X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=b87e4bf92c10de36e2a0b7cf827a5dd5341871f3;hb=85283704c950febdca739d7dd857a1068cd73bbb;hp=dc7283bfed29df19729799de0a75a98b89994e3f;hpb=5dc249708303dd777f4570bb66335150a8beab07;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index dc7283b..b87e4bf 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -82,7 +82,6 @@ import java.util.Map;
 import java.util.Set;
 
 import javax.help.HelpSetException;
-import javax.swing.AbstractButton;
 import javax.swing.AbstractCellEditor;
 import javax.swing.BorderFactory;
 import javax.swing.Icon;
@@ -165,6 +164,10 @@ public class FeatureSettings extends JPanel
 
   JSlider transparency = new JSlider();
 
+  private JCheckBox showComplementOnTop;
+
+  private JCheckBox showComplement;
+
   /*
    * when true, constructor is still executing - so ignore UI events
    */
@@ -180,6 +183,12 @@ public class FeatureSettings extends JPanel
   private boolean handlingUpdate = false;
 
   /*
+   * a change listener to ensure the dialog is updated if
+   * FeatureRenderer discovers new features
+   */
+  private PropertyChangeListener change;
+
+  /*
    * holds {featureCount, totalExtent} for each feature type
    */
   Map<String, float[]> typeWidth = null;
@@ -188,12 +197,22 @@ public class FeatureSettings extends JPanel
   {
     // save transparency for restore on Cancel
     originalTransparency = fr.getTransparency();
-    int originalTransparencyAsPercent = (int) (originalTransparency * 100);
-    transparency.setMaximum(100 - originalTransparencyAsPercent);
+
+    updateTransparencySliderFromFR();
 
     originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
     originalViewStyle = new ViewStyle(af.viewport.getViewStyle());
   }
+
+  private void updateTransparencySliderFromFR()
+  {
+    boolean incon = inConstruction;
+    inConstruction = true;
+
+    int transparencyAsPercent = (int) (fr.getTransparency() * 100);
+    transparency.setValue(100 - transparencyAsPercent);
+    inConstruction = incon;
+  }
   /**
    * Constructor
    * 
@@ -203,7 +222,9 @@ public class FeatureSettings extends JPanel
   {
     this.af = alignFrame;
     fr = af.getFeatureRenderer();
+
     storeOriginalSettings();
+
     try
     {
       jbInit();
@@ -436,12 +457,10 @@ public class FeatureSettings extends JPanel
     inConstruction = false;
   }
 
-  PropertyChangeListener change;
-
-  private JCheckBox showComplementOnTop;
-
-  private AbstractButton showComplement;
-
+  /**
+   * Sets the state of buttons to show complement features from viewport
+   * settings
+   */
   private void updateComplementButtons()
   {
     showComplement.setSelected(af.getViewport().isShowComplementFeatures());
@@ -472,32 +491,23 @@ public class FeatureSettings extends JPanel
     JMenuItem scr = new JMenuItem(
             MessageManager.getString("label.sort_by_score"));
     men.add(scr);
-    final FeatureSettings me = this;
     scr.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc
-                .sortAlignmentByFeatureScore(Arrays.asList(new String[]
-                { type }));
+        sortByScore(Arrays.asList(new String[] { type }));
       }
-
     });
     JMenuItem dens = new JMenuItem(
             MessageManager.getString("label.sort_by_density"));
     dens.addActionListener(new ActionListener()
     {
-
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        me.af.avc
-                .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
-                { type }));
+        sortByDensity(Arrays.asList(new String[] { type }));
       }
-
     });
     men.add(dens);
 
@@ -554,6 +564,47 @@ public class FeatureSettings extends JPanel
     men.show(table, x, y);
   }
 
