X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=65042906b728ed23ed1a00cf154ff7987fc219ce;hb=73d23396f9ed076d43e9416eeac708e1b300fd44;hp=ae84ba5332559440e5095c62dc57260e97207ca4;hpb=26ba864a6c290121fe6cf616794d2d0bea65fb7d;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index ae84ba5..6504290 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -31,12 +31,16 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileParse;
 import jalview.io.IdentifyFile;
 import jalview.io.JPredFile;
@@ -48,6 +52,7 @@ import jalview.javascript.JsCallBack;
 import jalview.javascript.MouseOverStructureListener;
 import jalview.structure.SelectionListener;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
 import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 
@@ -63,6 +68,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.WindowAdapter;
 import java.awt.event.WindowEvent;
 import java.io.BufferedReader;
+import java.io.IOException;
 import java.io.InputStreamReader;
 import java.net.URL;
 import java.util.ArrayList;
@@ -79,8 +85,8 @@ import netscape.javascript.JSObject;
  * @author $author$
  * @version $Revision: 1.92 $
  */
-public class JalviewLite extends Applet implements
-        StructureSelectionManagerProvider, JalviewLiteJsApi
+public class JalviewLite extends Applet
+        implements StructureSelectionManagerProvider, JalviewLiteJsApi
 {
 
