X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=0a6fabc3875b50edc9a8d2c6f6e6c3f51cd4642a;hb=140b350c1bb78f0d6b46f9fcbfc523a05c32beba;hp=9658abf97e15ea51745853385eeb7dce0d36f3cb;hpb=6c9f1f0278e44bdb3d777c0e4227c22fa09425bf;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9658abf..0a6fabc 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -57,7 +57,9 @@ import java.util.Deque;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Locale;
 import java.util.Vector;
+import java.util.concurrent.Callable;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
@@ -91,6 +93,7 @@ import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.bin.Jalview;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
@@ -144,6 +147,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.HttpUtils;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
@@ -346,6 +350,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   void init()
   {
+    setFrameIcon(null);
+
     // setBackground(Color.white); // BH 2019
 
     if (!Jalview.isHeadlessMode())
@@ -365,8 +371,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // modifyPID.setEnabled(false);
     }
 
-    String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
-            "No sort");
+    String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
 
     if (sortby.equals("Id"))
     {
@@ -408,7 +413,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       wrapMenuItem_actionPerformed(null);
     }
 
-    if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
+    if (Cache.getDefault("SHOW_OVERVIEW", false))
     {
       this.overviewMenuItem_actionPerformed(null);
     }
@@ -483,10 +488,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
               }
             });
-    if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+    if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
             .indexOf("devel") > -1
-            || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
-                    .indexOf("test") > -1)
+            || Cache.getDefault("VERSION", "DEVELOPMENT")
+                    .toLowerCase(Locale.ROOT).indexOf("test") > -1)
     {
       formatMenu.add(vsel);
     }
@@ -564,7 +569,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, 1);
+            alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
           }
           break;
 
@@ -575,7 +580,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, -1);
+            alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
           }
 
           break;
@@ -588,7 +593,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(-1, 0);
+            alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
           }
 
           break;
@@ -600,7 +605,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else
           {
-            alignPanel.getSeqPanel().moveCursor(1, 0);
+            alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
           }
           break;
 
@@ -1011,7 +1016,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public String getVersion()
   {
-    return jalview.bin.Cache.getProperty("VERSION");
+    return Cache.getProperty("VERSION");
   }
 
   public FeatureRenderer getFeatureRenderer()
@@ -1062,7 +1067,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         Desktop.instance.closeAssociatedWindows();
 
         FileLoader loader = new FileLoader();
-        DataSourceType protocol = fileName.startsWith("http:")
+        DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
                 ? DataSourceType.URL
                 : DataSourceType.FILE;
         loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
@@ -1078,9 +1083,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         if (fileObject == null)
         {
 
-          DataSourceType protocol = (fileName.startsWith("http:")
-                  ? DataSourceType.URL
-                  : DataSourceType.FILE);
+          DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
+                  fileName) ? DataSourceType.URL : DataSourceType.FILE;
           newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
                   currentFileFormat);
         }
@@ -1131,7 +1135,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void save_actionPerformed(ActionEvent e)
   {
     if (fileName == null || (currentFileFormat == null)
-            || fileName.startsWith("http"))
+            || HttpUtils.startsWithHttpOrHttps(fileName))
     {
       saveAs_actionPerformed();
     }
@@ -1204,11 +1208,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     if (!lastSaveSuccessful)
     {
-      JvOptionPane.showInternalMessageDialog(this, MessageManager
-              .formatMessage("label.couldnt_save_file", new Object[]
-              { lastFilenameSaved }),
-              MessageManager.getString("label.error_saving_file"),
-              JvOptionPane.WARNING_MESSAGE);
+      if (!Platform.isHeadless())
+      {
+        JvOptionPane.showInternalMessageDialog(this, MessageManager
+                .formatMessage("label.couldnt_save_file", new Object[]
+                { lastFilenameSaved }),
+                MessageManager.getString("label.error_saving_file"),
+                JvOptionPane.WARNING_MESSAGE);
+      }
+      else
+      {
+        Console.error(MessageManager
+                .formatMessage("label.couldnt_save_file", new Object[]
+                { lastFilenameSaved }));
+      }
     }
     else
     {
@@ -1248,118 +1261,103 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
               shortName);
 