+  /**
+   * Sort the sequences in the alignment by the number of features for the given
+   * feature types (or all features if null)
+   * 
+   * @param featureTypes
+   */
+  protected void sortByDensity(List<String> featureTypes)
+  {
+    af.avc.sortAlignmentByFeatureDensity(featureTypes);
+  }
+
+  /**
+   * Sort the sequences in the alignment by average score for the given feature
+   * types (or all features if null)
+   * 
+   * @param featureTypes
+   */
+  protected void sortByScore(List<String> featureTypes)
+  {
+    af.avc.sortAlignmentByFeatureScore(featureTypes);
+  }
+
+  /**
+   * Returns true if at least one feature type is visible. Else shows a warning
+   * dialog and returns false.
+   * 
+   * @param title
+   * @return
+   */
+  private boolean canSortBy(String title)
+  {
+    if (fr.getDisplayedFeatureTypes().isEmpty())
+    {
+      JvOptionPane.showMessageDialog(this,
+              MessageManager.getString("label.no_features_to_sort_by"),
+              title, JvOptionPane.OK_OPTION);
+      return false;
+    }
+    return true;
+  }
+
   @Override
   synchronized public void discoverAllFeatureData()
   {
@@ -1255,26 +1306,32 @@ public class FeatureSettings extends JPanel
       }
     });
 
-    JButton sortByScore = new JButton(
-            MessageManager.getString("label.seq_sort_by_score"));
+    final String byScoreLabel = MessageManager.getString("label.seq_sort_by_score");
+    JButton sortByScore = new JButton(byScoreLabel);
     sortByScore.setFont(JvSwingUtils.getLabelFont());
     sortByScore.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        af.avc.sortAlignmentByFeatureScore(null);
+        if (canSortBy(byScoreLabel))
+        {
+          sortByScore(null);
+        }
       }
     });
-    JButton sortByDens = new JButton(
-            MessageManager.getString("label.sequence_sort_by_density"));
+    final String byDensityLabel = MessageManager.getString("label.sequence_sort_by_density");
+    JButton sortByDens = new JButton(byDensityLabel);
     sortByDens.setFont(JvSwingUtils.getLabelFont());
     sortByDens.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        af.avc.sortAlignmentByFeatureDensity(null);
+        if (canSortBy(byDensityLabel))
+        {
+          sortByDensity(null);
+        }
       }
     });
 
@@ -1310,6 +1367,7 @@ public class FeatureSettings extends JPanel
       public void actionPerformed(ActionEvent e)
       {
         revert();
+        refreshDisplay();
         if (!hasComplement)
         {
           close();
@@ -1412,38 +1470,9 @@ public class FeatureSettings extends JPanel
         refreshDisplay();
       }
     });
-    // JButton viewComplementSettings = new JButton(MessageManager
-    // .formatMessage("label.show_linked_feature_settings",
-    // nucleotide
-    // ? MessageManager.getString("label.protein")
-    // .toLowerCase()
-    // : "CDS"));
-    // viewComplementSettings.addActionListener(new ActionListener()
-    // {
-    //
-    // @Override
-    // public void actionPerformed(ActionEvent e)
-    // {
-    // AlignViewControllerGuiI complAf = af.getSplitViewContainer()
-    // .getComplementAlignFrame(af);
-    // FeatureSettings complFeatureSettings = (FeatureSettings) complAf
-    // .getFeatureSettingsUI();
-    // if (complFeatureSettings != null)
-    // {
-    // complFeatureSettings.frame.setVisible(true);
-    // try
-    // {
-    // complFeatureSettings.frame.setSelected(true);
-    // return;
-    // } catch (Exception q)
-    // {
-    // }
-    // }
-    // {
-    // complAf.showFeatureSettingsUI();
-    // }
-    // }
-    // });
+
+    updateComplementButtons();
+
     JPanel lowerPanel = new JPanel(new GridLayout(1, 2));
     bigPanel.add(lowerPanel, BorderLayout.SOUTH);
 
@@ -2052,6 +2081,7 @@ public class FeatureSettings extends JPanel
     fr.setFeatureFilters(originalFilters);
     updateFeatureRenderer(originalData);
     af.getViewport().setViewStyle(originalViewStyle);
+    updateTransparencySliderFromFR();
     updateComplementButtons();
     refreshDisplay();
   }