apply version 2.7 copyright

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 1dc577e..fae5259 100755 (executable)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -134,7 +134,7 @@ public class FeatureSettings extends JPanel
 
     scrollPane.setViewportView(table);
 
-    dassourceBrowser = new DasSourceBrowser();
+    dassourceBrowser = new DasSourceBrowser(this);
     dasSettingsPane.add(dassourceBrowser, BorderLayout.CENTER);
 
     if (af.getViewport().featuresDisplayed == null
@@ -163,16 +163,24 @@ public class FeatureSettings extends JPanel
 
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
-    frame
-            .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
-            {
-              public void internalFrameClosed(
-                      javax.swing.event.InternalFrameEvent evt)
-              {
-                fr.removePropertyChangeListener(change);
-              };
-            });
+    if (new jalview.util.Platform().isAMac())
+    {
+      Desktop.addInternalFrame(frame, "Sequence Feature Settings", 475, 480);
+    }
+    else
+    {
+      Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 450);
+    }
+
+    frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+    {
+      public void internalFrameClosed(
+              javax.swing.event.InternalFrameEvent evt)
+      {
+        fr.removePropertyChangeListener(change);
+        dassourceBrowser.fs = null;
+      };
+    });
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
   }
 
@@ -272,8 +280,9 @@ public class FeatureSettings extends JPanel
                 // probably the color chooser!
                 table.setValueAt(colorChooser.getColor(), selectedRow, 1);
                 table.validate();
-                me.updateFeatureRenderer(((FeatureTableModel) table
-                        .getModel()).getData(), false);
+                me.updateFeatureRenderer(
+                        ((FeatureTableModel) table.getModel()).getData(),
+                        false);
               }
             }
           }
@@ -397,8 +406,8 @@ public class FeatureSettings extends JPanel
     {
       public void itemStateChanged(ItemEvent evt)
       {
-        fr.featureGroups.put(check.getText(), new Boolean(check
-                .isSelected()));
+        fr.featureGroups.put(check.getText(),
+                new Boolean(check.isSelected()));
         af.alignPanel.seqPanel.seqCanvas.repaint();
         if (af.alignPanel.overviewPanel != null)
         {
@@ -512,8 +521,8 @@ public class FeatureSettings extends JPanel
 
         data[dataIndex][0] = type;
         data[dataIndex][1] = fr.getFeatureStyle(type);
-        data[dataIndex][2] = new Boolean(af.getViewport().featuresDisplayed
-                .containsKey(type));
+        data[dataIndex][2] = new Boolean(
+                af.getViewport().featuresDisplayed.containsKey(type));
         dataIndex++;
         visibleChecks.removeElement(type);
       }
@@ -587,10 +596,10 @@ public class FeatureSettings extends JPanel
 
   void load()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"), new String[]
-    { "fc" }, new String[]
-    { "Sequence Feature Colours" }, "Sequence Feature Colours");
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            { "fc" }, new String[]
+            { "Sequence Feature Colours" }, "Sequence Feature Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Load Feature Colours");
     chooser.setToolTipText("Load");
@@ -627,8 +636,8 @@ public class FeatureSettings extends JPanel
               Cache.log.warn("Couldn't parse out graduated feature color.",
                       e);
             }
-            GraduatedColor gcol = new GraduatedColor(mincol, maxcol, newcol
-                    .getMin(), newcol.getMax());
+            GraduatedColor gcol = new GraduatedColor(mincol, maxcol,
+                    newcol.getMin(), newcol.getMax());
             if (newcol.hasAutoScale())
             {
               gcol.setAutoScaled(newcol.getAutoScale());
@@ -651,13 +660,11 @@ public class FeatureSettings extends JPanel
               }
               if (ttyp.equalsIgnoreCase("ABOVE"))
               {
-                gcol
-                        .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+                gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
               }
               if (ttyp.equalsIgnoreCase("BELOW"))
               {
-                gcol
-                        .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+                gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
               }
             }
             fr.setColour(name = newcol.getName(), gcol);
@@ -687,10 +694,10 @@ public class FeatureSettings extends JPanel
 
