed(ActionEvent e)
   {
@@ -5049,6 +5223,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
    * ActionEvent)
    */
+
   @Override
   protected void showNpFeats_actionPerformed(ActionEvent e)
   {
@@ -5061,6 +5236,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param av
    */
+
   public boolean closeView(AlignViewportI av)
   {
     if (viewport == av)
@@ -5104,6 +5280,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
     trimrs.addActionListener(new ActionListener()
     {
+
       @Override
       public void actionPerformed(ActionEvent e)
       {
@@ -5125,6 +5302,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         new Thread(new Runnable()
         {
+
           @Override
           public void run()
           {
@@ -5136,6 +5314,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     alignPanel.alignFrame.featureSettings, isNucleotide);
             dbRefFetcher.addListener(new FetchFinishedListenerI()
             {
+
               @Override
               public void finished()
               {
@@ -5159,16 +5338,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     rfetch.add(fetchr);
     new Thread(new Runnable()
     {
+
       @Override
       public void run()
       {
-        final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
-                .getSequenceFetcherSingleton();
+        // ??
+        // final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
+        // .getSequenceFetcherSingleton();
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+
           @Override
           public void run()
           {
+            jalview.ws.SequenceFetcher sf = jalview.ws.SequenceFetcher
+                    .getInstance();
             String[] dbclasses = sf.getNonAlignmentSources();
             List<DbSourceProxy> otherdb;
             JMenu dfetch = new JMenu();
@@ -5192,9 +5376,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               }
               if (otherdb.size() == 1)
               {
-                final DbSourceProxy[] dassource = otherdb
-                        .toArray(new DbSourceProxy[0]);
                 DbSourceProxy src = otherdb.get(0);
+                DbSourceProxy[] dassource = new DbSourceProxy[] { src };
                 fetchr = new JMenuItem(src.getDbSource());
                 fetchr.addActionListener(new ActionListener()
                 {
@@ -5219,6 +5402,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         dbRefFetcher
                                 .addListener(new FetchFinishedListenerI()
                                 {
+
                                   @Override
                                   public void finished()
                                   {
@@ -5253,6 +5437,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         { src.getDbSource() }));
                 fetchr.addActionListener(new ActionListener()
                 {
+
                   @Override
                   public void actionPerformed(ActionEvent e)
                   {
@@ -5273,6 +5458,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         dbRefFetcher
                                 .addListener(new FetchFinishedListenerI()
                                 {
+
                                   @Override
                                   public void finished()
                                   {
@@ -5341,6 +5527,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           dbRefFetcher
                                   .addListener(new FetchFinishedListenerI()
                                   {
+
                                     @Override
                                     public void finished()
                                     {
@@ -5392,23 +5579,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Left justify the whole alignment.
    */
+
   @Override
   protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
   {
-    AlignmentI al = viewport.getAlignment();
-    al.justify(false);
-    viewport.firePropertyChange("alignment", null, al);
+    viewport.getAlignment().justify(false);
+    viewport.notifyAlignment();
   }
 
   /**
    * Right justify the whole alignment.
    */
+
   @Override
   protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
   {
-    AlignmentI al = viewport.getAlignment();
-    al.justify(true);
-    viewport.firePropertyChange("alignment", null, al);
+    viewport.getAlignment().justify(true);
+    viewport.notifyAlignment();
   }
 
   @Override
@@ -5425,6 +5612,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
    * awt.event.ActionEvent)
    */
+
   @Override
   protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
   {
@@ -5439,6 +5627,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
    * .ActionEvent)
    */
+
   @Override
   protected void showGroupConsensus_actionPerformed(ActionEvent e)
   {
@@ -5454,6 +5643,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+
   @Override
   protected void showGroupConservation_actionPerformed(ActionEvent e)
   {
@@ -5468,6 +5658,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+
   @Override
   protected void showConsensusHistogram_actionPerformed(ActionEvent e)
   {
@@ -5482,6 +5673,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+
   @Override
   protected void showSequenceLogo_actionPerformed(ActionEvent e)
   {
@@ -5511,6 +5703,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
    * .event.ActionEvent)
    */
+
   @Override
   protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
   {
@@ -5562,6 +5755,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param alignmentPanel
    */
+
   public void setDisplayedView(AlignmentPanel alignmentPanel)
   {
     if (!viewport.getSequenceSetId()
@@ -5586,6 +5780,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param forAlignment
    *          update non-sequence-related annotations
    */
+
   @Override
   protected void setAnnotationsVisibility(boolean visible,
           boolean forSequences, boolean forAlignment)
@@ -5619,6 +5814,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Store selected annotation sort order for the view and repaint.
    */
+
   @Override
   protected void sortAnnotations_actionPerformed()
   {
@@ -5632,6 +5828,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return alignment panels in this alignment frame
    */
+
   public List<? extends AlignmentViewPanel> getAlignPanels()
   {
     // alignPanels is never null
@@ -5643,6 +5840,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Open a new alignment window, with the cDNA associated with this (protein)
    * alignment, aligned as is the protein.
    */
+
   protected void viewAsCdna_actionPerformed()
   {
     // TODO no longer a menu action - refactor as required
@@ -5693,6 +5891,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param show
    */
+
   @Override
   protected void showComplement_actionPerformed(boolean show)
   {
@@ -5707,6 +5906,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Generate the reverse (optionally complemented) of the selected sequences,
    * and add them to the alignment
    */
+
   @Override
   protected void showReverse_actionPerformed(boolean complement)
   {
@@ -5732,6 +5932,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
    * be targeted at this alignment.
    */
+
   @Override
   protected void runGroovy_actionPerformed()
   {
@@ -5765,6 +5966,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param columnsContaining
    * @return
    */
+
   public boolean hideFeatureColumns(String featureType,
           boolean columnsContaining)
   {
@@ -5797,6 +5999,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Rebuilds the Colour menu, including any user-defined colours which have
    * been loaded either on startup or during the session
    */
+
   public void buildColourMenu()
   {
     colourMenu.removeAll();
@@ -5824,6 +6027,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Open a dialog (if not already open) that allows the user to select and
    * calculate PCA or Tree analysis
    */
+
   protected void openTreePcaDialog()
   {
     if (alignPanel.getCalculationDialog() == null)
@@ -5843,6 +6047,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     final AlignFrame us = this;
     chooser.setResponseHandler(0, new Runnable()
     {
+
       @Override
       public void run()
       {
@@ -5894,6 +6099,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          true is visible
    * @return list
    */
+
   public String[] getFeatureGroupsOfState(boolean visible)
   {
     jalview.api.FeatureRenderer fr = null;
@@ -5911,6 +6117,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @return list of feature groups on the view
    */
+
   public String[] getFeatureGroups()
   {
     jalview.api.FeatureRenderer fr = null;
@@ -5930,48 +6137,47 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.getSeqPanel().selection(sel, csel, hidden, null);
   }
 