   private static final String TRUE = "true";
@@ -100,6 +106,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
    */
+  @Override
   public String getSelectedSequences()
   {
     return getSelectedSequencesFrom(getDefaultTargetFrame());
@@ -110,6 +117,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
    */
+  @Override
   public String getSelectedSequences(String sep)
   {
     return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
@@ -122,6 +130,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
    * .AlignFrame)
    */
+  @Override
   public String getSelectedSequencesFrom(AlignFrame alf)
   {
     return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
@@ -134,6 +143,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
    * .AlignFrame, java.lang.String)
    */
+  @Override
   public String getSelectedSequencesFrom(AlignFrame alf, String sep)
   {
     StringBuffer result = new StringBuffer("");
@@ -162,6 +172,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public void highlight(String sequenceId, String position,
           String alignedPosition)
   {
@@ -175,6 +186,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String, java.lang.String)
    */
+  @Override
   public void highlightIn(final AlignFrame alf, final String sequenceId,
           final String position, final String alignedPosition)
   {
@@ -196,9 +208,8 @@ public class JalviewLite extends Applet implements
       final StructureSelectionManagerProvider me = this;
       final int pos = apos;
       // use vamsas listener to broadcast to all listeners in scope
-      if (alignedPosition != null
-              && (alignedPosition.trim().length() == 0 || alignedPosition
-                      .toLowerCase().indexOf("false") > -1))
+      if (alignedPosition != null && (alignedPosition.trim().length() == 0
+              || alignedPosition.toLowerCase().indexOf("false") > -1))
       {
         java.awt.EventQueue.invokeLater(new Runnable()
         {
@@ -231,6 +242,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
    * java.lang.String)
    */
+  @Override
   public void select(String sequenceIds, String columns)
   {
     selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
@@ -242,6 +254,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public void select(String sequenceIds, String columns, String sep)
   {
     selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
@@ -253,6 +266,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public void selectIn(AlignFrame alf, String sequenceIds, String columns)
   {
     selectIn(alf, sequenceIds, columns, separator);
@@ -264,6 +278,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String, java.lang.String)
    */
+  @Override
   public void selectIn(final AlignFrame alf, String sequenceIds,
           String columns, String sep)
   {
@@ -327,8 +342,8 @@ public class JalviewLite extends Applet implements
             from--;
           } catch (NumberFormatException ex)
           {
-            System.err
-                    .println("ERROR: Couldn't parse first integer in range element column selection string '"
+            System.err.println(
+                    "ERROR: Couldn't parse first integer in range element column selection string '"
                             + cl + "' - format is 'from-to'");
             return;
           }
@@ -338,8 +353,8 @@ public class JalviewLite extends Applet implements
             to--;
           } catch (NumberFormatException ex)
           {
-            System.err
-                    .println("ERROR: Couldn't parse second integer in range element column selection string '"
+            System.err.println(
+                    "ERROR: Couldn't parse second integer in range element column selection string '"
                             + cl + "' - format is 'from-to'");
             return;
           }
@@ -405,8 +420,8 @@ public class JalviewLite extends Applet implements
             }
             else
             {
-              System.err
-                      .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
+              System.err.println(
+                      "ERROR: Couldn't parse integer from point selection element of column selection string '"
                               + cl + "'");
               return;
             }
@@ -456,14 +471,11 @@ public class JalviewLite extends Applet implements
         SequenceI rs = sel.getSequenceAt(0);
         start = rs.findIndex(start);
         end = rs.findIndex(end);
-        if (csel != null)
+        List<Integer> cs = new ArrayList<Integer>(csel.getSelected());
+        csel.clear();
+        for (Integer selectedCol : cs)
         {
-          List<Integer> cs = csel.getSelected();
-          csel.clear();
-          for (Integer selectedCol : cs)
-          {
-            csel.addElement(rs.findIndex(selectedCol));
-          }
+          csel.addElement(rs.findIndex(selectedCol));
         }
       }
       sel.setStartRes(start);
@@ -473,7 +485,8 @@ public class JalviewLite extends Applet implements
         @Override
         public void run()
         {
-          alf.select(sel, csel);
+          alf.select(sel, csel,
+                  alf.getAlignViewport().getAlignment().getHiddenColumns());
         }
       });
     }
@@ -486,7 +499,9 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
    * String, java.lang.String)
    */
-  public String getSelectedSequencesAsAlignment(String format, String suffix)
+  @Override
+  public String getSelectedSequencesAsAlignment(String format,
+          String suffix)
   {
     return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
             format, suffix);
@@ -499,26 +514,29 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
    * .appletgui.AlignFrame, java.lang.String, java.lang.String)
    */
+  @Override
   public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
           String format, String suffix)
   {
     try
     {
+      FileFormatI theFormat = FileFormats.getInstance().forName(format);
       boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
       if (alf.viewport.getSelectionGroup() != null)
       {
         // JBPNote: getSelectionAsNewSequence behaviour has changed - this
         // method now returns a full copy of sequence data
         // TODO consider using getSequenceSelection instead here
-        String reply = new AppletFormatAdapter().formatSequences(format,
+        String reply = new AppletFormatAdapter().formatSequences(theFormat,
                 new Alignment(alf.viewport.getSelectionAsNewSequence()),
                 seqlimits);
         return reply;
       }
-    } catch (Exception ex)
+    } catch (IllegalArgumentException ex)
     {
       ex.printStackTrace();
-      return "Error retrieving alignment in " + format + " format. ";
+      return "Error retrieving alignment, possibly invalid format specifier: "
+              + format;
     }
     return "";
   }
@@ -528,6 +546,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
    */
+  @Override
   public String getAlignmentOrder()
   {
     return getAlignmentOrderFrom(getDefaultTargetFrame());
@@ -540,6 +559,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
    * )
    */
+  @Override
   public String getAlignmentOrderFrom(AlignFrame alf)
   {
     return getAlignmentOrderFrom(alf, separator);
@@ -552,6 +572,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
    * , java.lang.String)
    */
+  @Override
   public String getAlignmentOrderFrom(AlignFrame alf, String sep)
   {
     AlignmentI alorder = alf.getAlignViewport().getAlignment();
@@ -569,6 +590,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
    * java.lang.String)
    */
+  @Override
   public String orderBy(String order, String undoName)
   {
     return orderBy(order, undoName, separator);
@@ -580,6 +602,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public String orderBy(String order, String undoName, String sep)
   {
     return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
@@ -592,6 +615,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String, java.lang.String)
    */
+  @Override
   public String orderAlignmentBy(AlignFrame alf, String order,
           String undoName, String sep)
   {
@@ -648,6 +672,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
    */
+  @Override
   public String getAlignment(String format)
   {
     return getAlignmentFrom(getDefaultTargetFrame(), format, TRUE);
@@ -660,6 +685,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
    * java.lang.String)
    */
+  @Override
   public String getAlignmentFrom(AlignFrame alf, String format)
   {
     return getAlignmentFrom(alf, format, TRUE);
@@ -671,6 +697,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
    * java.lang.String)
    */
+  @Override
   public String getAlignment(String format, String suffix)
   {
     return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
@@ -683,6 +710,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public String getAlignmentFrom(AlignFrame alf, String format,
           String suffix)
   {
@@ -690,13 +718,15 @@ public class JalviewLite extends Applet implements
     {
       boolean seqlimits = suffix.equalsIgnoreCase(TRUE);
 
-      String reply = new AppletFormatAdapter().formatSequences(format,
+      FileFormatI theFormat = FileFormats.getInstance().forName(format);
+      String reply = new AppletFormatAdapter().formatSequences(theFormat,
               alf.viewport.getAlignment(), seqlimits);
       return reply;
-    } catch (Exception ex)
+    } catch (IllegalArgumentException ex)
     {
       ex.printStackTrace();
-      return "Error retrieving alignment in " + format + " format. ";
+      return "Error retrieving alignment, possibly invalid format specifier: "
+              + format;
     }
   }
 
