JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...
[jalview.git] / src / jalview / gui / AnnotationColumnChooser.java
index 311b9d5..a1c082c 100644 (file)
@@ -25,6 +25,7 @@ import jalview.datamodel.HiddenColumns;
 import jalview.io.cache.JvCacheableInputBox;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
 
 import java.awt.BorderLayout;
@@ -33,10 +34,11 @@ import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.KeyEvent;
-import java.util.ArrayList;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBox;
@@ -50,8 +52,8 @@ import javax.swing.border.TitledBorder;
 import net.miginfocom.swing.MigLayout;
 
 @SuppressWarnings("serial")
-public class AnnotationColumnChooser extends AnnotationRowFilter implements
-        ItemListener
+public class AnnotationColumnChooser extends AnnotationRowFilter
+        implements ItemListener
 {
   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
 
@@ -77,19 +79,18 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   public static final int ACTION_OPTION_SELECT = 1;
 
-  public static int ACTION_OPTION_HIDE = 2;
+  public static final int ACTION_OPTION_HIDE = 2;
 
-  public static String NO_GRAPH_VIEW = "0";
+  public static final String NO_GRAPH_VIEW = "0";
 
-  public static String GRAPH_VIEW = "1";
+  public static final String GRAPH_VIEW = "1";
 
   private int actionOption = ACTION_OPTION_SELECT;
 
   private HiddenColumns oldHiddenColumns;
 
-  protected int MIN_WIDTH = 420;
-
-  protected int MIN_HEIGHT = 430;
+  protected static int MIN_WIDTH = (Platform.isJS() ? 370 : 420);
+  protected static int MIN_HEIGHT = (Platform.isJS() ? 370 : 430);
 
   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
   {
@@ -98,8 +99,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     Desktop.addInternalFrame(frame,
-            MessageManager.getString("label.select_by_annotation"), 520,
-            215);
+            MessageManager.getString("label.select_by_annotation"), 0,
+            0);
+    // BH note: MIGLayout ignores this completely, 
+    // possibly creating a frame smaller than specified:
     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 
     addSliderChangeListener();
@@ -119,18 +122,16 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     // restore Object state from the previous session if one exists
     if (lastChooser != null)
     {
-      currentSearchPanel = lastChooser
-              .getCurrentSearchPanel();
+      currentSearchPanel = lastChooser.getCurrentSearchPanel();
       currentStructureFilterPanel = lastChooser
               .getCurrentStructureFilterPanel();
-      annotations.setSelectedIndex(lastChooser
-              .getAnnotations().getSelectedIndex());
-      threshold.setSelectedIndex(lastChooser
-              .getThreshold().getSelectedIndex());
-      actionOption = lastChooser
-              .getActionOption();
-      percentThreshold.setSelected(lastChooser.percentThreshold
-              .isSelected());
+      annotations.setSelectedIndex(
+              lastChooser.getAnnotations().getSelectedIndex());
+      threshold.setSelectedIndex(
+              lastChooser.getThreshold().getSelectedIndex());
+      actionOption = lastChooser.getActionOption();
+      percentThreshold
+              .setSelected(lastChooser.percentThreshold.isSelected());
     }
 
     try
@@ -152,11 +153,11 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     super.jbInit();
 
     JPanel thresholdPanel = new JPanel();
-    thresholdPanel.setBorder(new TitledBorder(MessageManager
-            .getString("label.threshold_filter")));
+    thresholdPanel.setBorder(new TitledBorder(
+            MessageManager.getString("label.threshold_filter")));
     thresholdPanel.setBackground(Color.white);
     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
-    thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
+    thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]") );
 
     percentThreshold.setBackground(Color.white);
     percentThreshold.setFont(JvSwingUtils.getLabelFont());
@@ -205,7 +206,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
             AnnotationColumnChooser.NO_GRAPH_VIEW);
     switchableViewsPanel.add(graphFilterView,
             AnnotationColumnChooser.GRAPH_VIEW);
-
     this.setLayout(new BorderLayout());
     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
@@ -241,24 +241,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
       if (av.getAnnotationColumnSelectionState() != null)
       {
-        HiddenColumns oldHidden = av
-                .getAnnotationColumnSelectionState()
+        HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
-        if (oldHidden != null)
-        {
-          ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopyAsList();
-          for (int[] positions : regions)
-          {
-            av.hideColumns(positions[0], positions[1]);
-          }
-        }
-        // TODO not clear why we need to hide all the columns (above) if we are
-        // going to copy the hidden columns over wholesale anyway
         av.getAlignment().setHiddenColumns(oldHidden);
       }
-      ap.paintAlignment(true);
+      av.sendSelection();
+      ap.paintAlignment(true, true);
     }
-
   }
 
   @Override
@@ -270,7 +259,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       updateView();
       propagateSeqAssociatedThreshold(updateAllAnnotation,
               getCurrentAnnotation());
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -285,11 +274,12 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 
-    setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
-            .getSelectedIndex()]]);
+    setCurrentAnnotation(av.getAlignment()
+            .getAlignmentAnnotation()[annmap[getAnnotations()
+                    .getSelectedIndex()]]);
 
-    int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
-            .getSelectedIndex());
+    int selectedThresholdItem = getSelectedThresholdItem(
+            getThreshold().getSelectedIndex());
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
@@ -307,11 +297,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       if (getCurrentAnnotation().threshold == null)
       {
-        getCurrentAnnotation()
-                .setThreshold(
-                        new jalview.datamodel.GraphLine(
-                                (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
-                                "Threshold", Color.black));
+        getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
+                (getCurrentAnnotation().graphMax
+                        - getCurrentAnnotation().graphMin) / 2f,
+                "Threshold", Color.black));
       }
 
       adjusting = true;
@@ -320,8 +309,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
-      slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
-      
+      slider.setValue(
+              (int) (getCurrentAnnotation().threshold.value * 1000));
+
       setThresholdValueText();
 
       slider.setMajorTickSpacing((int) (range / 10f));
@@ -330,8 +320,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       adjusting = false;
 