-  
   public int getID()
   {
     return id;
   }
 
-}
-
-class PrintThread extends Thread
-{
-  AlignmentPanel ap;
-
-  public PrintThread(AlignmentPanel ap)
-  {
-    this.ap = ap;
-  }
-
-  static PageFormat pf;
-
-  @Override
-  public void run()
+  static class PrintThread extends Thread
   {
-    PrinterJob printJob = PrinterJob.getPrinterJob();
+    AlignmentPanel ap;
 
-    if (pf != null)
-    {
-      printJob.setPrintable(ap, pf);
-    }
-    else
+    public PrintThread(AlignmentPanel ap)
     {
-      printJob.setPrintable(ap);
+      this.ap = ap;
     }
 
-    if (printJob.printDialog())
+    static PageFormat pf;
+
+    @Override
+    public void run()
     {
-      try
+      PrinterJob printJob = PrinterJob.getPrinterJob();
+
+      if (pf != null)
       {
-        printJob.print();
-      } catch (Exception PrintException)
+        printJob.setPrintable(ap, pf);
+      }
+      else
       {
-        PrintException.printStackTrace();
+        printJob.setPrintable(ap);
+      }
+
+      if (printJob.printDialog())
+      {
+        try
+        {
+          printJob.print();
+        } catch (Exception PrintException)
+        {
+          PrintException.printStackTrace();
+        }
       }
     }
   }
 }
+
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index a5c899a..7ab84ad 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -223,7 +223,7 @@ f   */
 
     setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
     setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
-    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+    autoCalculateConsensusAndConservation = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
 
     setPadGaps(Cache.getDefault("PAD_GAPS", true));
     setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
@@ -754,7 +754,8 @@ f   */
     }
 
     ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
-    firePropertyChange("alignment", null, getAlignment().getSequences());
+    notifyAlignment();
+
   }
 
   /**
@@ -1147,4 +1148,5 @@ f   */
   {
     this.viewName = viewName;
   }
+
 }
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 5696c3a..cb2b3ed 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -20,29 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.AnnotationSorter;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.gui.ImageExporter.ImageWriterI;
-import jalview.io.HTMLOutput;
-import jalview.jbgui.GAlignmentPanel;
-import jalview.math.AlignmentDimension;
-import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.Comparison;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Container;
@@ -63,11 +40,34 @@ import java.beans.PropertyChangeListener;
 import java.io.File;
 import java.io.FileWriter;
 import java.io.PrintWriter;
-import java.util.ArrayList;
 import java.util.List;
 
 import javax.swing.SwingUtilities;
 
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.io.HTMLOutput;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
 /**
  * DOCUMENT ME!
  * 
@@ -123,7 +123,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
-//	setBackground(Color.white);  // BH 2019
+    // setBackground(Color.white); // BH 2019
     alignFrame = af;
     this.av = av;
     setSeqPanel(new SeqPanel(av, this));
@@ -174,6 +174,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
           ranges.setViewportWidth(widthInRes);
           ranges.setViewportHeight(heightInSeq);
         }
+        repaint();
       }
 
     });
@@ -184,10 +185,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
       @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
-        if (evt.getPropertyName().equals("alignment"))
-        {
+        switch (evt.getPropertyName()) {  
+        case AlignmentViewport.PROPERTY_SEQUENCE:
+          updateScrollBarsFromRanges();
+          if (annotationPanel != null)
+            annotationPanel.paintImmediately(0,  0, getWidth(), getHeight());
+          break;
+        case AlignmentViewport.PROPERTY_ALIGNMENT:
+          updateScrollBarsFromRanges();
           PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
           alignmentChanged();
+          break;
         }
       }
     };
@@ -260,32 +268,37 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int oldWidth = av.getIdWidth();
 
     // calculate sensible default width when no preference is available
-    Dimension r = null;
+    Dimension d = null;
     if (av.getIdWidth() < 0)
     {
-      int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
-      int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
-      int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
-      r = calculateIdWidth(maxwidth);
-      av.setIdWidth(r.width);
+      int maxWidth = getMaxWidth();
+      d = calculateIdWidth(maxWidth);
+      av.setIdWidth(d.width);
     }
     else
     {
-      r = new Dimension();
-      r.width = av.getIdWidth();
-      r.height = 0;
+      d = new Dimension();
+      d.width = av.getIdWidth();
+      d.height = 0;
     }
 
     /*
      * fudge: if desired width has changed, update layout
      * (see also paintComponent - updates layout on a repaint)
      */
-    if (r.width != oldWidth)
+    if (d.width != oldWidth)
     {
-      idPanelHolder.setPreferredSize(r);
+      idPanelHolder.setPreferredSize(d);
       validate();
     }
-    return r;
+    return d;
+  }
+
+  public int getMaxWidth()
+  {
+    int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+    int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
+    return Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
   }
 
   /**
@@ -297,10 +310,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * @return Dimension giving the maximum width of the alignment label panel
    *         that should be used.
    */
-  protected Dimension calculateIdWidth(int maxwidth)
+  public Dimension calculateIdWidth(int maxwidth)
   {
-    Container c = new Container();
-
+    Container c = this;// new Container();
     FontMetrics fm = c.getFontMetrics(
             new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
 
@@ -308,10 +320,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
     int i = 0;
     int idWidth = 0;
 
+    boolean withSuffix = av.getShowJVSuffix();
+
     while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
     {
       SequenceI s = al.getSequenceAt(i);
-      String id = s.getDisplayId(av.getShowJVSuffix());
+      String id = s.getDisplayId(withSuffix);
       int stringWidth = fm.stringWidth(id);
       idWidth = Math.max(idWidth, stringWidth);
       i++;
@@ -472,8 +486,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         /*
          * Scroll down to make end of search results visible
          */
-        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
-                + 1);
+        setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
       }
       /*
        * Else results are already visible - no need to scroll
@@ -573,7 +586,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
     Dimension e = idPanel.getSize();
     alabels.setSize(new Dimension(e.width, annotationHeight));
 
-
     annotationSpaceFillerHolder.setPreferredSize(new Dimension(
             annotationSpaceFillerHolder.getWidth(), annotationHeight));
     annotationScroller.validate();
@@ -588,10 +600,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
    */
   public void updateLayout()
   {
+    ViewportRanges ranges = av.getRanges();
     fontChanged();
     setAnnotationVisible(av.isShowAnnotation());
     boolean wrap = av.getWrapAlignment();
-    ViewportRanges ranges = av.getRanges();
     ranges.setStartSeq(0);
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
@@ -695,12 +707,17 @@ public class AlignmentPanel extends GAlignmentPanel implements
         x = 0;
       }
 
-      // update the scroll values
-      hscroll.setValues(x, hextent, 0, width);
-      vscroll.setValues(y, vextent, 0, height);
+      updateRanges(x, y);
+      updateScrollBars(x, y, width, height);
     }
   }
 