@@ -705,6 +735,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
    */
+  @Override
   public void loadAnnotation(String annotation)
   {
     loadAnnotationFrom(getDefaultTargetFrame(), annotation);
@@ -717,17 +748,18 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
    * , java.lang.String)
    */
+  @Override
   public void loadAnnotationFrom(AlignFrame alf, String annotation)
   {
     if (new AnnotationFile().annotateAlignmentView(alf.getAlignViewport(),
-            annotation, AppletFormatAdapter.PASTE))
+            annotation, DataSourceType.PASTE))
     {
       alf.alignPanel.fontChanged();
       alf.alignPanel.setScrollValues(0, 0);
     }
     else
     {
-      alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
+      alf.parseFeaturesFile(annotation, DataSourceType.PASTE);
     }
   }
 
@@ -736,6 +768,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
    */
+  @Override
   public void loadFeatures(String features, boolean autoenabledisplay)
   {
     loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
@@ -748,10 +781,11 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
    * , java.lang.String)
    */
+  @Override
   public boolean loadFeaturesFrom(AlignFrame alf, String features,
           boolean autoenabledisplay)
   {
-    return alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE,
+    return alf.parseFeaturesFile(features, DataSourceType.PASTE,
             autoenabledisplay);
   }
 
@@ -760,6 +794,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
    */
+  @Override
   public String getFeatures(String format)
   {
     return getFeaturesFrom(getDefaultTargetFrame(), format);
@@ -772,6 +807,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
    * java.lang.String)
    */
+  @Override
   public String getFeaturesFrom(AlignFrame alf, String format)
   {
     return alf.outputFeatures(false, format);
@@ -782,6 +818,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
    */
+  @Override
   public String getAnnotation()
   {
     return getAnnotationFrom(getDefaultTargetFrame());
@@ -794,6 +831,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
    * )
    */
+  @Override
   public String getAnnotationFrom(AlignFrame alf)
   {
     return alf.outputAnnotations(false);
@@ -804,6 +842,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#newView()
    */
+  @Override
   public AlignFrame newView()
   {
     return newViewFrom(getDefaultTargetFrame());
@@ -814,6 +853,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
    */
+  @Override
   public AlignFrame newView(String name)
   {
     return newViewFrom(getDefaultTargetFrame(), name);
@@ -824,6 +864,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
    */
+  @Override
   public AlignFrame newViewFrom(AlignFrame alf)
   {
     return alf.newView(null);
@@ -835,6 +876,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
    * java.lang.String)
    */
+  @Override
   public AlignFrame newViewFrom(AlignFrame alf, String name)
   {
     return alf.newView(name);
@@ -846,21 +888,22 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
    * java.lang.String)
    */
+  @Override
   public AlignFrame loadAlignment(String text, String title)
   {
     AlignmentI al = null;
 