+      Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
+      if (lastSaveSuccessful)
+      {
+        this.getViewport().setSavedUpToDate(true);
+      }
+
       statusBar.setText(MessageManager.formatMessage(
               "label.successfully_saved_to_file_in_format", new Object[]
-              { fileName, format }));
+              { file, format }));
 
       return;
     }
 
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
-    Runnable cancelAction = new Runnable()
-    {
-      @Override
-      public void run()
+    Callable<Void> cancelAction = () -> {
+      lastSaveSuccessful = false;
+      return null;
+    };
+    Callable<Void> outputAction = () -> {
+      // todo defer this to inside formatSequences (or later)
+      AlignmentExportData exportData = viewport.getAlignExportData(options);
+      String output = new FormatAdapter(alignPanel, options)
+              .formatSequences(format, exportData.getAlignment(),
+                      exportData.getOmitHidden(),
+                      exportData.getStartEndPostions(),
+                      viewport.getAlignment().getHiddenColumns());
+      if (output == null)
       {
         lastSaveSuccessful = false;
       }
-    };
-    Runnable outputAction = new Runnable()
-    {
-      @Override
-      public void run()
+      else
       {
-        // todo defer this to inside formatSequences (or later)
-        AlignmentExportData exportData = viewport
-                .getAlignExportData(options);
-        String output = new FormatAdapter(alignPanel, options)
-                .formatSequences(format, exportData.getAlignment(),
-                        exportData.getOmitHidden(),
-                        exportData.getStartEndPostions(),
-                        viewport.getAlignment().getHiddenColumns());
-        if (output == null)
+        // create backupfiles object and get new temp filename destination
+        boolean doBackup = BackupFiles.getEnabled();
+        BackupFiles backupfiles = null;
+        if (doBackup)
         {
-          lastSaveSuccessful = false;
+          Console.trace("ALIGNFRAME making backupfiles object for " + file);
+          backupfiles = new BackupFiles(file);
         }
-        else
+        try
         {
-          // create backupfiles object and get new temp filename destination
-          boolean doBackup = BackupFiles.getEnabled();
-          BackupFiles backupfiles = null;
-          if (doBackup)
-          {
-            Cache.log.debug(
-                    "ALIGNFRAME making backupfiles object for " + file);
-            backupfiles = new BackupFiles(file);
-          }
-          try
-          {
-            String tempFilePath = doBackup ? backupfiles.getTempFilePath()
-                    : file;
-            Cache.log.debug("ALIGNFRAME setting PrintWriter");
-            PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
-
-            if (backupfiles != null)
-            {
-              Cache.log.debug("ALIGNFRAME about to write to temp file "
-                      + backupfiles.getTempFilePath());
-            }
+          String tempFilePath = doBackup ? backupfiles.getTempFilePath()
+                  : file;
+          Console.trace("ALIGNFRAME setting PrintWriter");
+          PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
 
-            out.print(output);
-            Cache.log.debug("ALIGNFRAME about to close file");
-            out.close();
-            Cache.log.debug("ALIGNFRAME closed file");
-            AlignFrame.this.setTitle(file);
-            statusBar.setText(MessageManager.formatMessage(
-                    "label.successfully_saved_to_file_in_format",
-                    new Object[]
-                    { fileName, format.getName() }));
-            lastSaveSuccessful = true;
-          } catch (IOException e)
+          if (backupfiles != null)
           {
-            lastSaveSuccessful = false;
-            Cache.log.error(
-                    "ALIGNFRAME Something happened writing the temp file");
-            Cache.log.error(e.getMessage());
-            Cache.log.debug(e.getStackTrace());
-          } catch (Exception ex)
-          {
-            lastSaveSuccessful = false;
-            Cache.log.error(
-                    "ALIGNFRAME Something else happened writing the temp file");
-            Cache.log.error(ex.getMessage());
-            Cache.log.debug(ex.getStackTrace());
+            Console.trace("ALIGNFRAME about to write to temp file "
+                    + backupfiles.getTempFilePath());
           }
 