+  private void updateScrollBars(int x, int y, int width, int height) 
+  {
+    hscroll.setValues(x, hextent, 0, width);
+    vscroll.setValues(y, vextent, 0, height);
+  }
+
   /**
    * Respond to adjustment event when horizontal or vertical scrollbar is
    * changed
@@ -717,41 +734,54 @@ public class AlignmentPanel extends GAlignmentPanel implements
       return;
     }
 
-    ViewportRanges ranges = av.getRanges();
-
     if (evt.getSource() == hscroll)
     {
+      if (!updateRanges(hscroll.getValue(), Integer.MIN_VALUE))
+        return;
+    }
+    else if (evt.getSource() == vscroll)
+    {
+      if (!updateRanges(Integer.MIN_VALUE, vscroll.getValue()))
+        return;
+    }
+    repaint();
+  }
+
+  private boolean updateRanges(int x, int y)
+  {
+    ViewportRanges ranges = av.getRanges();
+    boolean isChanged = false;
+    if (x != Integer.MIN_VALUE)
+    {
       int oldX = ranges.getStartRes();
       int oldwidth = ranges.getViewportWidth();
-      int x = hscroll.getValue();
       int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
 
       // if we're scrolling to the position we're already at, stop
       // this prevents infinite recursion of events when the scroll/viewport
       // ranges values are the same
-      if ((x == oldX) && (width == oldwidth))
+      if (width > 0 && (x != oldX || width != oldwidth))
       {
-        return;
+        ranges.setViewportStartAndWidth(x, width);
+        isChanged = true;
       }
-      ranges.setViewportStartAndWidth(x, width);
     }
-    else if (evt.getSource() == vscroll)
+    if (y != Integer.MIN_VALUE)
     {
       int oldY = ranges.getStartSeq();
       int oldheight = ranges.getViewportHeight();
-      int y = vscroll.getValue();
       int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
       // if we're scrolling to the position we're already at, stop
       // this prevents infinite recursion of events when the scroll/viewport
       // ranges values are the same
-      if ((y == oldY) && (height == oldheight))
+      if (height > 0 && (y != oldY || height != oldheight))
       {
-        return;
+        ranges.setViewportStartAndHeight(y, height);
+        isChanged = true;
       }
-      ranges.setViewportStartAndHeight(y, height);
     }
-    repaint();
+    return isChanged;
   }
 
   /**
@@ -830,7 +860,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
             av.isShowAutocalculatedAbove());
     sorter.sort(getAlignment().getAlignmentAnnotation(),
             av.getSortAnnotationsBy());
-    repaint();
 
     if (updateStructures)
     {
@@ -838,11 +867,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     if (updateOverview)
     {
+      alignFrame.repaint();
 
       if (overviewPanel != null)
       {
         overviewPanel.updateOverviewImage();
       }
+    } else {
+      repaint();
     }
   }
 
@@ -862,7 +894,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * though I still think this call should be elsewhere.
      */
     ViewportRanges ranges = av.getRanges();
-    setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
+    // setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
     super.paintComponent(g);
   }
 
@@ -1021,8 +1053,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
      * single graphics context), then reset to (0, scale height)
      */
     alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
-    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
-            endRes, startSeq, endSeq - 1);
+    getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics,
+            startRes, endRes, startSeq, endSeq - 1);
     alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
 
     if (av.isShowAnnotation() && (endSeq == alignmentHeight))
@@ -1066,8 +1098,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * 
    * @throws PrinterException
    */
-  public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
-          Graphics g) throws PrinterException
+  public int printWrappedAlignment(int pageWidth, int pageHeight,
+          int pageNumber, Graphics g) throws PrinterException
   {
     getSeqPanel().seqCanvas.calculateWrappedGeometry();
     int annotationHeight = 0;
@@ -1118,8 +1150,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     g.translate(idWidth, 0);
 
-    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
-            totalHeight, 0);
+    getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g,
+            pageWidth - idWidth, totalHeight, 0);
 
     if ((pageNumber * pageHeight) < totalHeight)
     {
@@ -1284,13 +1316,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
             String triplet = null;
             if (av.getAlignment().isNucleotide())
             {
-              triplet = ResidueProperties.nucleotideName.get(seq
-                      .getCharAt(column) + "");
+              triplet = ResidueProperties.nucleotideName
+                      .get(seq.getCharAt(column) + "");
             }
             else
             {
-              triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
-                      + "");
+              triplet = ResidueProperties.aa2Triplet
+                      .get(seq.getCharAt(column) + "");
             }
 
             if (triplet == null)
@@ -1307,7 +1339,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
                 text.append("<area shape=\"rect\" coords=\"")
                         .append((idWidth + column * av.getCharWidth()))
                         .append(",").append(sy).append(",")
-                        .append((idWidth + (column + 1) * av.getCharWidth()))
+                        .append((idWidth
+                                + (column + 1) * av.getCharWidth()))
                         .append(",").append((av.getCharHeight() + sy))
                         .append("\"").append(" onMouseOver=\"toolTip('")
                         .append(seqPos).append(" ").append(triplet);
@@ -1333,7 +1366,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
             }
             if (!Comparison.isGap(seq.getCharAt(column)))
             {
-              List<SequenceFeature> features = seq.findFeatures(column, column);
+              List<SequenceFeature> features = seq.findFeatures(column,
+                      column);
               for (SequenceFeature sf : features)
               {
                 if (sf.isContactFeature())
@@ -1702,10 +1736,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
   public void propertyChange(PropertyChangeEvent evt)
   {
     // update this panel's scroll values based on the new viewport ranges values
-    ViewportRanges ranges = av.getRanges();
-    int x = ranges.getStartRes();
-    int y = ranges.getStartSeq();
-    setScrollValues(x, y);
+    updateScrollBarsFromRanges();
 
     // now update any complementary alignment (its viewport ranges object
     // is different so does not get automatically updated)
@@ -1717,6 +1748,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
   }
 
+  void updateScrollBarsFromRanges()
+  {
+    ViewportRanges ranges = av.getRanges();
+    setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
+  }
+
   /**
    * Set the reference to the PCA/Tree chooser dialog for this panel. This
    * reference should be nulled when the dialog is closed.
@@ -1920,7 +1957,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
     PaintRefresher.Refresh(this, av.getSequenceSetId());
   }
 
-  public void selectSequences(List<SequenceI> seqs) 
+  public void selectSequences(List<SequenceI> seqs)
   {
     SequenceGroup sg = new SequenceGroup(seqs);
     sg.setEndRes(av.getAlignment().getWidth() - 1);
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 35ae242..01be3b5 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1009,23 +1009,28 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     g.setColor(Color.white);
     g.fillRect(0, 0, visibleRect.width, visibleRect.height);
 
