X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColumnChooser.java;h=c321e5950b9388bac03c6a4f7c97587d4ac97204;hb=a5ab6cce3a64d41c3f91ba49f5e4d9536a2b0018;hp=1290d70249c3425ec508f0a9e2476629940c03b7;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 1290d70..c321e59 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -30,7 +30,6 @@ import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
 import java.awt.BorderLayout;
 import java.awt.CardLayout;
 import java.awt.Color;
-import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
@@ -55,28 +54,10 @@ import net.miginfocom.swing.MigLayout;
 public class AnnotationColumnChooser extends AnnotationRowFilter implements
         ItemListener
 {
-
-  private JComboBox<String> annotations;
-
-  private JPanel actionPanel = new JPanel();
-
-  private JPanel thresholdPanel = new JPanel();
-
   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
 
-  private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
-          .getLayout());
-
-  private JPanel noGraphFilterView = new JPanel();
-
-  private JPanel graphFilterView = new JPanel();
-
   private JPanel annotationComboBoxPanel = new JPanel();
 
-  private BorderLayout borderLayout1 = new BorderLayout();
-
-  private JComboBox<String> threshold = new JComboBox<String>();
-
   private StructureFilterPanel gStructureFilterPanel;
 
   private StructureFilterPanel ngStructureFilterPanel;
@@ -107,17 +88,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   private ColumnSelection oldColumnSelection;
 
-  public AnnotationColumnChooser()
-  {
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
   {
     super(av, ap);
@@ -169,72 +139,30 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     frame.pack();
   }
 
-  private void jbInit() throws Exception
+  @Override
+  protected void jbInit()
   {
-    ok.setOpaque(false);
-    ok.setText(MessageManager.getString("action.ok"));
-    ok.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed();
-      }
-    });
-
-    cancel.setOpaque(false);
-    cancel.setText(MessageManager.getString("action.cancel"));
-    cancel.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed();
-      }
-    });
-
-    annotations.addItemListener(this);
-    annotations.setToolTipText(MessageManager
-            .getString("info.select_annotation_row"));
-    threshold.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        threshold_actionPerformed();
-      }
-    });
-
-    thresholdValue.setEnabled(false);
-    thresholdValue.setColumns(7);
-    thresholdValue.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        thresholdValue_actionPerformed();
-      }
-    });
-
-    slider.setPaintLabels(false);
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setEnabled(false);
-    slider.setOpaque(false);
-    slider.setPreferredSize(new Dimension(100, 32));
+    super.jbInit();
 
+    JPanel thresholdPanel = new JPanel();
     thresholdPanel.setBorder(new TitledBorder(MessageManager
             .getString("label.threshold_filter")));
     thresholdPanel.setBackground(Color.white);
     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 
+    percentThreshold.setBackground(Color.white);
+    percentThreshold.setFont(JvSwingUtils.getLabelFont());
+
+    JPanel actionPanel = new JPanel();
     actionPanel.setBackground(Color.white);
     actionPanel.setFont(JvSwingUtils.getLabelFont());
 
+    JPanel graphFilterView = new JPanel();
     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
     graphFilterView.setBackground(Color.white);
 
+    JPanel noGraphFilterView = new JPanel();
     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
     noGraphFilterView.setBackground(Color.white);
 
@@ -249,8 +177,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     ngStructureFilterPanel = new StructureFilterPanel(this);
 
     thresholdPanel.add(getThreshold());
-    thresholdPanel.add(thresholdValue, "wrap");
-    thresholdPanel.add(slider, "grow, span, wrap");
+    thresholdPanel.add(percentThreshold, "wrap");
+    thresholdPanel.add(slider, "grow");
+    thresholdPanel.add(thresholdValue, "span, wrap");
 
     actionPanel.add(ok);
     actionPanel.add(cancel);
@@ -270,7 +199,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     switchableViewsPanel.add(graphFilterView,
             AnnotationColumnChooser.GRAPH_VIEW);
 
-    this.setLayout(borderLayout1);
+    this.setLayout(new BorderLayout());
     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
@@ -280,7 +209,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     this.validate();
   }
 
-  public void updateThresholdPanelToolTip()
+  protected void updateThresholdPanelToolTip()
   {
     thresholdValue.setToolTipText("");
     slider.setToolTipText("");
@@ -297,7 +226,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   }
 
   @Override
-  public void reset()
+  protected void reset()
   {
     if (this.getOldColumnSelection() != null)
     {
@@ -338,26 +267,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
   }
 
-  public JComboBox<String> getThreshold()
-  {
-    return threshold;
-  }
-
-  public void setThreshold(JComboBox<String> threshold)
-  {
-    this.threshold = threshold;
-  }
-
-  public JComboBox<String> getAnnotations()
-  {
-    return annotations;
-  }
-
-  public void setAnnotations(JComboBox<String> annotations)
-  {
-    this.annotations = annotations;
-  }
-
   @Override
   public void updateView()
   {
@@ -377,12 +286,14 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
+    percentThreshold.setEnabled(true);
 
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
       thresholdValue.setEnabled(false);
       thresholdValue.setText("");
+      percentThreshold.setEnabled(false);
       // build filter params
     }
     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
@@ -403,7 +314,18 @@ 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));
-      thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+      
+      if (percentThreshold.isSelected())
+      {
+        thresholdValue
+                .setText(""
+                        + ((getCurrentAnnotation().threshold.value - getCurrentAnnotation().graphMin) * 100f / (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin)));
+      }
+      else
+      {
+        thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+      }
+
       slider.setMajorTickSpacing((int) (range / 10f));
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
@@ -487,6 +409,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     ap.paintAlignment(true);
   }
 
+
   public ColumnSelection getOldColumnSelection()
   {
     return oldColumnSelection;
@@ -568,6 +491,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     selectedAnnotationChanged();
   }
 
+  @Override
   public void selectedAnnotationChanged()
   {
     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
@@ -585,6 +509,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     ngFurtherActionPanel.syncState();
     ngStructureFilterPanel.syncState();
 
+    CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
+            .getLayout();
     switchableViewsLayout.show(switchableViewsPanel, currentView);
     updateView();
   }