-    String format = new IdentifyFile().identify(text,
-            AppletFormatAdapter.PASTE);
     try
     {
-      al = new AppletFormatAdapter().readFile(text,
-              AppletFormatAdapter.PASTE, format);
+      FileFormatI format = new IdentifyFile().identify(text,
+              DataSourceType.PASTE);
+      al = new AppletFormatAdapter().readFile(text, DataSourceType.PASTE,
+              format);
       if (al.getHeight() > 0)
       {
         return new AlignFrame(al, this, title, false);
       }
-    } catch (java.io.IOException ex)
+    } catch (IOException ex)
     {
       ex.printStackTrace();
     }
@@ -872,6 +915,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
    */
+  @Override
   public void setMouseoverListener(String listener)
   {
     setMouseoverListener(currentAlignFrame, listener);
@@ -886,6 +930,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
    * , java.lang.String)
    */
+  @Override
   public void setMouseoverListener(AlignFrame af, String listener)
   {
     if (listener != null)
@@ -893,8 +938,8 @@ public class JalviewLite extends Applet implements
       listener = listener.trim();
       if (listener.length() == 0)
       {
-        System.err
-                .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
+        System.err.println(
+                "jalview Javascript error: Ignoring empty function for mouseover listener.");
         return;
       }
     }
@@ -906,8 +951,9 @@ public class JalviewLite extends Applet implements
     if (debug)
     {
       System.err.println("Added a mouseover listener for "
-              + ((af == null) ? "All frames" : "Just views for "
-                      + af.getAlignViewport().getSequenceSetId()));
+              + ((af == null) ? "All frames"
+                      : "Just views for "
+                              + af.getAlignViewport().getSequenceSetId()));
       System.err.println("There are now " + javascriptListeners.size()
               + " listeners in total.");
     }
@@ -918,6 +964,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
    */
+  @Override
   public void setSelectionListener(String listener)
   {
     setSelectionListener(null, listener);
@@ -930,6 +977,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
    * , java.lang.String)
    */
+  @Override
   public void setSelectionListener(AlignFrame af, String listener)
   {
     if (listener != null)
@@ -937,8 +985,8 @@ public class JalviewLite extends Applet implements
       listener = listener.trim();
       if (listener.length() == 0)
       {
-        System.err
-                .println("jalview Javascript error: Ignoring empty function for selection listener.");
+        System.err.println(
+                "jalview Javascript error: Ignoring empty function for selection listener.");
         return;
       }
     }
@@ -950,8 +998,9 @@ public class JalviewLite extends Applet implements
     if (debug)
     {
       System.err.println("Added a selection listener for "
-              + ((af == null) ? "All frames" : "Just views for "
-                      + af.getAlignViewport().getSequenceSetId()));
+              + ((af == null) ? "All frames"
+                      : "Just views for "
+                              + af.getAlignViewport().getSequenceSetId()));
       System.err.println("There are now " + javascriptListeners.size()
               + " listeners in total.");
     }
@@ -968,6 +1017,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
    *      java.lang.String)
    */
+  @Override
   public void setStructureListener(String listener, String modelSet)
   {
     if (listener != null)
@@ -975,8 +1025,8 @@ public class JalviewLite extends Applet implements
       listener = listener.trim();
       if (listener.length() == 0)
       {
-        System.err
-                .println("jalview Javascript error: Ignoring empty function for selection listener.");
+        System.err.println(
+                "jalview Javascript error: Ignoring empty function for selection listener.");
         return;
       }
     }
@@ -1001,6 +1051,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
    * .AlignFrame, java.lang.String)
    */
+  @Override
   public void removeJavascriptListener(AlignFrame af, String listener)
   {
     if (listener != null)
@@ -1016,9 +1067,8 @@ public class JalviewLite extends Applet implements
     {
       Object lstn = javascriptListeners.elementAt(ms);
       JsCallBack lstner = (JsCallBack) lstn;
-      if ((af == null || lstner.getAlignFrame() == af)
-              && (listener == null || lstner.getListenerFunction().equals(
-                      listener)))
+      if ((af == null || lstner.getAlignFrame() == af) && (listener == null
+              || lstner.getListenerFunction().equals(listener)))
       {
         javascriptListeners.removeElement(lstner);
         msSize--;
@@ -1050,12 +1100,14 @@ public class JalviewLite extends Applet implements
     }
   }
 
+  @Override
   public void stop()
   {
     System.err.println("Applet " + getName() + " stop().");
     tidyUp();
   }
 
+  @Override
   public void destroy()
   {
     System.err.println("Applet " + getName() + " destroy().");
@@ -1112,8 +1164,9 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
    * java.lang.String, java.lang.String)
    */
-  public void mouseOverStructure(final String pdbResNum,
-          final String chain, final String pdbfile)
+  @Override
+  public void mouseOverStructure(final String pdbResNum, final String chain,
+          final String pdbfile)
   {
     final StructureSelectionManagerProvider me = this;
     java.awt.EventQueue.invokeLater(new Runnable()
@@ -1128,9 +1181,9 @@ public class JalviewLite extends Applet implements
                           chain, pdbfile);
           if (debug)
           {
-            System.err.println("mouseOver for '" + pdbResNum
-                    + "' in chain '" + chain + "' in structure '" + pdbfile
-                    + "'");
+            System.err
+                    .println("mouseOver for '" + pdbResNum + "' in chain '"
+                            + chain + "' in structure '" + pdbfile + "'");
           }
         } catch (NumberFormatException e)
         {
@@ -1149,6 +1202,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String)
    */
+  @Override
   public void scrollViewToIn(final AlignFrame alf, final String topRow,
           final String leftHandColumn)
   {
@@ -1159,8 +1213,8 @@ public class JalviewLite extends Applet implements
       {
         try
         {
-          alf.scrollTo(new Integer(topRow).intValue(), new Integer(
-                  leftHandColumn).intValue());
+          alf.scrollTo(new Integer(topRow).intValue(),
+                  new Integer(leftHandColumn).intValue());
 
         } catch (Exception ex)
         {
@@ -1227,8 +1281,8 @@ public class JalviewLite extends Applet implements
 
         } catch (Exception ex)
         {
-          System.err
-                  .println("Couldn't parse integer arguments (leftHandColumn='"
+          System.err.println(
+                  "Couldn't parse integer arguments (leftHandColumn='"
                           + leftHandColumn + "')");
           ex.printStackTrace();
         }
@@ -1302,8 +1356,8 @@ public class JalviewLite extends Applet implements
       {
         try
         {
-          BufferedReader reader = new BufferedReader(new InputStreamReader(
-                  url.openStream()));
+          BufferedReader reader = new BufferedReader(
+                  new InputStreamReader(url.openStream()));
           String line;
           while ((line = reader.readLine()) != null)
           {
@@ -1370,8 +1424,8 @@ public class JalviewLite extends Applet implements
 