+    ViewportRanges ranges = av.getRanges();
+    
+    
+    
     if (image != null)
     {
     	// BH 2018 optimizing generation of new Rectangle().
       if (fastPaint || (visibleRect.width != (clipBounds = g.getClipBounds(clipBounds)).width)
             || (visibleRect.height != clipBounds.height))
       {
-
-    	  
     	  g.drawImage(image, 0, 0, this);
         fastPaint = false;
         return;
       }
     }
-    imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
+    
+    imgWidth = (ranges.getEndRes() - ranges.getStartRes()
             + 1) * av.getCharWidth();
+    
     if (imgWidth < 1)
     {
+      fastPaint = false;
       return;
     }
     Graphics2D gg;
@@ -1068,8 +1073,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         gg = (Graphics2D) image.getGraphics();
 
     }
-    
-    drawComponent(gg, av.getRanges().getStartRes(),
+   
+    drawComponent(gg, ranges.getStartRes(),
             av.getRanges().getEndRes() + 1);
     gg.dispose();
     imageFresh = false;
@@ -1077,11 +1082,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   /**
-   * set true to enable redraw timing debug output on stderr
-   */
-  private final boolean debugRedraw = false;
-
-  /**
    * non-Thread safe repaint
    * 
    * @param horizontal
@@ -1101,6 +1101,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     int sr = av.getRanges().getStartRes();
     int er = av.getRanges().getEndRes() + 1;
     int transX = 0;
+    
+    if (er == sr + 1) {
+      fastPaint = false;
+      return;
+    }
 
     Graphics2D gg = (Graphics2D) image.getGraphics();
 
diff --git a/src/jalview/gui/AssociatePdbFileWithSeq.java b/src/jalview/gui/AssociatePdbFileWithSeq.java
index 154582f..5b5bd18 100644
--- a/src/jalview/gui/AssociatePdbFileWithSeq.java
+++ b/src/jalview/gui/AssociatePdbFileWithSeq.java
@@ -20,18 +20,15 @@
  */
 package jalview.gui;
 
-import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
-import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 
-import javax.swing.JOptionPane;
-
 /**
- * GUI related routines for associating PDB files with sequences
+ * GUI related routines for associating PDB files with sequences. A single
+ * static method.
  * 
  * @author JimP
  * 
@@ -39,58 +36,56 @@ import javax.swing.JOptionPane;
 public class AssociatePdbFileWithSeq
 {
 
+  private AssociatePdbFileWithSeq()
+  {
+    // inaccessible
+  }
+
   /**
-   * assocate the given PDB file with
+   * Associate the given PDB file name or URL with a sequence. Do not map
+   * mouse-over events.
    * 
-   * @param choice
+   * @param fileName
+   *          or URL
+   * @param type
+   *          will be DataType.FILE or DataType.URL
    * @param sequence
+   *          to associate
+   * @param prompt
+   *          true if the user should be asked what to do if the specified file
+   *          does not seem to contain PDB information (StructureChooser only)
+   * @return null if file is not found
    */
-  public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,
-          SequenceI sequence, boolean prompt,
-          StructureSelectionManagerProvider ssmp)
+  public static PDBEntry associatePdbWithSeq(String fileName,
+          DataSourceType type, SequenceI sequence, boolean prompt)
   {
     PDBEntry entry = new PDBEntry();
     StructureFile pdbfile = null;
-    pdbfile = StructureSelectionManager.getStructureSelectionManager(ssmp)
+    pdbfile = Desktop.getStructureSelectionManager()
             .setMapping(false, new SequenceI[]
-            { sequence }, null, choice, file);
+            { sequence }, null, fileName, type);
     if (pdbfile == null)
     {
       // stacktrace already thrown so just return
       return null;
     }
-    if (pdbfile.getId() == null)
-    {
-      String reply = null;
-
-      if (prompt)
-      {
-        reply = JvOptionPane.showInternalInputDialog(Desktop.getDesktopPane(),
-                MessageManager
-                        .getString("label.couldnt_find_pdb_id_in_file"),
-                MessageManager.getString("label.no_pdb_id_in_file"),
-                JvOptionPane.QUESTION_MESSAGE);
-      }
-      if (reply == null)
-      {
-        return null;
-      }
-
-      entry.setId(reply);
-    }
-    else
+    String id = pdbfile.getId();
+    if (id == null && (id = (prompt
+            ? JvOptionPane.showInternalInputDialog(Desktop.getDesktopPane(),
+                    MessageManager
+                            .getString("label.couldnt_find_pdb_id_in_file"),
+                    MessageManager.getString("label.no_pdb_id_in_file"),
+                    JvOptionPane.QUESTION_MESSAGE)
+            : null)) == null)
     {
-      entry.setId(pdbfile.getId());
+      return null;
     }
+    entry.setId(id);
     entry.setType(PDBEntry.Type.FILE);
-
-    if (pdbfile != null)
-    {
-      entry.setFile(choice);
-      sequence.getDatasetSequence().addPDBId(entry);
-      StructureSelectionManager.getStructureSelectionManager(ssmp)
-              .registerPDBEntry(entry);
-    }
+    entry.setFile(fileName);
+    sequence.getDatasetSequence().addPDBId(entry);
+    Desktop.getStructureSelectionManager()
+            .registerPDBEntry(entry);
     return entry;
   }
 }
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 4b25ef2..a1d9a09 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -482,82 +482,89 @@ public class Desktop extends GDesktop
 
         experimentalFeatures.setSelected(showExperimental());
 
-        checkURLLinks();
+        if (Jalview.isInteractive())
+        {
+          // disabled for SeqCanvasTest
+          checkURLLinks();
 
-        // Spawn a thread that shows the splashscreen
+          checkURLLinks();
 
-        SwingUtilities.invokeLater(new Runnable()
-        {
-          @Override
-          public void run()
-          {
-            new SplashScreen(true);
-          }
-        });
+          // Spawn a thread that shows the splashscreen
 
-        // Thread off a new instance of the file chooser - this reduces the time
-        // it
-        // takes to open it later on.
-        new Thread(new Runnable()
-        {
-          @Override
-          public void run()
+          SwingUtilities.invokeLater(new Runnable()
           {
-            Cache.log.debug("Filechooser init thread started.");
-            String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
-            JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
-                    fileFormat);
-            Cache.log.debug("Filechooser init thread finished.");
-          }
-        }).start();
-        // Add the service change listener
-        changeSupport.addJalviewPropertyChangeListener("services",
-                new PropertyChangeListener()
-                {
+            @Override
+            public void run()
+            {
+              new SplashScreen(true);
+            }
+          });
 
-                  @Override
-                  public void propertyChange(PropertyChangeEvent evt)
+          // Thread off a new instance of the file chooser - this reduces the
+          // time
+          // it
+          // takes to open it later on.
+          new Thread(new Runnable()
+          {
+            @Override
+            public void run()
+            {
+              Cache.log.debug("Filechooser init thread started.");
+              String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+              JalviewFileChooser.forRead(
+                      Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+              Cache.log.debug("Filechooser init thread finished.");
+            }
+          }).start();
+          // Add the service change listener
+          changeSupport.addJalviewPropertyChangeListener("services",
+                  new PropertyChangeListener()
                   {
-                    Cache.log.debug("Firing service changed event for "
-                            + evt.getNewValue());
-                    JalviewServicesChanged(evt);
-                  }
-                });
-      }
-
-      this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this));
 