-          if (doBackup)
-          {
-            backupfiles.setWriteSuccess(lastSaveSuccessful);
-            Cache.log.debug("ALIGNFRAME writing temp file was "
-                    + (lastSaveSuccessful ? "" : "NOT ") + "successful");
-            // do the backup file roll and rename the temp file to actual file
-            Cache.log.debug(
-                    "ALIGNFRAME about to rollBackupsAndRenameTempFile");
-            lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
-            Cache.log.debug(
-                    "ALIGNFRAME performed rollBackupsAndRenameTempFile "
-                            + (lastSaveSuccessful ? "" : "un")
-                            + "successfully");
-          }
+          out.print(output);
+          Console.trace("ALIGNFRAME about to close file");
+          out.close();
+          Console.trace("ALIGNFRAME closed file");
+          AlignFrame.this.setTitle(file);
+          statusBar.setText(MessageManager.formatMessage(
+                  "label.successfully_saved_to_file_in_format", new Object[]
+                  { fileName, format.getName() }));
+          lastSaveSuccessful = true;
+        } catch (IOException e)
+        {
+          lastSaveSuccessful = false;
+          Console.error(
+                  "ALIGNFRAME Something happened writing the temp file");
+          Console.error(e.getMessage());
+          Console.debug(Cache.getStackTraceString(e));
+        } catch (Exception ex)
+        {
+          lastSaveSuccessful = false;
+          Console.error(
+                  "ALIGNFRAME Something unexpected happened writing the temp file");
+          Console.error(ex.getMessage());
+          Console.debug(Cache.getStackTraceString(ex));
+        }
 
-          if (!lastSaveSuccessful)
-          {
-            if (!Platform.isHeadless())
-            {
-              JvOptionPane.showInternalMessageDialog(AlignFrame.this,
-                      MessageManager.formatMessage(
-                              "label.couldnt_save_file", new Object[]
-                              { fileName }),
-                      MessageManager.getString("label.error_saving_file"),
-                      JvOptionPane.WARNING_MESSAGE);
-            }
-          }
+        if (doBackup)
+        {
+          backupfiles.setWriteSuccess(lastSaveSuccessful);
+          Console.debug("ALIGNFRAME writing temp file was "
+                  + (lastSaveSuccessful ? "" : "NOT ") + "successful");
+          // do the backup file roll and rename the temp file to actual file
+          Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
+          lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+          Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
+                  + (lastSaveSuccessful ? "" : "un") + "successfully");
+        }
+
+        Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
+        if (lastSaveSuccessful)
+        {
+          AlignFrame.this.getViewport().setSavedUpToDate(true);
         }
       }
+      return null;
     };
 
     /*
@@ -1375,7 +1373,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      outputAction.run();
+      try
+      {
+        outputAction.call();
+      } catch (Exception e)
+      {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+      }
     }
   }
 
@@ -1392,34 +1397,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     FileFormatI fileFormat = FileFormats.getInstance()
             .forName(fileFormatName);
     AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
-    Runnable outputAction = new Runnable()
-    {
-      @Override
-      public void run()
+    Callable<Void> outputAction = () -> {
+      // todo defer this to inside formatSequences (or later)
+      AlignmentExportData exportData = viewport.getAlignExportData(options);
+      CutAndPasteTransfer cap = new CutAndPasteTransfer();
+      cap.setForInput(null);
+      try
       {
-        // todo defer this to inside formatSequences (or later)
-        AlignmentExportData exportData = viewport
-                .getAlignExportData(options);
-        CutAndPasteTransfer cap = new CutAndPasteTransfer();
-        cap.setForInput(null);
-        try
-        {
-          FileFormatI format = fileFormat;
-          cap.setText(new FormatAdapter(alignPanel, options)
-                  .formatSequences(format, exportData.getAlignment(),
-                          exportData.getOmitHidden(),
-                          exportData.getStartEndPostions(),
-                          viewport.getAlignment().getHiddenColumns()));
-          Desktop.addInternalFrame(cap, MessageManager.formatMessage(
-                  "label.alignment_output_command", new Object[]
-                  { fileFormat.getName() }), 600, 500);
-        } catch (OutOfMemoryError oom)
-        {
-          new OOMWarning("Outputting alignment as " + fileFormat.getName(),
-                  oom);
-          cap.dispose();
-        }
+        FileFormatI format = fileFormat;
+        cap.setText(new FormatAdapter(alignPanel, options).formatSequences(
+                format, exportData.getAlignment(),
+                exportData.getOmitHidden(),
+                exportData.getStartEndPostions(),
+                viewport.getAlignment().getHiddenColumns()));
+        Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+                "label.alignment_output_command", new Object[]
+                { fileFormat.getName() }), 600, 500);
+      } catch (OutOfMemoryError oom)
+      {
+        new OOMWarning("Outputting alignment as " + fileFormat.getName(),
+                oom);
+        cap.dispose();
       }
+      return null;
     };
 
     /*
@@ -1434,7 +1434,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      outputAction.run();
+      try
+      {
+        outputAction.call();
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+      }
     }
   }
 