     } catch (Exception ex)
     {
-      System.err
-              .println("Warning: No JalviewLite javascript callbacks available.");
+      System.err.println(
+              "Warning: No JalviewLite javascript callbacks available.");
       if (debug)
       {
         ex.printStackTrace();
@@ -1413,9 +1467,8 @@ public class JalviewLite extends Applet implements
       }
       else
       {
-        throw new Error(
-                MessageManager
-                        .getString("error.invalid_separator_parameter"));
+        throw new Error(MessageManager
+                .getString("error.invalid_separator_parameter"));
       }
     }
     int r = 255;
@@ -1488,6 +1541,7 @@ public class JalviewLite extends Applet implements
         add(launcher);
         launcher.addActionListener(new java.awt.event.ActionListener()
         {
+          @Override
           public void actionPerformed(ActionEvent e)
           {
             LoadingThread loader = new LoadingThread(file, file2,
@@ -1571,8 +1625,8 @@ public class JalviewLite extends Applet implements
         {
           // do onInit with the JS executor thread
           new JSFunctionExec(this).executeJavascriptFunction(true,
-                  initjscallback, null, "Calling oninit callback '"
-                          + initjscallback + "'.");
+                  initjscallback, null,
+                  "Calling oninit callback '" + initjscallback + "'.");
         } catch (Exception e)
         {
           System.err.println("Exception when executing _oninit callback '"
@@ -1610,6 +1664,7 @@ public class JalviewLite extends Applet implements
     frame.setTitle(title);
     frame.addWindowListener(new WindowAdapter()
     {
+      @Override
       public void windowClosing(WindowEvent e)
       {
         if (frame instanceof AlignFrame)
@@ -1634,6 +1689,7 @@ public class JalviewLite extends Applet implements
         frame.dispose();
       }
 
+      @Override
       public void windowActivated(WindowEvent e)
       {
         if (frame instanceof AlignFrame)
@@ -1671,6 +1727,7 @@ public class JalviewLite extends Applet implements
    * @param g
    *          graphics context
    */
+  @Override
   public void paint(Graphics g)
   {
     if (!fileFound)
@@ -1680,8 +1737,8 @@ public class JalviewLite extends Applet implements
       g.fillRect(0, 0, getSize().width, getSize().height);
       g.setColor(Color.red);
       g.drawString(
-              MessageManager.getString("label.jalview_cannot_open_file"),
-              5, 15);
+              MessageManager.getString("label.jalview_cannot_open_file"), 5,
+              15);
       g.drawString("\"" + file + "\"", 5, 30);
     }
     else if (embedded)
@@ -1722,6 +1779,7 @@ public class JalviewLite extends Applet implements
   {
     private boolean running = false;
 
+    @Override
     public void run()
     {
       if (running || checkedForJmol)
@@ -1740,8 +1798,8 @@ public class JalviewLite extends Applet implements
           }
           if (!jmolAvailable)
           {
-            System.out
-                    .println("Jmol not available - Using MCview for structures");
+            System.out.println(
+                    "Jmol not available - Using MCview for structures");
           }
         } catch (java.lang.ClassNotFoundException ex)
         {
@@ -1752,8 +1810,8 @@ public class JalviewLite extends Applet implements
         jmolAvailable = false;
         if (debug)
         {
-          System.err
-                  .println("Skipping Jmol check. Will use MCView (probably)");
+          System.err.println(
+                  "Skipping Jmol check. Will use MCView (probably)");
         }
       }
       checkedForJmol = true;
@@ -1771,7 +1829,7 @@ public class JalviewLite extends Applet implements
     /**
      * State variable: protocol for access to file source
      */
-    String protocol;
+    DataSourceType protocol;
 
     String _file; // alignment file or URL spec
 
@@ -1801,7 +1859,7 @@ public class JalviewLite extends Applet implements
        */
       if (path.startsWith("PASTE"))
       {
-        protocol = AppletFormatAdapter.PASTE;
+        protocol = DataSourceType.PASTE;
         return path.substring(5);
       }
 
@@ -1810,7 +1868,7 @@ public class JalviewLite extends Applet implements
        */
       if (path.indexOf("://") != -1)
       {
-        protocol = AppletFormatAdapter.URL;
+        protocol = DataSourceType.URL;
         return path;
       }
 
@@ -1826,7 +1884,7 @@ public class JalviewLite extends Applet implements
           System.err.println("Prepended document base '" + documentBase
                   + "' to make: '" + withDocBase + "'");
         }
-        protocol = AppletFormatAdapter.URL;
+        protocol = DataSourceType.URL;
         return withDocBase;
       }
 