-      this.addWindowListener(new WindowAdapter()
-      {
-        @Override
-        public void windowClosing(WindowEvent evt)
-        {
-          quit();
+                    @Override
+                    public void propertyChange(PropertyChangeEvent evt)
+                    {
+                      Cache.log.debug("Firing service changed event for "
+                              + evt.getNewValue());
+                      JalviewServicesChanged(evt);
+                    }
+                  });
         }
-      });
 
-      MouseAdapter ma;
-      this.addMouseListener(ma = new MouseAdapter()
-      {
-        @Override
-        public void mousePressed(MouseEvent evt)
+        this.setDropTarget(new java.awt.dnd.DropTarget(desktopPane, this));
+
+        this.addWindowListener(new WindowAdapter()
         {
-          if (evt.isPopupTrigger()) // Mac
+          @Override
+          public void windowClosing(WindowEvent evt)
           {
-            showPasteMenu(evt.getX(), evt.getY());
+            quit();
           }
-        }
+        });
 
-        @Override
-        public void mouseReleased(MouseEvent evt)
+        MouseAdapter ma;
+        this.addMouseListener(ma = new MouseAdapter()
         {
-          if (evt.isPopupTrigger()) // Windows
+          @Override
+          public void mousePressed(MouseEvent evt)
           {
-            showPasteMenu(evt.getX(), evt.getY());
+            if (evt.isPopupTrigger()) // Mac
+            {
+              showPasteMenu(evt.getX(), evt.getY());
+            }
           }
-        }
-      });
-      desktopPane.addMouseListener(ma);
+
+          @Override
+          public void mouseReleased(MouseEvent evt)
+          {
+            if (evt.isPopupTrigger()) // Windows
+            {
+              showPasteMenu(evt.getX(), evt.getY());
+            }
+          }
+        });
+        desktopPane.addMouseListener(ma);
+      }
     } catch (Throwable t)
     {
       t.printStackTrace();
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ff70162..dc7fea3 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -2040,8 +2040,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                   ap.paintAlignment(false, false);
                 }
                 sequence.setDescription(dialog.getDescription());
-                ap.av.firePropertyChange("alignment", null,
-                        ap.av.getAlignment().getSequences());
+                ap.av.notifyAlignment();
               }
             });
   }
@@ -2172,9 +2171,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
               startEnd, caseChange);
 
       ap.alignFrame.addHistoryItem(caseCommand);
+      ap.av.notifyAlignment();
 
-      ap.av.firePropertyChange("alignment", null,
-              ap.av.getAlignment().getSequences());
 
     }
   }
@@ -2281,8 +2279,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
                           sg.getStartRes(), sg.getEndRes() + 1,
                           ap.av.getAlignment());
                   ap.alignFrame.addHistoryItem(editCommand);
-                  ap.av.firePropertyChange("alignment", null,
-                          ap.av.getAlignment().getSequences());
+                  ap.av.notifyAlignment();
                 }
               });
     }
diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 1725a8a..c7e2b8e 100755
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -263,8 +263,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
       ap.alignFrame.addHistoryItem(cut);
 
       PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
-      ap.av.firePropertyChange("alignment", null,
-              ap.av.getAlignment().getSequences());
+      ap.av.notifyAlignment();
     }
 
   }
@@ -289,8 +288,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     {
       command.undoCommand(af.getViewAlignments());
       ap.av.getHistoryList().remove(command);
-      ap.av.firePropertyChange("alignment", null,
-              ap.av.getAlignment().getSequences());
+      ap.av.notifyAlignment();
       af.updateEditMenuBar();
     }
 
diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index a6b4b49..fda1e03 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -180,9 +180,7 @@ public class ScalePanel extends JPanel
         {
           av.showColumn(hiddenRange[0]);
           reveal = null;
-          ap.updateLayout();
-          ap.paintAlignment(true, true);
-          av.sendSelection();
+          updatePanel();
         }
       });
       pop.add(item);
@@ -197,9 +195,7 @@ public class ScalePanel extends JPanel
           {
             av.showAllHiddenColumns();
             reveal = null;
-            ap.updateLayout();
-            ap.paintAlignment(true, true);
-            av.sendSelection();
+            updatePanel();
           }
         });
         pop.add(item);
@@ -221,10 +217,7 @@ public class ScalePanel extends JPanel
           {
             av.setSelectionGroup(null);
           }
-
-          ap.updateLayout();
-          ap.paintAlignment(true, true);
-          av.sendSelection();
+          updatePanel();
         }
       });
       pop.add(item);
@@ -232,6 +225,14 @@ public class ScalePanel extends JPanel
     return pop;
   }
 
+  protected void updatePanel()
+  {
+    ap.updateLayout();
+    ap.paintAlignment(true, true);
+    ap.updateScrollBarsFromRanges();
+    av.sendSelection();
+  }
+
   /**
    * Handles left mouse button press
    * 
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 4e789b9..3de631f 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -423,8 +423,7 @@ public class SeqPanel extends JPanel
       if (editCommand != null && editCommand.getSize() > 0)
       {
         ap.alignFrame.addHistoryItem(editCommand);
-        av.firePropertyChange("alignment", null,
-                av.getAlignment().getSequences());
+        ap.av.notifyAlignment();
       }
     } finally
     {
diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 5b94831..c30d8c7 100644
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -1001,10 +1001,8 @@ public class StructureChooser extends GStructureChooser
           {
             selectedSequence = userSelectedSeq;
           }
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(selectedPdbFileName,
-                          DataSourceType.FILE, selectedSequence, true,
-                          Desktop.getInstance());
+          PDBEntry fileEntry = AssociatePdbFileWithSeq.associatePdbWithSeq(selectedPdbFileName,
+                          DataSourceType.FILE, selectedSequence, true);
           sViewer = StructureViewer.launchStructureViewer(ap, new PDBEntry[] { fileEntry },
                   new SequenceI[]
                   { selectedSequence }, superimpose, theViewer,
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 37b4dac..d242892 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -174,11 +174,12 @@ public class TreePanel extends GTreePanel
   {
     final PropertyChangeListener listener = new PropertyChangeListener()
     {
+      @SuppressWarnings("unchecked")
       @Override
       public void propertyChange(PropertyChangeEvent evt)
       {
-        if (evt.getPropertyName().equals("alignment"))
-        {
+        switch (evt.getPropertyName()) {
+        case AlignmentViewport.PROPERTY_ALIGNMENT:
           if (tree == null)
           {
             System.out.println("tree is null");
@@ -191,12 +192,14 @@ public class TreePanel extends GTreePanel
           {
             System.out.println(
                     "new alignment sequences vector value is null");
+            return;
           }
 
           tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
           treeCanvas.nameHash.clear(); // reset the mapping between canvas
           // rectangles and leafnodes
           repaint();
+          break;
         }
       }
     };
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 4f399f0..4148c72 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -83,6 +83,9 @@ import java.util.Map;
 public abstract class AlignmentViewport
         implements AlignViewportI, CommandListener, VamsasSource
 {
+  public static final String PROPERTY_ALIGNMENT = "alignment";
+  public static final String PROPERTY_SEQUENCE = "sequence";
+
   protected ViewportRanges ranges;
 
   protected ViewStyleI viewStyle = new ViewStyle();
@@ -605,10 +608,31 @@ public abstract class AlignmentViewport
 
   protected ColumnSelection colSel = new ColumnSelection();
 