@@ -1536,21 +1542,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void associatedData_actionPerformed(ActionEvent e)
   {
     final JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     String tooltip = MessageManager
             .getString("label.load_jalview_annotations");
     chooser.setDialogTitle(tooltip);
     chooser.setToolTipText(tooltip);
-    chooser.setResponseHandler(0, new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        String choice = chooser.getSelectedFile().getPath();
-        jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
-        loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
-      }
+    chooser.setResponseHandler(0, () -> {
+      String choice = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", choice);
+      loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
+      return null;
     });
 
     chooser.showOpenDialog(this);
@@ -1735,7 +1737,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       if (originalSource != viewport)
       {
-        Cache.log.warn(
+        Console.warn(
                 "Implementation worry: mismatch of viewport origin for undo");
       }
       originalSource.updateHiddenColumns();
@@ -1775,7 +1777,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (originalSource != viewport)
       {
-        Cache.log.warn(
+        Console.warn(
                 "Implementation worry: mismatch of viewport origin for redo");
       }
       originalSource.updateHiddenColumns();
@@ -2472,36 +2474,31 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       return;
     }
 
-    Runnable okAction = new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        SequenceI[] cut = sg.getSequences()
-                .toArray(new SequenceI[sg.getSize()]);
+    Callable okAction = () -> {
+      SequenceI[] cut = sg.getSequences()
+              .toArray(new SequenceI[sg.getSize()]);
 
-        addHistoryItem(new EditCommand(
-                MessageManager.getString("label.cut_sequences"), Action.CUT,
-                cut, sg.getStartRes(),
-                sg.getEndRes() - sg.getStartRes() + 1,
-                viewport.getAlignment()));
+      addHistoryItem(new EditCommand(
+              MessageManager.getString("label.cut_sequences"), Action.CUT,
+              cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+              viewport.getAlignment()));
 
-        viewport.setSelectionGroup(null);
-        viewport.sendSelection();
-        viewport.getAlignment().deleteGroup(sg);
+      viewport.setSelectionGroup(null);
+      viewport.sendSelection();
+      viewport.getAlignment().deleteGroup(sg);
 
-        viewport.firePropertyChange("alignment", null,
-                viewport.getAlignment().getSequences());
-        if (viewport.getAlignment().getHeight() < 1)
+      viewport.firePropertyChange("alignment", null,
+              viewport.getAlignment().getSequences());
+      if (viewport.getAlignment().getHeight() < 1)
+      {
+        try
+        {
+          AlignFrame.this.setClosed(true);
+        } catch (Exception ex)
         {
-          try
-          {
-            AlignFrame.this.setClosed(true);
-          } catch (Exception ex)
-          {
-          }
         }
       }
+      return null;
     };
 
     /*
@@ -2525,7 +2522,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      okAction.run();
+      try
+      {
+        okAction.call();
+      } catch (Exception e)
+      {
+        e.printStackTrace();
+      }
     }
   }
 
@@ -2829,7 +2832,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void findMenuItem_actionPerformed(ActionEvent e)
   {
-    new Finder(alignPanel);
+    new Finder(alignPanel, false, null);
   }
 
   /**
@@ -3446,6 +3449,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             .formatMessage("label.overview_params", new Object[]
             { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
             true, true);
+    frame.setFrameIcon(null);
     frame.pack();
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     frame.addInternalFrameListener(
@@ -4071,43 +4075,38 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     // Pick the tree file
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
+            Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
             MessageManager.getString("label.select_newick_like_tree_file"));
     chooser.setToolTipText(
             MessageManager.getString("label.load_tree_file"));
 