@@ -1839,7 +1897,7 @@ public class JalviewLite extends Applet implements
       if (!withCodeBase.equals(withDocBase)
               && HttpUtils.isValidUrl(withCodeBase))
       {
-        protocol = AppletFormatAdapter.URL;
+        protocol = DataSourceType.URL;
         if (debug)
         {
           System.err.println("Prepended codebase '" + codeBase
@@ -1854,7 +1912,7 @@ public class JalviewLite extends Applet implements
        */
       if (inArchive(path))
       {
-        protocol = AppletFormatAdapter.CLASSLOADER;
+        protocol = DataSourceType.CLASSLOADER;
       }
       return path;
     }
@@ -1866,6 +1924,7 @@ public class JalviewLite extends Applet implements
       applet = _applet;
     }
 
+    @Override
     public void run()
     {
       LoadJmolThread jmolchecker = new LoadJmolThread();
@@ -1890,7 +1949,8 @@ public class JalviewLite extends Applet implements
      */
     private void startLoading()
     {
-      dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
+      dbgMsg("Loading thread started with:\n>>file\n" + _file
+              + ">>endfile");
 
       dbgMsg("Loading started.");
 
@@ -1967,11 +2027,12 @@ public class JalviewLite extends Applet implements
         return null;
       }
       String resolvedFile = resolveFileProtocol(fileParam);
-      String format = new IdentifyFile().identify(resolvedFile, protocol);
-      dbgMsg("File identified as '" + format + "'");
       AlignmentI al = null;
       try
       {
+        FileFormatI format = new IdentifyFile().identify(resolvedFile,
+                protocol);
+        dbgMsg("File identified as '" + format + "'");
         al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
                 format);
         if ((al != null) && (al.getHeight() > 0))
@@ -1988,16 +2049,16 @@ public class JalviewLite extends Applet implements
           // update the focus.
           currentAlignFrame = newAlignFrame;
 
-          if (protocol == AppletFormatAdapter.PASTE)
+          if (protocol == DataSourceType.PASTE)
           {
-            newAlignFrame.setTitle(MessageManager.formatMessage(
-                    "label.sequences_from", new Object[] { applet
-                            .getDocumentBase().toString() }));
+            newAlignFrame.setTitle(MessageManager
+                    .formatMessage("label.sequences_from", new Object[]
+                    { applet.getDocumentBase().toString() }));
           }
 
           newAlignFrame.statusBar.setText(MessageManager.formatMessage(
-                  "label.successfully_loaded_file",
-                  new Object[] { resolvedFile }));
+                  "label.successfully_loaded_file", new Object[]
+                  { resolvedFile }));
 
           return newAlignFrame;
         }
@@ -2020,8 +2081,8 @@ public class JalviewLite extends Applet implements
             dbgMsg(">>>Dump finished.");
           } catch (Exception e)
           {
-            System.err
-                    .println("Exception when trying to dump the content of the file parameter.");
+            System.err.println(
+                    "Exception when trying to dump the content of the file parameter.");
             e.printStackTrace();
           }
         }
@@ -2044,8 +2105,8 @@ public class JalviewLite extends Applet implements
        * related to JAL-434
        */
 
-      applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
-              false));
+      applet.setAlignPdbStructures(
+              getDefaultParameter("alignpdbfiles", false));
       /*
        * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
        * PDB|1GAQ|1GAQ|C">
@@ -2061,9 +2122,11 @@ public class JalviewLite extends Applet implements
       Vector pdbs = new Vector();
       // create a lazy matcher if we're asked to
       jalview.analysis.SequenceIdMatcher matcher = (applet
-              .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
-              alignFrame.getAlignViewport().getAlignment()
-                      .getSequencesArray()) : null;
+              .getDefaultParameter("relaxedidmatch", false))
+                      ? new jalview.analysis.SequenceIdMatcher(
+                              alignFrame.getAlignViewport().getAlignment()
+                                      .getSequencesArray())
+                      : null;
 
       String param;
       do
@@ -2092,8 +2155,9 @@ public class JalviewLite extends Applet implements
             String sequence = applet.getParameter("PDBSEQ");
             if (sequence != null)
             {
-              seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
-                      .getAlignViewport().getAlignment().findName(sequence)
+              seqs = new SequenceI[] { matcher == null
+                      ? (Sequence) alignFrame.getAlignViewport()
+                              .getAlignment().findName(sequence)
                       : matcher.findIdMatch(sequence) };
             }
 
