JAL-2432 desktop: filter/select columns by threshold as a percentage

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 4ebca62..cc52620 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -908,6 +908,7 @@ label.webservice_job_title_on = {0} using {1} on {2}
 label.updating_vamsas_session = Updating vamsas session
 label.loading_file = Loading File: {0}
 label.edit_params = Edit {0}
+label.as_percentage = As Percentage
 error.not_implemented = Not implemented
 error.no_such_method_as_clone1_for = No such method as clone1 for {0}
 error.null_from_clone1 = Null from clone1!

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 637eb30..c321e59 100644 (file)
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -151,6 +151,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     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());
@@ -174,8 +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);
@@ -282,12 +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)
@@ -308,7 +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);
@@ -392,6 +409,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     ap.paintAlignment(true);
   }
 
+
   public ColumnSelection getOldColumnSelection()
   {
     return oldColumnSelection;

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index c2bf41b..1035a6c 100644 (file)
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -62,6 +62,8 @@ public abstract class AnnotationRowFilter extends JPanel
 
   protected JCheckBox seqAssociated = new JCheckBox();
 
+  protected JCheckBox percentThreshold = new JCheckBox();
+
   protected JSlider slider = new JSlider();
 
   protected JTextField thresholdValue = new JTextField(20);
@@ -120,13 +122,27 @@ public abstract class AnnotationRowFilter extends JPanel
       {
         if (!adjusting)
         {
-          thresholdValue.setText((slider.getValue() / 1000f) + "");
+          setThresholdValueText();
           valueChanged(!sliderDragging);
         }
       }
     });
   }
 
+  protected void setThresholdValueText()
+  {
+    adjusting = true;
+    if (percentThreshold.isSelected())
+    {
+      thresholdValue.setText("" + (slider.getValue() - slider.getMinimum())
+              * 100f / (slider.getMaximum() - slider.getMinimum()));
+    }
+    else
+    {
+      thresholdValue.setText((slider.getValue() / 1000f) + "");
+    }
+    adjusting = false;
+  }
   protected void addSliderMouseListeners()
   {
 
@@ -275,13 +291,27 @@ public abstract class AnnotationRowFilter extends JPanel
     try
     {
       float f = Float.parseFloat(thresholdValue.getText());
-      slider.setValue((int) (f * 1000));
+      if (percentThreshold.isEnabled())
+      {
+        slider.setValue(slider.getMinimum()
+                + ((int) ((f / 100f) * (slider.getMaximum() - slider
+                        .getMinimum()))));
+      }
+      else
+      {
+        slider.setValue((int) (f * 1000));
+      }
       updateView();
     } catch (NumberFormatException ex)
     {
     }
   }
 
+  protected void percentageValue_actionPerformed()
+  {
+    setThresholdValueText();
+  }
+
   protected void thresholdIsMin_actionPerformed()
   {
     updateView();
@@ -439,6 +469,18 @@ public abstract class AnnotationRowFilter extends JPanel
       }
     });
 
+    percentThreshold.setText(MessageManager.getString("label.as_percentage"));
+    percentThreshold.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        if (!adjusting)
+        {
+          percentageValue_actionPerformed();
+        }
+      }
+    });
     slider.setPaintLabels(false);
     slider.setPaintTicks(true);
     slider.setBackground(Color.white);