JAL-2577 mirror select/hide by annotation in split frame applet, and on

[jalview.git] / src / jalview / appletgui / AnnotationColumnChooser.java

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index 852512d..22978c3 100644 (file)
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -167,20 +167,22 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
 
     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.select(av.getAnnotationColumnSelectionState()
+      annotations.select(lastChooser
               .getAnnotations().getSelectedIndex());
-      threshold.select(av.getAnnotationColumnSelectionState()
+      threshold.select(lastChooser
               .getThreshold().getSelectedIndex());
-      actionOption = av.getAnnotationColumnSelectionState()
+      actionOption = lastChooser
               .getActionOption();
+      percentThreshold.setState(lastChooser.percentThreshold.getState());
     }
 
     try
@@ -204,6 +206,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     thresholdValue.setEnabled(false);
     thresholdValue.setColumns(7);
+    thresholdValue.setCaretPosition(0);
 
     ok.addActionListener(this);
     cancel.addActionListener(this);
@@ -219,6 +222,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 
+    percentThreshold.setLabel("As percentage");
+    percentThreshold.addItemListener(this);
+
     actionPanel.setBackground(Color.white);
     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 
@@ -242,6 +248,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     thresholdPanel.add(getThreshold());
     thresholdPanel.add(slider);
     thresholdPanel.add(thresholdValue);
+    thresholdPanel.add(percentThreshold);
 
     actionPanel.add(ok);
     actionPanel.add(cancel);
@@ -303,6 +310,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
         av.getAlignment().setHiddenColumns(oldHidden);
       }
+      av.sendSelection();
       ap.paintAlignment(true);
     }
 
@@ -313,7 +321,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   {
     if (!adjusting)
     {
-      thresholdValue.setText((slider.getValue() / 1000f) + "");
+      setThresholdValueText();
       valueChanged(!sliderDragging);
     }
   }
@@ -399,12 +407,14 @@ 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)
@@ -419,22 +429,23 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
 
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * 1000
-              - getCurrentAnnotation().graphMin * 1000;
+      // float range = getCurrentAnnotation().graphMax * 1000
+      // - getCurrentAnnotation().graphMin * 1000;
 
       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);
+      percentThreshold.setEnabled(true);
       adjusting = false;
 
       // build filter params
       filterParams
               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
-      if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+      if (getCurrentAnnotation().isQuantitative())
       {
         filterParams
                 .setThresholdValue(getCurrentAnnotation().threshold.value);
@@ -494,10 +505,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
     }
 
+    // show hidden columns here, before changing the column selection in
+    // filterAnnotations, because showing hidden columns has the side effect of
+    // adding them to the selection
+    av.showAllHiddenColumns();
     av.getColumnSelection().filterAnnotations(
             getCurrentAnnotation().annotations, filterParams);
 
-    av.showAllHiddenColumns();
     if (getActionOption() == ACTION_OPTION_HIDE)
     {
       av.hideSelectedColumns();
@@ -505,6 +519,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     filterParams = null;
     av.setAnnotationColumnSelectionState(this);
+    av.sendSelection();
     ap.paintAlignment(true);
   }
 
@@ -574,13 +589,21 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       threshold_actionPerformed(null);
     }
+    else if (e.getSource() == percentThreshold)
+    {
+      if (!adjusting)
+      {
+        percentageValue_actionPerformed();
+      }
+
+    }
   }
 
   public void selectedAnnotationChanged()
   {
     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
-            .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
+            .getSelectedIndex()].isQuantitative())
     {
       currentView = AnnotationColumnChooser.GRAPH_VIEW;
     }
@@ -877,19 +900,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   @Override
   public void actionPerformed(ActionEvent evt)
   {
-    if (evt.getSource() == thresholdValue)
-    {
-      try
-      {
-        float f = new Float(thresholdValue.getText()).floatValue();
-        slider.setValue((int) (f * 1000));
-        adjustmentValueChanged(null);
-      } catch (NumberFormatException ex)
-      {
-      }
-    }
 
-    else if (evt.getSource() == ok)
+    if (evt.getSource() == ok)
     {
       ok_actionPerformed(null);
     }