       // build filter params
-      filterParams
-              .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
+      filterParams.setThresholdType(
+              AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
       if (getCurrentAnnotation().isQuantitative())
       {
         filterParams
@@ -339,13 +329,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
         {
-          filterParams
-                  .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
+          filterParams.setThresholdType(
+                  AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
         }
         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
         {
-          filterParams
-                  .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
+          filterParams.setThresholdType(
+                  AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
         }
       }
     }
@@ -371,17 +361,17 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
       {
-        filterParams.setRegexString(currentSearchPanel.searchBox
-                .getUserInput());
+        filterParams.setRegexString(
+                currentSearchPanel.searchBox.getUserInput());
         if (currentSearchPanel.displayName.isSelected())
         {
-          filterParams
-                  .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
+          filterParams.addRegexSearchField(
+                  AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
         }
         if (currentSearchPanel.description.isSelected())
         {
-          filterParams
-                  .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
+          filterParams.addRegexSearchField(
+                  AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
         }
       }
     }
@@ -393,14 +383,17 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     av.getColumnSelection().filterAnnotations(
             getCurrentAnnotation().annotations, filterParams);
 
-    if (getActionOption() == ACTION_OPTION_HIDE)
+    boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
+    if (hideCols)
     {
       av.hideSelectedColumns();
     }
+    av.sendSelection();
 
     filterParams = null;
     av.setAnnotationColumnSelectionState(this);
-    ap.paintAlignment(true);
+    // only update overview and structures if columns were hidden
+    ap.paintAlignment(hideCols, hideCols);
   }
 
   public HiddenColumns getOldHiddenColumns()
@@ -488,8 +481,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   public void selectedAnnotationChanged()
   {
     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
-    if (av.getAlignment()
-            .getAlignmentAnnotation()[annmap[getAnnotations()
+    if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
             .getSelectedIndex()]].isQuantitative())
     {
       currentView = AnnotationColumnChooser.GRAPH_VIEW;
@@ -505,7 +497,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
             .getLayout();
-    switchableViewsLayout.show(switchableViewsPanel, currentView);
+       switchableViewsLayout.show(switchableViewsPanel, currentView);
     updateView();
   }
 
@@ -567,7 +559,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     public void syncState()
     {
-      if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
+      if (aColChooser
+              .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
       {
         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
       }
@@ -634,8 +627,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      this.setBorder(new TitledBorder(MessageManager
-              .getString("label.structures_filter")));
+      this.setBorder(new TitledBorder(
+              MessageManager.getString("label.structures_filter")));
       JvSwingUtils.jvInitComponent(this);
 
       this.add(all);
@@ -735,14 +728,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
       this.aColChooser = aColChooser;
       JvSwingUtils.jvInitComponent(this);
-      this.setBorder(new TitledBorder(MessageManager
-              .getString("label.search_filter")));
+      this.setBorder(new TitledBorder(
+              MessageManager.getString("label.search_filter")));
 
       searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
-      searchBox.setToolTipText(MessageManager
-              .getString("info.enter_search_text_here"));
-      searchBox.getEditor().getEditorComponent()
-              .addKeyListener(new java.awt.event.KeyAdapter()
+      searchBox.getComponent().setToolTipText(
+              MessageManager.getString("info.enter_search_text_here"));
+      searchBox.addKeyListener(new java.awt.event.KeyAdapter()
               {
                 @Override
                 public void keyPressed(KeyEvent e)
@@ -754,8 +746,14 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
                   }
                 }
               });
-
-
+      searchBox.addFocusListener(new FocusAdapter()
+      {
+        @Override
+        public void focusLost(FocusEvent e)
+        {
+          searchStringAction();
+        }
+      });
 
       JvSwingUtils.jvInitComponent(displayName, "label.label");
       displayName.addActionListener(new ActionListener()
@@ -773,12 +771,12 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         @Override
         public void actionPerformed(ActionEvent actionEvent)
         {
-          discriptionCheckboxAction();
+          descriptionCheckboxAction();
         }
       });
 
       syncState();
-      this.add(searchBox);
+      this.add(searchBox.getComponent());
       this.add(displayName);
       this.add(description);
     }
@@ -789,7 +787,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       aColChooser.updateView();
     }
 
-    public void discriptionCheckboxAction()
+    public void descriptionCheckboxAction()
     {
       aColChooser.setCurrentSearchPanel(this);
       aColChooser.updateView();
@@ -824,15 +822,15 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       String defaultTtip = MessageManager
               .getString("info.enter_search_text_to_enable");
       String labelTtip = MessageManager.formatMessage(
-              "info.search_in_annotation_label", annotations
-                      .getSelectedItem().toString());
+              "info.search_in_annotation_label",
+              annotations.getSelectedItem().toString());
       String descTtip = MessageManager.formatMessage(
-              "info.search_in_annotation_description", annotations
-                      .getSelectedItem().toString());
-      displayName.setToolTipText(displayName.isEnabled() ? labelTtip
-              : defaultTtip);
-      description.setToolTipText(description.isEnabled() ? descTtip
-              : defaultTtip);
+              "info.search_in_annotation_description",
+              annotations.getSelectedItem().toString());
+      displayName.setToolTipText(
+              displayName.isEnabled() ? labelTtip : defaultTtip);
+      description.setToolTipText(
+              description.isEnabled() ? descTtip : defaultTtip);
     }
   }