-  public boolean autoCalculateConsensus = true;
+  protected boolean autoCalculateConsensusAndConservation = true;
+
+  public boolean getAutoCalculateConsensusAndConservation()
+  { // BH 2019.07.24
+    return autoCalculateConsensusAndConservation;
+  }
+
+  public void setAutoCalculateConsensusAndConservation(boolean b)
+  {
+    autoCalculateConsensusAndConservation = b;
+  }
 
   protected boolean autoCalculateStrucConsensus = true;
 
+  public boolean getAutoCalculateStrucConsensus()
+  { // BH 2019.07.24
+    return autoCalculateStrucConsensus;
+  }
+
+  public void setAutoCalculateStrucConsensus(boolean b)
+  {
+    autoCalculateStrucConsensus = b;
+  }
+
+
   protected boolean ignoreGapsInConsensusCalculation = false;
 
   protected ResidueShaderI residueShading = new ResidueShader();
@@ -824,7 +848,7 @@ public abstract class AlignmentViewport
     // see note in mantis : issue number 8585
     if (alignment.isNucleotide()
             || (conservation == null && quality == null)
-            || !autoCalculateConsensus)
+            || !autoCalculateConsensusAndConservation)
     {
       return;
     }
@@ -842,7 +866,7 @@ public abstract class AlignmentViewport
   public void updateConsensus(final AlignmentViewPanel ap)
   {
     // see note in mantis : issue number 8585
-    if (consensus == null || !autoCalculateConsensus)
+    if (consensus == null || !autoCalculateConsensusAndConservation)
     {
       return;
     }
@@ -1275,21 +1299,22 @@ public abstract class AlignmentViewport
    * checks current colsel against record of last hash value, and optionally
    * updates record.
    * 
-   * @param b
+   * @param updateHash
    *          update the record of last hash value
    * @return true if colsel changed since last call (when b is true)
    */
-  public boolean isColSelChanged(boolean b)
+  public boolean isColSelChanged(boolean updateHash)
   {
     int hc = (colSel == null || colSel.isEmpty()) ? -1 : colSel.hashCode();
     if (hc != -1 && hc != colselhash)
     {
-      if (b)
+      if (updateHash)
       {
         colselhash = hc;
       }
       return true;
     }
+    notifySequence();
     return false;
   }
 
@@ -1350,22 +1375,6 @@ public abstract class AlignmentViewport
     }
   }
 
-  /**
-   * Property change listener for changes in alignment
-   * 
-   * @param prop
-   *          DOCUMENT ME!
-   * @param oldvalue
-   *          DOCUMENT ME!
-   * @param newvalue
-   *          DOCUMENT ME!
-   */
-  public void firePropertyChange(String prop, Object oldvalue,
-          Object newvalue)
-  {
-    changeSupport.firePropertyChange(prop, oldvalue, newvalue);
-  }
-
   // common hide/show column stuff
 
   public void hideSelectedColumns()
@@ -1430,13 +1439,14 @@ public abstract class AlignmentViewport
 
       ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
 
-      firePropertyChange("alignment", null, alignment.getSequences());
       // used to set hasHiddenRows/hiddenRepSequences here, after the property
       // changed event
+      notifySequence();
       sendSelection();
     }
   }
 
+
   public void showSequence(int index)
   {
     int startSeq = ranges.getStartSeq();
@@ -1459,8 +1469,7 @@ public abstract class AlignmentViewport
       }
 
       ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
-
-      firePropertyChange("alignment", null, alignment.getSequences());
+      notifyAlignment();
       sendSelection();
     }
   }
@@ -1494,7 +1503,7 @@ public abstract class AlignmentViewport
         setSequenceAnnotationsVisible(seq[i], false);
       }
       ranges.setStartSeq(startSeq);
-      firePropertyChange("alignment", null, alignment.getSequences());
+      notifyAlignment();
     }
   }
 
@@ -1859,11 +1868,11 @@ public abstract class AlignmentViewport
     {
       alignment.padGaps();
     }
-    if (autoCalculateConsensus)
+    if (autoCalculateConsensusAndConservation)
     {
       updateConsensus(ap);
     }
-    if (hconsensus != null && autoCalculateConsensus)
+    if (hconsensus != null && autoCalculateConsensusAndConservation)
     {
       updateConservation(ap);
     }
@@ -3078,4 +3087,22 @@ public abstract class AlignmentViewport
       codingComplement.setUpdateStructures(needToUpdateStructureViews);
     }
   }
+  
+
+  /**
+   * Notify TreePanel and AlignmentPanel of some sort of alignment change.
+   */
+  public void notifyAlignment()
+  {
+    changeSupport.firePropertyChange(PROPERTY_ALIGNMENT, null, alignment.getSequences());
+  }
+  
+  /**
+   * Notify AlignmentPanel of a sequence column selection or visibility changes.
+   */
+  public void notifySequence()
+  {
+    changeSupport.firePropertyChange(PROPERTY_SEQUENCE, null, null);
+  }
+
 }
diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index 4f671da..5a4fc57 100644
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -136,13 +136,25 @@ public class ViewportRanges extends ViewportProperties
     int[] oldvalues = updateStartEndRes(start, end);
     int oldstartres = oldvalues[0];
     int oldendres = oldvalues[1];
+    
+    if (oldstartres == startRes && oldendres == endRes)
+    {
+      return; // BH 2019.07.27 standard check for no changes
+    }
 
+    // "STARTRES" is a misnomer here -- really "STARTORENDRES"
+    // note that this could be "no change" if the range is just being expanded
     changeSupport.firePropertyChange(STARTRES, oldstartres, startRes);
     if (oldstartres == startRes)
     {
+      // only caught in ViewportRangesTest
+      // No listener cares about this
+      // "ENDRES" is a misnomer here -- really "ENDONLYRES"
+      // BH 2019.07.27 adds end change check
+      // fire only if only the end is changed
       // event won't be fired if start positions are same
       // fire an event for the end positions in case they changed
-      changeSupport.firePropertyChange(ENDRES, oldendres, endRes);
+     changeSupport.firePropertyChange(ENDRES, oldendres, endRes);
     }
   }
 
