(JAL-969) refactored alignmentViewport base class to own package and pulled up most...

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 1997dc9..18d17f4 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 2.6)
- * 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, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -313,15 +313,15 @@ public class FeatureSettings extends JPanel
     Vector allGroups = new Vector();
     SequenceFeature[] tmpfeatures;
     String group;
-    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+    for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
     {
-      if (af.getViewport().alignment.getSequenceAt(i).getDatasetSequence()
+      if (af.getViewport().getAlignment().getSequenceAt(i).getDatasetSequence()
               .getSequenceFeatures() == null)
       {
         continue;
       }
 
-      tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
               .getDatasetSequence().getSequenceFeatures();
 
       int index = 0;
@@ -442,10 +442,10 @@ public class FeatureSettings extends JPanel
     // Find out which features should be visible depending on which groups
     // are selected / deselected
     // and recompute average width ordering
-    for (int i = 0; i < af.getViewport().alignment.getHeight(); i++)
+    for (int i = 0; i < af.getViewport().getAlignment().getHeight(); i++)
     {
 
-      tmpfeatures = af.getViewport().alignment.getSequenceAt(i)
+      tmpfeatures = af.getViewport().getAlignment().getSequenceAt(i)
               .getDatasetSequence().getSequenceFeatures();
       if (tmpfeatures == null)
       {
@@ -904,7 +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()
     {
@@ -913,7 +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()
     {
@@ -922,7 +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()
     {
@@ -931,7 +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()
     {
@@ -940,7 +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()
     {
@@ -950,7 +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()
     {
@@ -959,7 +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()
     {
@@ -968,7 +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()
     {