X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureTypeSettings.java;h=b3e6917354fecc9e87ddde3122f72d2edebff219;hb=ccc53e88e3260886f5d3bdacc619c0f374be9b8f;hp=aaf81acf6071091a7479141bb0f69b809a2668ca;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;p=jalview.git

diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index aaf81ac..b3e6917 100644
--- a/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@ -23,7 +23,7 @@ package jalview.gui;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.features.FeatureAttributes;
 import jalview.datamodel.features.FeatureAttributes.Datatype;
@@ -155,7 +155,7 @@ public class FeatureTypeSettings extends JalviewDialog
   JRadioButton graduatedColour = new JRadioButton();
 
   JPanel coloursPanel;
-  
+
   JPanel filtersPanel;
 
   JPanel singleColour = new JPanel();
@@ -204,22 +204,27 @@ public class FeatureTypeSettings extends JalviewDialog
 
   private JPanel chooseFiltersPanel;
 
+  public boolean originalDisplay;
+
   /**
    * Constructor
    * 
    * @param frender
    * @param theType
+   * @param last
+   *          - visibility of feature prior to adjustment
    */
-  public FeatureTypeSettings(FeatureRenderer frender, String theType)
+  public FeatureTypeSettings(FeatureRenderer frender, String theType,
+          boolean last)
   {
     this.fr = frender;
     this.featureType = theType;
     ap = fr.ap;
     originalFilter = fr.getFeatureFilter(theType);
     originalColour = fr.getFeatureColours().get(theType);
-    
+    originalDisplay = last;
     adjusting = true;
-    
+
     try
     {
       initialise();
@@ -228,15 +233,15 @@ public class FeatureTypeSettings extends JalviewDialog
       ex.printStackTrace();
       return;
     }
-    
+
     updateColoursPanel();
-    
+
     updateFiltersPanel();
-    
+
     adjusting = false;
-    
+
     colourChanged(false);
-    
+
     String title = MessageManager
             .formatMessage("label.display_settings_for", new String[]
             { theType });
@@ -245,8 +250,8 @@ public class FeatureTypeSettings extends JalviewDialog
   }
 
   /**
-   * Configures the widgets on the Colours panel according to the current feature
-   * colour scheme
+   * Configures the widgets on the Colours panel according to the current
+   * feature colour scheme
    */
   private void updateColoursPanel()
   {
@@ -537,7 +542,8 @@ public class FeatureTypeSettings extends JalviewDialog
       {
         if (minColour.isEnabled())
         {
-          String ttl = MessageManager.getString("label.select_colour_minimum_value");
+          String ttl = MessageManager
+                  .getString("label.select_colour_minimum_value");
           showColourChooser(minColour, ttl);
         }
       }
@@ -554,7 +560,8 @@ public class FeatureTypeSettings extends JalviewDialog
       {
         if (maxColour.isEnabled())
         {
-          String ttl = MessageManager.getString("label.select_colour_maximum_value");
+          String ttl = MessageManager
+                  .getString("label.select_colour_maximum_value");
           showColourChooser(maxColour, ttl);
         }
       }
@@ -762,8 +769,8 @@ public class FeatureTypeSettings extends JalviewDialog
     // }
     // else
     // {
-      singleColour.setBackground(originalColour.getColour());
-      singleColour.setForeground(originalColour.getColour());
+    singleColour.setBackground(originalColour.getColour());
+    singleColour.setForeground(originalColour.getColour());
     // }
     singleColour.addMouseListener(new MouseAdapter()
     {
@@ -772,7 +779,8 @@ public class FeatureTypeSettings extends JalviewDialog
       {
         if (simpleColour.isSelected())
         {
-          String ttl = MessageManager.formatMessage("label.select_colour_for",  featureType);
+          String ttl = MessageManager
+                  .formatMessage("label.select_colour_for", featureType);
           showColourChooser(singleColour, ttl);
         }
       }
@@ -857,8 +865,8 @@ public class FeatureTypeSettings extends JalviewDialog
         colourChanged(true);
       }
     };
-	JalviewColourChooser.showColourChooser(this, title, 
-	  colourPanel.getBackground(), listener);
+    JalviewColourChooser.showColourChooser(this, title,
+            colourPanel.getBackground(), listener);
   }
 
   /**
@@ -1029,6 +1037,10 @@ public class FeatureTypeSettings extends JalviewDialog
   {
     fr.setColour(featureType, originalColour);
     fr.setFeatureFilter(featureType, originalFilter);
+    if (!originalDisplay)
+    {
+      fr.getFeaturesDisplayed().setHidden(featureType);
+    }
     refreshDisplay(true);
   }
 
@@ -1045,7 +1057,7 @@ public class FeatureTypeSettings extends JalviewDialog
        */
       adjusting = true;
       float f = Float.parseFloat(thresholdValue.getText());
-      f = Float.max(f,  this.min);
+      f = Float.max(f, this.min);
       f = Float.min(f, this.max);
       setThresholdValueText(f);
       slider.setSliderValue(f);
@@ -1061,7 +1073,8 @@ public class FeatureTypeSettings extends JalviewDialog
   }
 
   /**
-   * Sets the text field for threshold value, rounded to four significant figures
+   * Sets the text field for threshold value, rounded to four significant
+   * figures
    * 
    * @param f
    */
@@ -1092,7 +1105,7 @@ public class FeatureTypeSettings extends JalviewDialog
   {
     if (featureSettings != null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
     }
     featureSettings = listener;
@@ -1160,7 +1173,7 @@ public class FeatureTypeSettings extends JalviewDialog
     List<Object> displayAttsObjects = new ArrayList<>(displayAtts);
     JComboBox<Object> attCombo = JvSwingUtils
             .buildComboWithTooltips(displayAttsObjects, tooltips);
-    
+
     return attCombo;
   }
 
@@ -1696,7 +1709,7 @@ public class FeatureTypeSettings extends JalviewDialog
       attName = (String) attCombo.getSelectedItem();
     } catch (Exception e)
     {
-      Cache.error("Problem casting Combo box entry to String");
+      Console.error("Problem casting Combo box entry to String");
       attName = attCombo.getSelectedItem().toString();
     }
     Condition cond = (Condition) condCombo.getSelectedItem();