   void save()
   {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
-            .getProperty("LAST_DIRECTORY"), new String[]
-    { "fc" }, new String[]
-    { "Sequence Feature Colours" }, "Sequence Feature Colours");
+    JalviewFileChooser chooser = new JalviewFileChooser(
+            jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+            { "fc" }, new String[]
+            { "Sequence Feature Colours" }, "Sequence Feature Colours");
     chooser.setFileView(new jalview.io.JalviewFileView());
     chooser.setDialogTitle("Save Feature Colour Scheme");
     chooser.setToolTipText("Save");
@@ -897,7 +904,7 @@ public class FeatureSettings extends JPanel
     settingsPane.setLayout(borderLayout2);
     dasSettingsPane.setLayout(borderLayout3);
     bigPanel.setLayout(borderLayout4);
-    invert.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    invert.setFont(JvSwingUtils.getLabelFont());
     invert.setText("Invert Selection");
     invert.addActionListener(new ActionListener()
     {
@@ -906,7 +913,7 @@ public class FeatureSettings extends JPanel
         invertSelection();
       }
     });
-    optimizeOrder.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    optimizeOrder.setFont(JvSwingUtils.getLabelFont());
     optimizeOrder.setText("Optimise Order");
     optimizeOrder.addActionListener(new ActionListener()
     {
@@ -915,7 +922,7 @@ public class FeatureSettings extends JPanel
         orderByAvWidth();
       }
     });
-    sortByScore.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    sortByScore.setFont(JvSwingUtils.getLabelFont());
     sortByScore.setText("Seq sort by Score");
     sortByScore.addActionListener(new ActionListener()
     {
@@ -924,7 +931,7 @@ public class FeatureSettings extends JPanel
         sortByScore(null);
       }
     });
-    sortByDens.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    sortByDens.setFont(JvSwingUtils.getLabelFont());
     sortByDens.setText("Seq Sort by density");
     sortByDens.addActionListener(new ActionListener()
     {
@@ -933,7 +940,7 @@ public class FeatureSettings extends JPanel
         sortByDens(null);
       }
     });
-    cancel.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    cancel.setFont(JvSwingUtils.getLabelFont());
     cancel.setText("Cancel");
     cancel.addActionListener(new ActionListener()
     {
@@ -943,7 +950,7 @@ public class FeatureSettings extends JPanel
         close();
       }
     });
-    ok.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    ok.setFont(JvSwingUtils.getLabelFont());
     ok.setText("OK");
     ok.addActionListener(new ActionListener()
     {
@@ -952,7 +959,7 @@ public class FeatureSettings extends JPanel
         close();
       }
     });
-    loadColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    loadColours.setFont(JvSwingUtils.getLabelFont());
     loadColours.setText("Load Colours");
     loadColours.addActionListener(new ActionListener()
     {
@@ -961,7 +968,7 @@ public class FeatureSettings extends JPanel
         load();
       }
     });
-    saveColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    saveColours.setFont(JvSwingUtils.getLabelFont());
     saveColours.setText("Save Colours");
     saveColours.addActionListener(new ActionListener()
     {
@@ -1158,6 +1165,7 @@ public class FeatureSettings extends JPanel
   {
     fetchDAS.setEnabled(false);
     cancelDAS.setEnabled(true);
+    dassourceBrowser.setGuiEnabled(false);
     Vector selectedSources = dassourceBrowser.getSelectedSources();
     doDasFeatureFetch(selectedSources, true, true);
   }
@@ -1285,6 +1293,8 @@ public class FeatureSettings extends JPanel
   {
     fetchDAS.setEnabled(true);
     cancelDAS.setEnabled(false);
+    dassourceBrowser.setGuiEnabled(true);
+
   }
 
   public void cancelDAS_actionPerformed(ActionEvent e)
@@ -1293,8 +1303,7 @@ public class FeatureSettings extends JPanel
     {
       dasFeatureFetcher.cancel();
     }
-    fetchDAS.setEnabled(true);
-    cancelDAS.setEnabled(false);
+    complete();
   }
 
   public void noDasSourceActive()