JAL-3549 JAL-3305 no Sort By Score / Density if no features visible

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index c5589cf..a4b24ed 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1407,8 +1407,8 @@ label.create_image_of = Create {0} image of {1}
 label.click_to_edit = Click to edit, right-click for menu
 label.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu
 label.show_linked_features = Show {0} features
-label.show_linked_feature_settings = Open {0} settings
 label.on_top = on top
 label.include_linked_features = Include {0} features
 label.include_linked_tooltip = Include visible {0} features<br>converted to local sequence coordinates
-label.features_not_shown = {0} feature(s) not shown
\ No newline at end of file
+label.features_not_shown = {0} feature(s) not shown
+label.no_features_to_sort_by = No features to sort by

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 42f145b..4e0fb1f 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -1405,4 +1405,5 @@ label.show_linked_features = Caracter
 label.on_top = encima
 label.include_linked_features = Incluir características de {0}
 label.include_linked_tooltip = Incluir características de {0}<br>convertidas a coordenadas de secuencia local
-label.features_not_shown = {0} característica(s) no mostradas
\ No newline at end of file
+label.features_not_shown = {0} característica(s) no mostradas
+label.no_features_to_sort_by = No hay características para ordenar

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index f45afa5..8087210 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -310,16 +310,31 @@ public class AlignViewController implements AlignViewControllerI
   @Override
   public void sortAlignmentByFeatureDensity(List<String> typ)
   {
-    sortBy(typ, "Sort by Density", AlignmentSorter.FEATURE_DENSITY);
+    String methodText = MessageManager.getString("label.sort_by_density");
+    sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_DENSITY);
   }
 
-  protected void sortBy(List<String> typ, String methodText,
+  /**
+   * Sorts the alignment (or current selection) by either average score or
+   * density of the specified feature types, and adds to the command history. If
+   * {@code types} is null, all visible feature types are used for the sort. If
+   * no feature types apply, does nothing.
+   * 
+   * @param types
+   * @param methodText
+   * @param method
+   */
+  protected void sortByFeatures(List<String> types, String methodText,
           final String method)
   {
     FeatureRenderer fr = alignPanel.getFeatureRenderer();
-    if (typ == null && fr != null)
+    if (types == null && fr != null)
+    {
+      types = fr.getDisplayedFeatureTypes();
+    }
+    if (types.isEmpty())
     {
-      typ = fr.getDisplayedFeatureTypes();
+      return; // nothing to do
     }
     List<String> gps = null;
     if (fr != null)
@@ -341,7 +356,7 @@ public class AlignViewController implements AlignViewControllerI
       stop = al.getWidth();
     }
     SequenceI[] oldOrder = al.getSequencesArray();
-    AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
+    AlignmentSorter.sortByFeature(types, gps, start, stop, al, method);
     avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
             viewport.getAlignment()));
     alignPanel.paintAlignment(true, false);
@@ -351,7 +366,8 @@ public class AlignViewController implements AlignViewControllerI
   @Override
   public void sortAlignmentByFeatureScore(List<String> typ)
   {
-    sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
+    String methodText = MessageManager.getString("label.sort_by_score");
+    sortByFeatures(typ, methodText, AlignmentSorter.FEATURE_SCORE);
   }
 
   @Override

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 3efc63e..b87e4bf 100644 (file)
--- 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;
@@ -448,12 +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());
@@ -484,32 +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);
 
@@ -566,6 +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()
   {
@@ -1267,26 +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);
+        }
       }
     });
 
@@ -1425,38 +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);