@@ -797,4 +809,10 @@ public class ViewportRanges extends ViewportProperties
 
     return maxScroll;
   }
+  
+
+  @Override
+  public String toString() {
+     return "[ViewportRange " + startSeq + "-" + endSeq + ", "+ startRes + "-" + endRes + "]";
+  }
 }
diff --git a/test/jalview/gui/AlignmentPanelTest.java b/test/jalview/gui/AlignmentPanelTest.java
index 24b658f..3d06bc8 100644
--- a/test/jalview/gui/AlignmentPanelTest.java
+++ b/test/jalview/gui/AlignmentPanelTest.java
@@ -40,6 +40,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.util.Platform;
 import jalview.viewmodel.ViewportRanges;
 
 public class AlignmentPanelTest
@@ -49,8 +50,9 @@ public class AlignmentPanelTest
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws InvocationTargetException, InterruptedException
   {
-    Jalview.main(new String[] { "-nonews", "-props",
-        "test/jalview/testProps.jvprops" });
+    Jalview.main(new String[] { "-nonews", 
+        "-props", "test/jalview/testProps.jvprops",
+        "-jabaws", "none"});
 
     Cache.setPropertyNoSave("SHOW_IDENTITY",
             Boolean.TRUE.toString());
@@ -94,22 +96,29 @@ public class AlignmentPanelTest
     af.alignPanel.setScrollValues(-1, 5);
 
     // setting -ve x value does not change residue
+    // no update necessary now
     assertEquals(ranges.getEndRes(), oldres);
 
     af.alignPanel.setScrollValues(0, 5);
-
+    // no update necessary now
     // setting 0 as x value does not change residue
+    // no update necessary now
     assertEquals(ranges.getEndRes(), oldres);
 
     af.alignPanel.setScrollValues(5, 5);
     // setting x value to 5 extends endRes by 5 residues
+    System.out.println(ranges);
+    // no update necessary now
     assertEquals(ranges.getEndRes(), oldres + 5);
 
     // scroll to position after hidden columns sets endres to oldres (width) +
     // position
-    int scrollpos = 60;
+
+    int scrollpos = 53; // was 60, but this is too high to allow full scrolling
+                        // in Windows
     af.getViewport().hideColumns(30, 50);
     af.alignPanel.setScrollValues(scrollpos, 5);
+    // no update necessary now
     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 
     // scroll to position within hidden columns, still sets endres to oldres +
@@ -120,6 +129,7 @@ public class AlignmentPanelTest
     af.getViewport().showAllHiddenColumns();
     af.getViewport().hideColumns(30, 50);
     af.alignPanel.setScrollValues(scrollpos, 5);
+    // no update necessary now
     assertEquals(ranges.getEndRes(), oldres + scrollpos);
 
     // scroll to position within <width> distance of the end of the alignment
@@ -127,8 +137,9 @@ public class AlignmentPanelTest
     scrollpos = 130;
     af.getViewport().showAllHiddenColumns();
     af.alignPanel.setScrollValues(scrollpos, 5);
-    assertEquals(ranges.getEndRes(), af.getViewport()
-            .getAlignment().getWidth() - 1);
+    // no update necessary now
+    assertEquals(ranges.getEndRes(),
+            af.getViewport().getAlignment().getWidth() - 1);
 
     // now hide some columns, and scroll to position within <width>
     // distance of the end of the alignment
@@ -136,9 +147,12 @@ public class AlignmentPanelTest
     // columns
     af.getViewport().hideColumns(30, 50);
     af.alignPanel.setScrollValues(scrollpos, 5);
-    assertEquals(ranges.getEndRes(), af.getViewport()
-            .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
-                                                  // columns
+    // no update necessary now
+    assertEquals(ranges.getEndRes(),
+            af.getViewport().getAlignment().getWidth() - 1 - 21); // 21 is the
+                                                                  // number of
+                                                                  // hidden
+                                                                  // columns
   }
 
   /**
@@ -192,8 +206,9 @@ public class AlignmentPanelTest
      * note 4 pixels padding are added to the longest sequence name width
      */
     av.setIdWidth(-1); // force recalculation
+    
     d = af.alignPanel.calculateIdWidth();
-    assertEquals(d.width, 166); // 4 + pixel width of "Q93Z60_ARATH/1-118"
+    assertEquals(d.width, Platform.isWin() ? 172 : 166); // 4 + pixel width of "Q93Z60_ARATH/1-118"
     assertEquals(d.height, 12);
     assertEquals(d.width, av.getIdWidth());
   }
@@ -215,7 +230,7 @@ public class AlignmentPanelTest
      * note 4 pixels 'padding' are added to the longest seq name/annotation label
      */
     Dimension d = af.alignPanel.calculateIdWidth(2000);
-    assertEquals(d.width, 166); // 4 + pixel width of "Q93Z60_ARATH/1-118"
+    assertEquals(d.width, Platform.isWin() ? 172 : 166); // 4 + pixel width of "Q93Z60_ARATH/1-118"
     assertEquals(d.height, 12); // fixed value (not used?)
     assertEquals(av.getIdWidth(), 18); // not changed by this method
 
@@ -224,11 +239,14 @@ public class AlignmentPanelTest
      */
     SequenceI seq = af.viewport.getAlignment()
             .findSequenceMatch("Q93Z60_ARATH")[0];
-    seq.setName(seq.getName() + "MMMMM");
+    String orig = seq.getName();
+    seq.setName(orig + "MMMMM");
     d = af.alignPanel.calculateIdWidth(2000);
-    assertEquals(d.width, 211); // 4 + pixel width of "Q93Z60_ARATHMMMMM/1-118"
+    assertEquals(d.width, Platform.isWin() ? 219 : 211); // 4 + pixel width of "Q93Z60_ARATHMMMMM/1-118"
     assertEquals(d.height, 12);
     assertEquals(av.getIdWidth(), 18); // unchanged
+    // for next test:
+    seq.setName(orig);
 
     /*
      * make the longest annotation name even longer
@@ -239,17 +257,19 @@ public class AlignmentPanelTest
     FontMetrics fmfor = af.alignPanel
             .getFontMetrics(af.alignPanel.getAlabels().getFont());
     // Assumption ID_WIDTH_PADDING == 4
+    // AH! But with those added MMMM above, this was NOT the longest label!
     int expwidth = 4 + fmfor.stringWidth(aa.label);
     d = af.alignPanel.calculateIdWidth(2000);
-    assertEquals(d.width, expwidth); // 228 == ID_WIDTH_PADDING + pixel width of "THIS IS A VERY LONG LABEL INDEED"
+    assertEquals(d.width, expwidth); // 191 == ID_WIDTH_PADDING + pixel width of "THIS IS A VERY LONG LABEL INDEED"
     assertEquals(d.height, 12);
 
     /*
      * override with maxwidth
      * note the 4 pixels padding is added to this value
      */
-    d = af.alignPanel.calculateIdWidth(213);
-    assertEquals(d.width, 217);
+    // BH but we have to be under the max width
+    d = af.alignPanel.calculateIdWidth(180);
+    assertEquals(d.width, 184);
     assertEquals(d.height, 12);
   }
 
