X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationColumnChooser.java;h=999d217f6296143922c788b9cd9ad446a22b549a;hb=95702b58b4a81f53147aa5e4add078f965966437;hp=fde6ce8d1fe86ce7f92fbd3b1283a3518528a709;hpb=b59839dfda0a767318fc3c89d9604c39ff298d83;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index fde6ce8..999d217 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -21,7 +21,6 @@
 
 package jalview.gui;
 
-import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
@@ -116,20 +115,23 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
     populateThresholdComboBox(threshold);
-
+    AnnotationColumnChooser lastChooser = av
+            .getAnnotationColumnSelectionState();
     // restore Object state from the previous session if one exists
-    if (av.getAnnotationColumnSelectionState() != null)
+    if (lastChooser != null)
     {
-      currentSearchPanel = av.getAnnotationColumnSelectionState()
+      currentSearchPanel = lastChooser
               .getCurrentSearchPanel();
-      currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
+      currentStructureFilterPanel = lastChooser
               .getCurrentStructureFilterPanel();
-      annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
+      annotations.setSelectedIndex(lastChooser
               .getAnnotations().getSelectedIndex());
-      threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
+      threshold.setSelectedIndex(lastChooser
               .getThreshold().getSelectedIndex());
-      actionOption = av.getAnnotationColumnSelectionState()
+      actionOption = lastChooser
               .getActionOption();
+      percentThreshold.setSelected(lastChooser.percentThreshold
+              .isSelected());
     }
 
     try
@@ -157,6 +159,9 @@ 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());
@@ -180,8 +185,9 @@ 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);
@@ -288,12 +294,14 @@ 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)
@@ -314,7 +322,9 @@ 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));
-      thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+      
+      setThresholdValueText();
+
       slider.setMajorTickSpacing((int) (range / 10f));
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
@@ -323,7 +333,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       // build filter params
       filterParams
               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
-      if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+      if (getCurrentAnnotation().isQuantitative())
       {
         filterParams
                 .setThresholdValue(getCurrentAnnotation().threshold.value);
@@ -398,6 +408,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     ap.paintAlignment(true);
   }
 
+
   public ColumnSelection getOldColumnSelection()
   {
     return oldColumnSelection;
@@ -483,8 +494,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   public void selectedAnnotationChanged()
   {
     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
-    if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
-            .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
+    if (av.getAlignment()
+            .getAlignmentAnnotation()[annmap[getAnnotations()
+            .getSelectedIndex()]].isQuantitative())
     {
       currentView = AnnotationColumnChooser.GRAPH_VIEW;
     }