Merge branch 'features/JAL-2447experimentalFlag' into develop

[jalview.git] / src / jalview / gui / Desktop.java

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index cc897e3..4877d7f 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -20,7 +20,6 @@
  */
 package jalview.gui;
 
-import static jalview.util.UrlConstants.EMBLEBI_STRING;
 import static jalview.util.UrlConstants.SEQUENCE_ID;
 
 import jalview.api.AlignViewportI;
@@ -31,6 +30,7 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatException;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.IdentifyFile;
 import jalview.io.JalviewFileChooser;
@@ -38,11 +38,14 @@ import jalview.io.JalviewFileView;
 import jalview.jbgui.GSplitFrame;
 import jalview.jbgui.GStructureViewer;
 import jalview.structure.StructureSelectionManager;
+import jalview.urls.IdOrgSettings;
 import jalview.util.ImageMaker;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.UrlConstants;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.ParamManager;
+import jalview.ws.utils.UrlDownloadClient;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -77,6 +80,7 @@ import java.beans.PropertyChangeListener;
 import java.io.BufferedInputStream;
 import java.io.File;
 import java.io.FileOutputStream;
+import java.io.IOException;
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -125,6 +129,11 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         DropTargetListener, ClipboardOwner, IProgressIndicator,
         jalview.api.StructureSelectionManagerProvider
 {
+  private static int DEFAULT_MIN_WIDTH = 300;
+
+  private static int DEFAULT_MIN_HEIGHT = 250;
+
+  private static final String EXPERIMENTAL_FEATURES = "EXPERIMENTAL_FEATURES";
 
   private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
 
@@ -323,19 +332,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     instance = this;
     doVamsasClientCheck();
 
-    groovyShell = new JMenuItem();
-    groovyShell.setText(MessageManager.getString("label.groovy_console"));
-    groovyShell.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        groovyShell_actionPerformed();
-      }
-    });
-    toolsMenu.add(groovyShell);
-    groovyShell.setVisible(true);
-
     doConfigureStructurePrefs();
     setTitle("Jalview " + jalview.bin.Cache.getProperty("VERSION"));
     setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
@@ -390,6 +386,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     showConsole(showjconsole);
 
     showNews.setVisible(false);
+    
+    experimentalFeatures.setSelected(showExperimental());
+
+    getIdentifiersOrgData();
 
     checkURLLinks();
 
@@ -484,6 +484,19 @@ public class Desktop extends jalview.jbgui.GDesktop implements
             });
   }
 
+  /**
+   * Answers true if user preferences to enable experimental features is True
+   * (on), else false
+   * 
+   * @return
+   */
+  public boolean showExperimental()
+  {
+    String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES,
+            Boolean.FALSE.toString());
+    return Boolean.valueOf(experimental).booleanValue();
+  }
+
   public void doConfigureStructurePrefs()
   {
     // configure services
@@ -524,6 +537,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     });
   }
 
+  public void getIdentifiersOrgData()
+  {
+    // Thread off the identifiers fetcher
+    addDialogThread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        Cache.log.debug("Downloading data from identifiers.org");
+        UrlDownloadClient client = new UrlDownloadClient();
+        try
+        {
+          client.download(IdOrgSettings.getUrl(),
+                  IdOrgSettings.getDownloadLocation());
+        } catch (IOException e)
+        {
+          Cache.log.debug("Exception downloading identifiers.org data"
+                  + e.getMessage());
+        }
+      }
+    });
+  }
+
   @Override
   protected void showNews_actionPerformed(ActionEvent e)
   {
@@ -804,6 +840,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     openFrameCount++;
 
+    frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH,
+            DEFAULT_MIN_HEIGHT));
     frame.setVisible(makeVisible);
     frame.setClosable(true);
     frame.setResizable(resizable);
@@ -890,9 +928,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     });
 
+    desktop.add(frame);
+
     windowMenu.add(menuItem);
 
-    desktop.add(frame);
     frame.toFront();
     try
     {
@@ -1024,20 +1063,21 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       Cache.setProperty("LAST_DIRECTORY", chooser
               .getSelectedFile().getParent());
 
-      FileFormatI format = null;
-      FileFormatI selectedFormat = chooser.getSelectedFormat();
-      if (FileFormat.Jalview.equals(selectedFormat))
-      {
-        format = FileFormat.Jalview;
-      }
-      else
+      FileFormatI format = chooser.getSelectedFormat();
+
+      /*
+       * Call IdentifyFile to verify the file contains what its extension implies.
+       * Skip this step for dynamically added file formats, because
+       * IdentifyFile does not know how to recognise them.
+       */
+      if (FileFormats.getInstance().isIdentifiable(format))
       {
         try
         {
           format = new IdentifyFile().identify(choice, DataSourceType.FILE);
         } catch (FileFormatException e)
         {
-          // format is null
+          // format = null; //??
         }
       }
 
@@ -1528,8 +1568,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   @Override
   public void saveState_actionPerformed(ActionEvent e)
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(
-            Cache.getProperty("LAST_DIRECTORY"), "jvp", "Jalview Project");
+    JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+            "Jalview Project");
 
     chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(MessageManager.getString("label.save_state"));
@@ -2182,8 +2222,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   {
     if (v_client != null)
     {
-      JalviewFileChooser chooser = new JalviewFileChooser(
-              Cache.getProperty("LAST_DIRECTORY"), "vdj",// TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+   // TODO: VAMSAS DOCUMENT EXTENSION is VDJ
+      JalviewFileChooser chooser = new JalviewFileChooser("vdj",
               "Vamsas Document");
 
       chooser.setFileView(new JalviewFileView());
@@ -2287,7 +2327,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
         {
           // check what the actual links are - if it's just the default don't
           // bother with the warning
-          Vector<String> links = Preferences.sequenceURLLinks;
+          List<String> links = Preferences.sequenceUrlLinks
+                  .getLinksForMenu();
 
           // only need to check links if there is one with a
           // SEQUENCE_ID which is not the default EMBL_EBI link
@@ -2297,7 +2338,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
           while (li.hasNext())
           {
             String link = li.next();
-            if (link.contains(SEQUENCE_ID) && !link.equals(EMBLEBI_STRING))
+            if (link.contains(SEQUENCE_ID)
+                    && !link.equals(UrlConstants.DEFAULT_STRING))
             {
               check = true;
               int barPos = link.indexOf("|");
@@ -2459,8 +2501,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
   }
 
-  protected JMenuItem groovyShell;
-
   /**
    * Accessor method to quickly get all the AlignmentFrames loaded.
    * 
@@ -2546,6 +2586,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
   /**
    * Add Groovy Support to Jalview
    */
+  @Override
   public void groovyShell_actionPerformed()
   {
     try
@@ -2821,13 +2862,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements
 
     if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
     {
-      if (jalview.ws.jws2.Jws2Discoverer.getDiscoverer().isRunning())
-      {
-        jalview.ws.jws2.Jws2Discoverer.getDiscoverer().setAborted(true);
-      }
       t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(
               changeSupport);
-
     }
     Thread t3 = null;
     {
@@ -3365,4 +3401,14 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     }
   }
+
+  /**
+   * Sets the Preferences property for experimental features to True or False
+   * depending on the state of the controlling menu item
+   */
+  @Override
+  protected void showExperimental_actionPerformed(boolean selected)
+  {
+    Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
+  }
 }