X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColumnChooser.java;h=f1f78fa1d4fa450e9e7956f9e9ddeb5ad0f7c9fe;hb=HEAD;hp=8b66b8e540f48cffad5d6a72c02e756bfb37c1c9;hpb=6b13a606027284408286d1cd2833470d1f9b9bfe;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 8b66b8e..f1f78fa 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -21,14 +21,6 @@
 
 package jalview.gui;
 
-import jalview.datamodel.AlignmentAnnotation;
-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;
 import java.awt.CardLayout;
 import java.awt.Color;
@@ -50,6 +42,14 @@ import javax.swing.JPanel;
 import javax.swing.JRadioButton;
 import javax.swing.border.TitledBorder;
 
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentAnnotation;
+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 net.miginfocom.swing.MigLayout;
 
 @SuppressWarnings("serial")
@@ -91,18 +91,25 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
   private HiddenColumns oldHiddenColumns;
 
   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)
   {
+    this(av, ap, null);
+  }
+
+  public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap,
+          AlignmentAnnotation selectedAnnotation)
+  {
     super(av, ap);
     frame = new JInternalFrame();
+    frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     Desktop.addInternalFrame(frame,
-            MessageManager.getString("label.select_by_annotation"), 0,
-            0);
-    // BH note: MIGLayout ignores this completely, 
+            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));
 
@@ -134,6 +141,18 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       percentThreshold
               .setSelected(lastChooser.percentThreshold.isSelected());
     }
+    if (selectedAnnotation != null)
+    {
+      try
+      {
+        setCurrentAnnotation(selectedAnnotation);
+        annotations.setSelectedItem(
+                getAnnotationMenuLabel(selectedAnnotation));
+      } catch (Exception x)
+      {
+        Console.error("Couldn't select annotation in column chooser", x);
+      }
+    }
 
     try
     {
@@ -158,7 +177,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
             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());
@@ -300,15 +319,14 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       if (currentAnnotation.threshold == null)
       {
         currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
-                (currentAnnotation.graphMax
-                        - currentAnnotation.graphMin) / 2f,
+                (currentAnnotation.graphMax - currentAnnotation.graphMin)
+                        / 2f,
                 "Threshold", Color.black));
       }
 
       adjusting = true;
 
-      setSliderModel(currentAnnotation.graphMin,
-              currentAnnotation.graphMax,
+      setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
               currentAnnotation.threshold.value);
 
       setThresholdValueText();
@@ -322,8 +340,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
       if (currentAnnotation.isQuantitative())
       {
-        filterParams
-                .setThresholdValue(currentAnnotation.threshold.value);
+        filterParams.setThresholdValue(currentAnnotation.threshold.value);
 
         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
         {
@@ -378,8 +395,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     // filterAnnotations, because showing hidden columns has the side effect of
     // adding them to the selection
     av.showAllHiddenColumns();
-    av.getColumnSelection().filterAnnotations(
-            currentAnnotation.annotations, filterParams);
+    av.getColumnSelection().filterAnnotations(currentAnnotation,
+            filterParams);
 
     boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
     if (hideCols)
@@ -495,7 +512,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
 
     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
             .getLayout();
-    	switchableViewsLayout.show(switchableViewsPanel, currentView);
+    switchableViewsLayout.show(switchableViewsPanel, currentView);
     updateView();
   }
 
@@ -732,17 +749,17 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       searchBox.getComponent().setToolTipText(
               MessageManager.getString("info.enter_search_text_here"));
       searchBox.addKeyListener(new java.awt.event.KeyAdapter()
-              {
-                @Override
-                public void keyPressed(KeyEvent e)
-                {
-                  if (e.getKeyCode() == KeyEvent.VK_ENTER)
-                  {
-                    e.consume();
-                    searchStringAction();
-                  }
-                }
-              });
+      {
+        @Override
+        public void keyPressed(KeyEvent e)
+        {
+          if (e.getKeyCode() == KeyEvent.VK_ENTER)
+          {
+            e.consume();
+            searchStringAction();
+          }
+        }
+      });
       searchBox.addFocusListener(new FocusAdapter()
       {
         @Override
@@ -852,4 +869,11 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     gSearchPanel.searchBox.updateCache();
     ngSearchPanel.searchBox.updateCache();
   }
+
+  public static void displayFor(AlignViewport av, AlignmentPanel ap,
+          AlignmentAnnotation alignmentAnnotation)
+  {
+    AnnotationColumnChooser colchooser = new AnnotationColumnChooser(av, ap,
+            alignmentAnnotation);
+  }
 }