@@ -2114,9 +2178,10 @@ public class JalviewLite extends Applet implements
                 tmp2.add(st2.nextToken());
                 seqstring = st2.nextToken();
               }
-              tmp.add(matcher == null ? (Sequence) alignFrame
-                      .getAlignViewport().getAlignment()
-                      .findName(seqstring) : matcher.findIdMatch(seqstring));
+              tmp.add(matcher == null
+                      ? (Sequence) alignFrame.getAlignViewport()
+                              .getAlignment().findName(seqstring)
+                      : matcher.findIdMatch(seqstring));
             }
 
             seqs = tmp.toArray(new SequenceI[tmp.size()]);
@@ -2136,8 +2201,9 @@ public class JalviewLite extends Applet implements
               if (seqs[i] != null)
               {
                 ((Sequence) seqs[i]).addPDBId(pdb);
-                StructureSelectionManager.getStructureSelectionManager(
-                        applet).registerPDBEntry(pdb);
+                StructureSelectionManager
+                        .getStructureSelectionManager(applet)
+                        .registerPDBEntry(pdb);
               }
               else
               {
@@ -2145,8 +2211,8 @@ public class JalviewLite extends Applet implements
                 {
                   // this may not really be a problem but we give a warning
                   // anyway
-                  System.err
-                          .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
+                  System.err.println(
+                          "Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
                                   + i + ")");
                 }
               }
@@ -2159,8 +2225,7 @@ public class JalviewLite extends Applet implements
             }
             else
             {
-              pdbs.addElement(new Object[] { pdb, seqs, chains,
-                  new String(protocol) });
+              pdbs.addElement(new Object[] { pdb, seqs, chains, protocol });
             }
           }
         }
@@ -2173,7 +2238,8 @@ public class JalviewLite extends Applet implements
         PDBEntry[] pdb = new PDBEntry[pdbs.size()];
         String[][] chains = new String[pdbs.size()][];
         String[] protocols = new String[pdbs.size()];
-        for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
+        for (int pdbsi = 0, pdbsiSize = pdbs
+                .size(); pdbsi < pdbsiSize; pdbsi++)
         {
           Object[] o = (Object[]) pdbs.elementAt(pdbsi);
           pdb[pdbsi] = (PDBEntry) o[0];
@@ -2199,6 +2265,11 @@ public class JalviewLite extends Applet implements
     {
       boolean result = false;
       String param = applet.getParameter("jnetfile");
+      if (param == null)
+      {
+        // jnet became jpred around 2016
+        param = applet.getParameter("jpredfile");
+      }
       if (param != null)
       {
         try
@@ -2211,9 +2282,9 @@ public class JalviewLite extends Applet implements
           SequenceI repseq = alignFrame.viewport.getAlignment()
                   .getSequenceAt(0);
           alignFrame.viewport.getAlignment().setSeqrep(repseq);
-          ColumnSelection cs = new ColumnSelection();
+          HiddenColumns cs = new HiddenColumns();
           cs.hideInsertionsFor(repseq);
-          alignFrame.viewport.setColumnSelection(cs);
+          alignFrame.viewport.getAlignment().setHiddenColumns(cs);
           alignFrame.alignPanel.fontChanged();
           alignFrame.alignPanel.setScrollValues(0, 0);
           result = true;
@@ -2249,8 +2320,8 @@ public class JalviewLite extends Applet implements
         }
         else
         {
-          System.err
-                  .println("Annotations were not added from annotation file '"
+          System.err.println(
+                  "Annotations were not added from annotation file '"
                           + param + "'");
         }
       }
@@ -2321,14 +2392,14 @@ public class JalviewLite extends Applet implements
         {
           if (debug)
           {
-            System.err
-                    .println("Attempting to load T-COFFEE score file from the scoreFile parameter");
+            System.err.println(
+                    "Attempting to load T-COFFEE score file from the scoreFile parameter");
           }
           result = alignFrame.loadScoreFile(sScoreFile);
           if (!result)
           {
-            System.err
-                    .println("Failed to parse T-COFFEE parameter as a valid score file ('"
+            System.err.println(
+                    "Failed to parse T-COFFEE parameter as a valid score file ('"
                             + sScoreFile + "')");
           }
         } catch (Exception e)
@@ -2425,8 +2496,8 @@ public class JalviewLite extends Applet implements
     {
       return initialAlignFrame;
     }
-    System.err
-            .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
+    System.err.println(
+            "Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
     return null;
   }
 
@@ -2504,8 +2575,8 @@ public class JalviewLite extends Applet implements
     }
     if (debug)
     {
-      System.err.println("Empty Array from '" + separator
-              + "' separated List");
+      System.err.println(
+              "Empty Array from '" + separator + "' separated List");
     }
     return null;
   }
@@ -2547,16 +2618,16 @@ public class JalviewLite extends Applet implements
       }
       if (debug)
       {
-        System.err.println("Returning '" + separator
-                + "' separated List:\n");
+        System.err
+                .println("Returning '" + separator + "' separated List:\n");
         System.err.println(v);
       }
       return v.toString();
     }
     if (debug)
     {
-      System.err.println("Returning empty '" + separator
-              + "' separated List\n");
+      System.err.println(
+              "Returning empty '" + separator + "' separated List\n");
     }
     return "" + separator;
   }
@@ -2566,10 +2637,11 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
    */
+  @Override
   public String getFeatureGroups()
   {
-    String lst = arrayToSeparatorList(getDefaultTargetFrame()
-            .getFeatureGroups());
+    String lst = arrayToSeparatorList(
+            getDefaultTargetFrame().getFeatureGroups());
     return lst;
   }
 