-    chooser.setResponseHandler(0, new Runnable()
-    {
-      @Override
-      public void run()
+    chooser.setResponseHandler(0, () -> {
+      String filePath = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", filePath);
+      NewickFile fin = null;
+      try
       {
-        String filePath = chooser.getSelectedFile().getPath();
-        Cache.setProperty("LAST_DIRECTORY", filePath);
-        NewickFile fin = null;
-        try
-        {
-          fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
-                  DataSourceType.FILE));
-          viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
-        } catch (Exception ex)
-        {
-          JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
-                  MessageManager
-                          .getString("label.problem_reading_tree_file"),
-                  JvOptionPane.WARNING_MESSAGE);
-          ex.printStackTrace();
-        }
-        if (fin != null && fin.hasWarningMessage())
-        {
-          JvOptionPane.showMessageDialog(Desktop.desktop,
-                  fin.getWarningMessage(),
-                  MessageManager.getString(
-                          "label.possible_problem_with_tree_file"),
-                  JvOptionPane.WARNING_MESSAGE);
-        }
+        fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
+                DataSourceType.FILE));
+        viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
+      } catch (Exception ex)
+      {
+        JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+                MessageManager.getString("label.problem_reading_tree_file"),
+                JvOptionPane.WARNING_MESSAGE);
+        ex.printStackTrace();
       }
+      if (fin != null && fin.hasWarningMessage())
+      {
+        JvOptionPane.showMessageDialog(Desktop.desktop,
+                fin.getWarningMessage(),
+                MessageManager
+                        .getString("label.possible_problem_with_tree_file"),
+                JvOptionPane.WARNING_MESSAGE);
+      }
+      return null;
     });
     chooser.showOpenDialog(this);
   }
@@ -4290,9 +4289,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   webService.add(me.webServiceNoServices);
                 }
                 // TODO: move into separate menu builder class.
-                boolean new_sspred = false;
-                if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
                 {
+                  // logic for 2.11.1.4 is
+                  // always look to see if there is a discover. if there isn't
+                  // we can't show any Jws2 services
+                  // if there are services available, show them - regardless of
+                  // the 'show JWS2 preference'
+                  // if the discoverer is running then say so
+                  // otherwise offer to trigger discovery if 'show JWS2' is not
+                  // enabled
                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
                   if (jws2servs != null)
                   {
@@ -4301,7 +4306,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       jws2servs.attachWSMenuEntry(webService, me);
                       for (Jws2Instance sv : jws2servs.getServices())
                       {
-                        if (sv.description.toLowerCase().contains("jpred"))
+                        if (sv.description.toLowerCase(Locale.ROOT)
+                                .contains("jpred"))
                         {
                           for (JMenuItem jmi : legacyItems)
                           {
@@ -4309,8 +4315,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           }
                         }
                       }
-
                     }
+
                     if (jws2servs.isRunning())
                     {
                       JMenuItem tm = new JMenuItem(
@@ -4318,6 +4324,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       tm.setEnabled(false);
                       webService.add(tm);
                     }
+                    else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
+                    {
+                      JMenuItem enableJws2 = new JMenuItem(
+                              "Discover Web Services");
+                      enableJws2.setToolTipText(
+                              "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
+                      enableJws2.setEnabled(true);
+                      enableJws2.addActionListener(new ActionListener()
+                      {
+
+                        @Override
+                        public void actionPerformed(ActionEvent e)
+                        {
+                          // start service discoverer, but ignore preference
+                          Desktop.instance.startServiceDiscovery(false,
+                                  true);
+                        }
+                      });
+                      webService.add(enableJws2);
+                    }
                   }
                 }
                 build_urlServiceMenu(me.webService);
@@ -4335,7 +4361,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 }
               } catch (Exception e)
               {
-                Cache.log.debug(
+                Console.debug(
                         "Exception during web service menu building process.",
                         e);
               }
@@ -4432,7 +4458,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       showProducts.setEnabled(showp);
     } catch (Exception e)
     {
-      Cache.log.warn(
+      Console.warn(
               "canShowProducts threw an exception - please report to help@jalview.org",
               e);
       return false;
@@ -4473,8 +4499,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       al = dna.translateCdna(codeTable);
     } catch (Exception ex)
     {
-      jalview.bin.Cache.log.error(
-              "Exception during translation. Please report this !", ex);
+      Console.error("Exception during translation. Please report this !",
+              ex);
       final String msg = MessageManager.getString(
               "label.error_when_translating_sequences_submit_bug_report");
       final String errorTitle = MessageManager
@@ -4836,7 +4862,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
         } catch (Exception x)
         {
-          Cache.log.debug(
+          Console.debug(
                   "Exception when processing data source as T-COFFEE score file",
                   x);
           tcf = null;
@@ -5852,16 +5878,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
     chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
     final AlignFrame us = this;
-    chooser.setResponseHandler(0, new Runnable()
-    {
-      @Override
-      public void run()
-      {
-        String choice = chooser.getSelectedFile().getPath();
-        Cache.setProperty("LAST_DIRECTORY", choice);
-        SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
-        new VCFLoader(choice).loadVCF(seqs, us);
-      }
+    chooser.setResponseHandler(0, () -> {
+      String choice = chooser.getSelectedFile().getPath();
+      Cache.setProperty("LAST_DIRECTORY", choice);
+      SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+      new VCFLoader(choice).loadVCF(seqs, us);
+      return null;
     });
     chooser.showOpenDialog(null);