JAL-1160 support horizontal mouse wheel scrolling events

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 1997dc9..1928382 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.
  * 
@@ -19,11 +19,10 @@ package jalview.gui;
 
 import java.io.*;
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 
@@ -38,6 +37,7 @@ import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.GraduatedColor;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
 
 public class FeatureSettings extends JPanel
 {
@@ -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)
       {
@@ -714,13 +714,13 @@ public class FeatureSettings extends JPanel
         PrintWriter out = new PrintWriter(new OutputStreamWriter(
                 new FileOutputStream(choice), "UTF-8"));
 
-        Enumeration e = fr.featureColours.keys();
+        Iterator e = fr.featureColours.keySet().iterator();
         float[] sortOrder = new float[fr.featureColours.size()];
         String[] sortTypes = new String[fr.featureColours.size()];
         int i = 0;
-        while (e.hasMoreElements())
+        while (e.hasNext())
         {
-          sortTypes[i] = e.nextElement().toString();
+          sortTypes[i] = e.next().toString();
           sortOrder[i] = fr.getOrder(sortTypes[i]);
           i++;
         }
@@ -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()
     {
@@ -1134,13 +1134,13 @@ public class FeatureSettings extends JPanel
 
       if (fr.featureGroups != null)
       {
-        Enumeration en = fr.featureGroups.keys();
+        Iterator en = fr.featureGroups.keySet().iterator();
         gps = new String[fr.featureColours.size()];
         int g = 0;
         boolean valid = false;
-        while (en.hasMoreElements())
+        while (en.hasNext())
         {
-          String gp = (String) en.nextElement();
+          String gp = (String) en.next();
           Boolean on = (Boolean) fr.featureGroups.get(gp);
           if (on != null && on.booleanValue())
           {
@@ -1177,7 +1177,7 @@ public class FeatureSettings extends JPanel
    * @param checkDbRefs
    * @param promptFetchDbRefs
    */
-  private void doDasFeatureFetch(Vector selectedSources,
+  private void doDasFeatureFetch(List<jalviewSourceI> selectedSources,
           boolean checkDbRefs, boolean promptFetchDbRefs)
   {
     SequenceI[] dataset, seqs;
@@ -1225,9 +1225,9 @@ public class FeatureSettings extends JPanel
    *          Vector of Strings to resolve to DAS source nicknames.
    * @return sources that are present in source list.
    */
-  public Vector resolveSourceNicknames(Vector sources)
+  public List<jalviewSourceI> resolveSourceNicknames(Vector sources)
   {
-    return dassourceBrowser.resolveSourceNicknames(sources);
+    return dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
   }
 
   /**
@@ -1253,14 +1253,14 @@ public class FeatureSettings extends JPanel
   public void fetchDasFeatures(Vector sources, boolean block)
   {
     initDasSources();
-    Vector resolved = resolveSourceNicknames(sources);
+    List<jalviewSourceI> resolved = dassourceBrowser.sourceRegistry.resolveSourceNicknames(sources);
     if (resolved.size() == 0)
     {
       resolved = dassourceBrowser.getSelectedSources();
     }
     if (resolved.size() > 0)
     {
-      final Vector dassources = resolved;
+      final List<jalviewSourceI> dassources = resolved;
       fetchDAS.setEnabled(false);
       // cancelDAS.setEnabled(true); doDasFetch does this.
       Runnable fetcher = new Runnable()