@@ -261,7 +281,7 @@ public class AlignmentPanelTest
      */
     int w = af.alignPanel.getVisibleIdWidth(true);
     assertEquals(w, af.alignPanel.getIdPanel().getWidth());
-    assertEquals(w, 115);
+    assertEquals(w, Platform.isWin() ? 112 : 115);
 
     /*
      * width for offscreen rendering is the same
@@ -281,6 +301,6 @@ public class AlignmentPanelTest
      * preference for auto id width overrides fixed width
      */
     Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
-    assertEquals(115, af.alignPanel.getVisibleIdWidth(false));
+    assertEquals(Platform.isWin() ? 106 : 115, af.alignPanel.getVisibleIdWidth(false));
   }
 }
diff --git a/test/jalview/gui/PairwiseAlignmentPanelTest.java b/test/jalview/gui/PairwiseAlignmentPanelTest.java
index 3322ee8..ca9ac22 100644
--- a/test/jalview/gui/PairwiseAlignmentPanelTest.java
+++ b/test/jalview/gui/PairwiseAlignmentPanelTest.java
@@ -37,7 +37,7 @@ public class PairwiseAlignmentPanelTest
 
     PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
 
-    String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
+    String text = ((JTextArea) PA.getValue(testee, "textarea")).getText().replace("\r\n", "\n");
     String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
             + "Sequence     FER1_PEA/29-32 (Sequence length = 7)\n"
             + "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
@@ -62,7 +62,7 @@ public class PairwiseAlignmentPanelTest
 
     PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
 
-    String text = ((JTextArea) PA.getValue(testee, "textarea")).getText();
+    String text = ((JTextArea) PA.getValue(testee, "textarea")).getText().replace("\r\n", "\n");
     String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
             + "Sequence     FER1_PEA/29-32 (Sequence length = 7)\n"
             + "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
diff --git a/test/jalview/gui/SeqCanvasTest.java b/test/jalview/gui/SeqCanvasTest.java
index 78f6cd3..0e14a6b 100644
--- a/test/jalview/gui/SeqCanvasTest.java
+++ b/test/jalview/gui/SeqCanvasTest.java
@@ -23,10 +23,12 @@ package jalview.gui;
 import static org.testng.Assert.assertEquals;
 
 import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.util.Platform;
+import jalview.viewmodel.ViewportRanges;
 
 import java.awt.Font;
 import java.awt.FontMetrics;
@@ -41,6 +43,7 @@ public class SeqCanvasTest
   @BeforeClass(alwaysRun = true)
   public void setUp()
   {
+    Jalview.setInteractive(false);
     Cache.initLogger();
   }
 
@@ -65,8 +68,8 @@ public class SeqCanvasTest
     av.setFont(new Font("SansSerif", Font.PLAIN, 14), true);
     int charHeight = av.getCharHeight();
     int charWidth = av.getCharWidth();
-    assertEquals(charHeight, Platform.isMac() ? 17 : 19);
-    assertEquals(charWidth, Platform.isMac() ? 12 : 11);
+    assertEquals(charHeight, !Platform.isWin() ? 17 : 19);
+    assertEquals(charWidth, !Platform.isWin() ? 12 : 11);
 
     /*
      * first with scales above, left, right
@@ -78,7 +81,7 @@ public class SeqCanvasTest
     FontMetrics fm = testee.getFontMetrics(av.getFont());
     int labelWidth = fm.stringWidth("000") + charWidth;
     assertEquals(labelWidth,
-            Platform.isMac() ? 3 * 9 + charWidth : 3 * 8 + charWidth);
+            !Platform.isWin() ? 3 * 9 + charWidth : 3 * 8 + charWidth);
 
     /*
      * width 400 pixels leaves (400 - 2*labelWidth) for residue columns
@@ -200,7 +203,7 @@ public class SeqCanvasTest
     canvasWidth += 2;
     wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
             canvasHeight);
-    assertEquals(wrappedWidth, Platform.isMac() ? 24 : 25); // 2px not enough
+    assertEquals(wrappedWidth, !Platform.isWin() ? 24 : 25); // 2px not enough
     canvasWidth += 1;
     wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
             canvasHeight);
@@ -235,8 +238,8 @@ public class SeqCanvasTest
     int charHeight = av.getCharHeight();
     int charWidth = av.getCharWidth();
 
-    assertEquals(charHeight, Platform.isMac() ? 17 : 19);
-    assertEquals(charWidth, Platform.isMac() ? 12 : 11);
+    assertEquals(charHeight, !Platform.isWin() ? 17 : 19);
+    assertEquals(charWidth, !Platform.isWin() ? 12 : 11);
 
     SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas;
   
@@ -251,7 +254,7 @@ public class SeqCanvasTest
     FontMetrics fm = testee.getFontMetrics(av.getFont());
     int labelWidth = fm.stringWidth("000") + charWidth;
     assertEquals(labelWidth,
-            Platform.isMac() ? 3 * 9 + charWidth : 3 * 8 + charWidth);
+            !Platform.isWin() ? 3 * 9 + charWidth : 3 * 8 + charWidth);
 
     int annotationHeight = testee.getAnnotationHeight();
 
@@ -330,24 +333,31 @@ public class SeqCanvasTest
     AlignmentI al = av.getAlignment();
     assertEquals(al.getWidth(), 157);
     assertEquals(al.getHeight(), 15);
-    av.getRanges().setStartEndSeq(0, 3);
+
+    ViewportRanges ranges = av.getRanges();
+    ranges.setStartEndSeq(0, 3);
+    System.out.println(ranges);
     av.setShowAnnotation(false);
     av.setScaleAboveWrapped(true);
 
+    System.out.println(ranges);
     SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas;
     av.setWrapAlignment(true);
+    System.out.println(ranges);
     av.setFont(new Font("SansSerif", Font.PLAIN, 14), true);
     int charHeight = av.getCharHeight();
     int charWidth = av.getCharWidth();
+    System.out.println(ranges);
     // Windows h=19, w=11.
-    assertEquals(charHeight, Platform.isMac() ? 17 : 19);
-    assertEquals(charWidth, Platform.isMac() ? 12 : 11);
-
+    assertEquals(charHeight, !Platform.isWin() ? 17 : 19);
+    assertEquals(charWidth, !Platform.isWin() ? 12 : 11);
+    System.out.println(ranges);
+    
     int canvasWidth = 400;
     int canvasHeight = 300;
     testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
-
-    assertEquals(av.getRanges().getEndSeq(), 3); // unchanged
+    System.out.println(ranges);
+    assertEquals(ranges.getEndSeq(), 3); // unchanged
     int repeatingHeight = (int) PA.getValue(testee,
             "wrappedRepeatHeightPx");
     int h = charHeight * (2 + al.getHeight());