X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=a1846bc75695384dbd950a69c3353da00dda744e;hb=ce26ffcae5e876cf4127173c92f0eddffc9830da;hp=dcd4f7d7782cee5f3bab77555d4e4fb121942e75;hpb=2373f90e6077de127c55ec6cb7671d8ba2436684;p=jalview.git

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index dcd4f7d..a1846bc 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -174,7 +174,8 @@ public class AppJmol extends StructureViewerBase
       _alignwith = new Vector<AlignmentPanel>();
     }
 
-    seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
+    seqColourBy = new ViewSelectionMenu(
+            MessageManager.getString("label.colour_by"), this, _colourwith,
             new ItemListener()
             {
 
@@ -194,7 +195,8 @@ public class AppJmol extends StructureViewerBase
             });
     viewMenu.add(seqColourBy);
     final ItemListener handler;
-    JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
+    JMenu alpanels = new ViewSelectionMenu(
+            MessageManager.getString("label.superpose_with"), this,
             _alignwith, handler = new ItemListener()
             {
 
@@ -205,8 +207,8 @@ public class AppJmol extends StructureViewerBase
                 alignStructs.setToolTipText(MessageManager
                         .formatMessage(
                                 "label.align_structures_using_linked_alignment_views",
-                                new String[]
-                                { new Integer(_alignwith.size()).toString() }));
+                                new String[] { new Integer(_alignwith
+                                        .size()).toString() }));
               }
             });
     handler.itemStateChanged(null);
@@ -381,6 +383,7 @@ public class AppJmol extends StructureViewerBase
       command = "";
     }
     jmb.evalStateCommand(command);
+    jmb.evalStateCommand("set hoverDelay=0.1");
     jmb.setFinishedInit(true);
   }
 
@@ -395,6 +398,7 @@ public class AppJmol extends StructureViewerBase
             MessageManager.getString("label.all"));
     menuItem.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent evt)
       {
         allChainsSelected = true;
@@ -417,6 +421,7 @@ public class AppJmol extends StructureViewerBase
       menuItem = new JCheckBoxMenuItem(chain, true);
       menuItem.addItemListener(new ItemListener()
       {
+        @Override
         public void itemStateChanged(ItemEvent evt)
         {
           if (!allChainsSelected)
@@ -449,6 +454,7 @@ public class AppJmol extends StructureViewerBase
     jmb.centerViewer(toshow);
   }
 
+  @Override
   public void closeViewer(boolean closeExternalViewer)
   {
     // Jmol does not use an external viewer
@@ -465,6 +471,7 @@ public class AppJmol extends StructureViewerBase
     jmb = null;
   }
 
+  @Override
   public void run()
   {
     _started = true;
@@ -488,7 +495,8 @@ public class AppJmol extends StructureViewerBase
           long hdl = pdbid.hashCode() - System.currentTimeMillis();
           if (progressBar != null)
           {
-            progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl);
+            progressBar.setProgressBar(MessageManager.formatMessage(
+                    "status.fetching_pdb", new String[] { pdbid }), hdl);
           }
           try
           {
@@ -503,7 +511,8 @@ public class AppJmol extends StructureViewerBase
           }
           if (progressBar != null)
           {
-            progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl);
+            progressBar.setProgressBar(
+                    MessageManager.getString("label.state_completed"), hdl);
           }
           if (pdbseq != null)
           {
@@ -554,9 +563,8 @@ public class AppJmol extends StructureViewerBase
 
       JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
               .formatMessage("label.pdb_entries_couldnt_be_retrieved",
-                      new String[]
-                      { errormsgs.toString() }), MessageManager
-              .getString("label.couldnt_load_file"),
+                      new String[] { errormsgs.toString() }),
+              MessageManager.getString("label.couldnt_load_file"),
               JOptionPane.ERROR_MESSAGE);
 
     }
@@ -623,10 +631,11 @@ public class AppJmol extends StructureViewerBase
         jmb.updateColours(ap);
       }
       // do superposition if asked to
-      if (alignAddedStructures)
+      if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
       {
         javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
+          @Override
           public void run()
           {
             if (jmb.viewer.isScriptExecuting())
@@ -674,8 +683,7 @@ public class AppJmol extends StructureViewerBase
       try
       {
         // TODO: cope with multiple PDB files in view
-        in = new BufferedReader(new FileReader(
-                jmb.getPdbFile()[0]));
+        in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
         File outFile = chooser.getSelectedFile();
 
         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
@@ -749,22 +757,21 @@ public class AppJmol extends StructureViewerBase
     if (type == jalview.util.ImageMaker.TYPE.PNG)
     {
       im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.PNG,
-              "Make PNG image from view", width, height, null, null);
+              jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view",
+              width, height, null, null, null, 0, false);
     }
     else if (type == jalview.util.ImageMaker.TYPE.EPS)
     {
       im = new jalview.util.ImageMaker(this,
-              jalview.util.ImageMaker.TYPE.EPS,
-              "Make EPS file from view", width, height, null,
-              this.getTitle());
+              jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view",
+              width, height, null, this.getTitle(), null, 0, false);
     }
     else
     {
 
       im = new jalview.util.ImageMaker(this,
               jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA",
-              width, height, null, this.getTitle());
+              width, height, null, this.getTitle(), null, 0, false);
     }
 
     if (im.getGraphics() != null)
@@ -889,8 +896,9 @@ public class AppJmol extends StructureViewerBase
   @Override
   public void backGround_actionPerformed(ActionEvent actionEvent)
   {
-    java.awt.Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_backgroud_colour"), null);
+    java.awt.Color col = JColorChooser
+            .showDialog(this, MessageManager
+                    .getString("label.select_backgroud_colour"), null);
     if (col != null)
     {
       jmb.setBackgroundColour(col);
@@ -1067,6 +1075,7 @@ public class AppJmol extends StructureViewerBase
 
   }
 
+  @Override
   public void setJalviewColourScheme(ColourSchemeI ucs)
   {
     jmb.setJalviewColourScheme(ucs);