X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=1c156dc43f934ad415c6de77981372787894885d;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=f1e983580161ce62352dc453b406019d97195c78;hpb=619cc880371f3228e6a1fb33c6bfb6e7a7e2622c;p=jalview.git

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index f1e9835..1c156dc 100755
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -119,7 +119,8 @@ public class FeatureSettings extends Panel implements ItemListener,
     this.setLayout(new BorderLayout());
     scrollPane = new ScrollPane();
     scrollPane.add(featurePanel);
-    if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
+    if (fr.getAllFeatureColours() != null
+            && fr.getAllFeatureColours().size() > 0)
     {
       add(scrollPane, BorderLayout.CENTER);
     }
@@ -150,10 +151,11 @@ public class FeatureSettings extends Panel implements ItemListener,
 
     if (groupPanel != null)
     {
-      groupPanel
-              .setLayout(new GridLayout(
-                      (fr.getFeatureGroupsSize()) / 4 + 1,
-                      4)); // JBPNote - this was scaled on number of visible groups. seems broken
+      groupPanel.setLayout(new GridLayout(
+              (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was
+                                                        // scaled on number of
+                                                        // visible groups. seems
+                                                        // broken
       groupPanel.validate();
 
       add(groupPanel, BorderLayout.NORTH);
@@ -180,8 +182,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     int width = 300;
     jalview.bin.JalviewLite.addFrame(frame,
             MessageManager.getString("label.sequence_feature_settings"),
-            width,
-            height);
+            width, height);
   }
 
   public void paint(Graphics g)
@@ -203,8 +204,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     final String type = check.type;
     final Object typeCol = fr.getFeatureStyle(type);
     java.awt.PopupMenu men = new PopupMenu(MessageManager.formatMessage(
-            "label.settings_for_type", new String[]
-            { type }));
+            "label.settings_for_type", new String[] { type }));
     java.awt.MenuItem scr = new MenuItem(
             MessageManager.getString("label.sort_by_score"));
     men.add(scr);
@@ -214,8 +214,8 @@ public class FeatureSettings extends Panel implements ItemListener,
 
       public void actionPerformed(ActionEvent e)
       {
-        me.ap.alignFrame.avc.sortAlignmentByFeatureScore(new String[]
-        { type });
+        me.ap.alignFrame.avc
+                .sortAlignmentByFeatureScore(new String[] { type });
       }
 
     });
@@ -226,8 +226,8 @@ public class FeatureSettings extends Panel implements ItemListener,
 
       public void actionPerformed(ActionEvent e)
       {
-        me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(new String[]
-        { type });
+        me.ap.alignFrame.avc
+                .sortAlignmentByFeatureDensity(new String[] { type });
       }
 
     });
@@ -283,7 +283,8 @@ public class FeatureSettings extends Panel implements ItemListener,
   @Override
   public void discoverAllFeatureData()
   {
-    if (fr.getAllFeatureColours()!=null && fr.getAllFeatureColours().size()>0)
+    if (fr.getAllFeatureColours() != null
+            && fr.getAllFeatureColours().size() > 0)
     {
       rebuildGroups();
 
@@ -308,7 +309,7 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
     // TODO: JAL-964 - smoothly incorporate new group entries if panel already
     // displayed and new groups present
-    for (String group:fr.getFeatureGroups())
+    for (String group : fr.getFeatureGroups())
     {
       boolean vis = fr.checkGroupVisibility(group, false);
       Checkbox check = new MyCheckbox(group, vis,
@@ -326,6 +327,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       groupPanel.validate();
     }
   }
+
   // This routine adds and removes checkboxes depending on
   // Group selection states
   void resetTable(boolean groupsChanged)
@@ -482,11 +484,12 @@ public class FeatureSettings extends Panel implements ItemListener,
     selectionChanged();
   }
 
-  private ItemListener groupItemListener = new ItemListener() {
-    public void itemStateChanged(ItemEvent evt) {
+  private ItemListener groupItemListener = new ItemListener()
+  {
+    public void itemStateChanged(ItemEvent evt)
+    {
       Checkbox source = (Checkbox) evt.getSource();
-      fr.setGroupVisibility(source.getLabel(),
-              source.getState());
+      fr.setGroupVisibility(source.getLabel(), source.getState());
       ap.seqPanel.seqCanvas.repaint();
       if (ap.overviewPanel != null)
       {
@@ -496,6 +499,7 @@ public class FeatureSettings extends Panel implements ItemListener,
       return;
     };
   };
+
   public void itemStateChanged(ItemEvent evt)
   {
     selectionChanged();
@@ -615,7 +619,9 @@ public class FeatureSettings extends Panel implements ItemListener,
     }
     else
     {
-      throw new Error(MessageManager.getString("error.implementation_error_unsupported_feature_colour_object"));
+      throw new Error(
+              MessageManager
+                      .getString("error.implementation_error_unsupported_feature_colour_object"));
     }
     refreshTable();
   }
@@ -711,7 +717,9 @@ public class FeatureSettings extends Panel implements ItemListener,
       }
       else
       {
-        throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
+        throw new Error(
+                MessageManager
+                        .getString("error.invalid_colour_for_mycheckbox"));
       }
       if (col != null)
       {