@@ -2580,6 +2652,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
    * )
    */
+  @Override
   public String getFeatureGroupsOn(AlignFrame alf)
   {
     String lst = arrayToSeparatorList(alf.getFeatureGroups());
@@ -2591,10 +2664,11 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
    */
+  @Override
   public String getFeatureGroupsOfState(boolean visible)
   {
-    return arrayToSeparatorList(getDefaultTargetFrame()
-            .getFeatureGroupsOfState(visible));
+    return arrayToSeparatorList(
+            getDefaultTargetFrame().getFeatureGroupsOfState(visible));
   }
 
   /*
@@ -2604,6 +2678,7 @@ public class JalviewLite extends Applet implements
    * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
    * .AlignFrame, boolean)
    */
+  @Override
   public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
   {
     return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
@@ -2615,6 +2690,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
    * AlignFrame, java.lang.String, boolean)
    */
+  @Override
   public void setFeatureGroupStateOn(final AlignFrame alf,
           final String groups, boolean state)
   {
@@ -2636,6 +2712,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
    * boolean)
    */
+  @Override
   public void setFeatureGroupState(String groups, boolean state)
   {
     setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
@@ -2646,6 +2723,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#getSeparator()
    */
+  @Override
   public String getSeparator()
   {
     return separator;
@@ -2656,6 +2734,7 @@ public class JalviewLite extends Applet implements
    * 
    * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
    */
+  @Override
   public void setSeparator(String separator)
   {
     if (separator == null || separator.length() < 1)
@@ -2700,6 +2779,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
    * java.lang.String, java.lang.String, java.lang.String)
    */
+  @Override
   public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
           String pdbEntryString, String pdbFile)
   {
@@ -2716,6 +2796,7 @@ public class JalviewLite extends Applet implements
     return alignPdbStructures;
   }
 
+  @Override
   public void start()
   {
     // callInitCallback();
@@ -2749,6 +2830,7 @@ public class JalviewLite extends Applet implements
    * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
    * java.lang.String)
    */
+  @Override
   public String getJsMessage(String messageclass, String viewId)
   {
     Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
@@ -2816,22 +2898,13 @@ public class JalviewLite extends Applet implements
     {
       return defcolour;
     }
-    Color col = jalview.schemes.ColourSchemeProperty
-            .getAWTColorFromName(colprop);
+    Color col = ColorUtils.parseColourString(colprop);
     if (col == null)
     {
-      try
-      {
-        col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
-      } catch (Exception ex)
-      {
-        System.err.println("Couldn't parse '" + colprop
-                + "' as a colour for " + colparam);
-        col = null;
-      }
+      System.err.println("Couldn't parse '" + colprop + "' as a colour for "
+              + colparam);
     }
     return (col == null) ? defcolour : col;
-
   }
 
   public void openJalviewHelpUrl()
@@ -2864,8 +2937,7 @@ public class JalviewLite extends Applet implements
       String codebase = localref.toString();
       String localfile = localref.getFile();
       resolvedPath = codebase.substring(0,
-              codebase.length() - localfile.length())
-              + targetPath;
+              codebase.length() - localfile.length()) + targetPath;
       return resolvedPath;
     }
 
@@ -2899,8 +2971,8 @@ public class JalviewLite extends Applet implements
     }
     if (debug)
     {
-      System.err.println("resolveUrlForLocalOrAbsolute returning "
-              + resolvedPath);
+      System.err.println(
+              "resolveUrlForLocalOrAbsolute returning " + resolvedPath);
     }
     return resolvedPath;
   }
@@ -2922,17 +2994,15 @@ public class JalviewLite extends Applet implements
         // form valid URL
         // Should really use docbase, not codebase.
         URL prepend;
-        url = resolveUrlForLocalOrAbsolute(
-                url,
-                prepend = getDefaultParameter("resolvetocodebase", false) ? getCodeBase()
+        url = resolveUrlForLocalOrAbsolute(url,
+                prepend = getDefaultParameter("resolvetocodebase", false)
+                        ? getCodeBase()
                         : getDocumentBase());
         if (debug)
         {
-          System.err
-                  .println("Show url (prepended "
-                          + prepend
-                          + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
-                          + url);
+          System.err.println("Show url (prepended " + prepend
+                  + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
+                  + url);
         }
       }
       else