X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAnnotationColumnChooser.java;h=96299e7ce9a405bac8d704cdfa89ab7fd1c76da0;hb=1499d3297cf70ff34df05362449dbf36873c5bc1;hp=fa63e0dfd1d13658be592efeb7973743f75d21e7;hpb=d1707d4c26db76cfeb640f0dbeb3e3427fd40eb7;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index fa63e0d..96299e7 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.HiddenColumns;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
@@ -30,6 +29,7 @@ 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;
@@ -88,6 +88,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   private HiddenColumns oldHiddenColumns;
 
+  protected int MIN_WIDTH = 420;
+
+  protected int MIN_HEIGHT = 430;
+
   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
   {
     super(av, ap);
@@ -97,6 +101,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     Desktop.addInternalFrame(frame,
             MessageManager.getString("label.select_by_annotation"), 520,
             215);
+    frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 
     addSliderChangeListener();
     addSliderMouseListeners();
@@ -110,20 +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
@@ -151,6 +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());
@@ -174,8 +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);
@@ -233,10 +245,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         HiddenColumns oldHidden = av
                 .getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
-        if (oldHidden != null && oldHidden.getListOfCols() != null
-                && !oldHidden.getListOfCols().isEmpty())
+        if (oldHidden != null && oldHidden.getHiddenRegions() != null
+                && !oldHidden.getHiddenRegions().isEmpty())
         {
-          for (Iterator<int[]> itr = oldHidden.getListOfCols()
+          for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
                   .iterator(); itr.hasNext();)
           {
             int positions[] = itr.next();
@@ -282,12 +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)
@@ -308,7 +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);
@@ -317,7 +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);
@@ -477,8 +493,9 @@ 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;
     }