X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=ad013f5bb1a90478c99967c3ce79a70c6c862b24;hb=4160e6f1fa6aa45849153cce5794faa93e3a19c4;hp=f0887915c40ce6b8f833613767dbcf2b9d9b6f26;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index f088791..ad013f5 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -24,6 +24,7 @@ import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceGroup;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
@@ -42,7 +43,6 @@ import java.util.Vector;
 import javax.swing.BorderFactory;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
-import javax.swing.JColorChooser;
 import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
 import javax.swing.JLayeredPane;
@@ -53,8 +53,6 @@ import net.miginfocom.swing.MigLayout;
 @SuppressWarnings("serial")
 public class AnnotationColourChooser extends AnnotationRowFilter
 {
-  private static final int ONETHOUSAND = 1000;
-
   private ColourSchemeI oldcs;
 
   private JButton defColours;
@@ -63,9 +61,9 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
   private JCheckBox useOriginalColours = new JCheckBox();
 
-  private JPanel minColour = new JPanel();
+  JPanel minColour = new JPanel();
 
-  private JPanel maxColour = new JPanel();
+  JPanel maxColour = new JPanel();
 
   private JCheckBox thresholdIsMin = new JCheckBox();
 
@@ -79,7 +77,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
-      oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
+      oldgroupColours = new Hashtable<>();
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
         if (sg.getColourScheme() != null)
@@ -122,7 +120,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     }
     Vector<String> annotItems = getAnnotationItems(
             seqAssociated.isSelected());
-    annotations = new JComboBox<String>(annotItems);
+    annotations = new JComboBox<>(annotItems);
 
     populateThresholdComboBox(threshold);
 
@@ -147,7 +145,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
                 "error.implementation_error_dont_know_about_threshold_setting"));
       }
       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
-      thresholdValue.setText("" + acg.getAnnotationThreshold());
+      thresholdValue
+              .setText(String.valueOf(acg.getAnnotationThreshold()));
     }
 
     jbInit();
@@ -174,7 +173,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       {
         if (minColour.isEnabled())
         {
-          minColour_actionPerformed();
+          showColourChooser(minColour, "label.select_colour_minimum_value");
         }
       }
     });
@@ -189,7 +188,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       {
         if (maxColour.isEnabled())
         {
-          maxColour_actionPerformed();
+          showColourChooser(maxColour, "label.select_colour_maximum_value");
         }
       }
     });
@@ -288,36 +287,27 @@ public class AnnotationColourChooser extends AnnotationRowFilter
             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
   }
 
-  public void minColour_actionPerformed()
+  protected void showColourChooser(JPanel colourPanel, String titleKey)
   {
-    Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_minimum_value"),
-            minColour.getBackground());
-    if (col != null)
+    String ttl = MessageManager.getString(titleKey);
+    ColourChooserListener listener = new ColourChooserListener()
     {
-      minColour.setBackground(col);
-    }
-    minColour.repaint();
-    updateView();
-  }
-
-  public void maxColour_actionPerformed()
-  {
-    Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_colour_maximum_value"),
-            maxColour.getBackground());
-    if (col != null)
-    {
-      maxColour.setBackground(col);
-    }
-    maxColour.repaint();
-    updateView();
+      @Override
+      public void colourSelected(Color c)
+      {
+        colourPanel.setBackground(c);
+        colourPanel.repaint();
+        updateView();
+      }
+    };
+    JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl,
+            colourPanel.getBackground(), listener);
   }
 
   @Override
   public void reset()
   {
-    av.setGlobalColourScheme(oldcs);
+    this.ap.alignFrame.changeColour(oldcs);
     if (av.getAlignment().getGroups() != null)
     {
 
@@ -338,10 +328,10 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       {
         updateView();
       }
-      getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+      getCurrentAnnotation().threshold.value = getSliderValue();
       propagateSeqAssociatedThreshold(updateAllAnnotation,
               getCurrentAnnotation());
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -378,6 +368,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     thresholdValue.setEnabled(true);
     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 
+    final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
@@ -386,41 +377,31 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       thresholdIsMin.setEnabled(false);
     }
     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
-            && getCurrentAnnotation().threshold == null)
+            && currentAnnotation.threshold == null)
     {
-      getCurrentAnnotation().setThreshold(new GraphLine(
-              (getCurrentAnnotation().graphMax
-                      - getCurrentAnnotation().graphMin) / 2f,
+      currentAnnotation.setThreshold(new GraphLine(
+              (currentAnnotation.graphMax - currentAnnotation.graphMin)
+                      / 2f,
               "Threshold", Color.black));
     }
 
     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * ONETHOUSAND
-              - getCurrentAnnotation().graphMin * ONETHOUSAND;
-
-      slider.setMinimum(
-              (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
-      slider.setMaximum(
-              (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
-      slider.setValue(
-              (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
-      thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
-      slider.setMajorTickSpacing((int) (range / 10f));
+      setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
+              currentAnnotation.threshold.value);
       slider.setEnabled(true);
+
+      setThresholdValueText();
       thresholdValue.setEnabled(true);
       adjusting = false;
     }
-    colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
+    colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
 
     ap.alignmentChanged();
-    // ensure all associated views (overviews, structures, etc) are notified of
-    // updated colours.
-    ap.paintAlignment(true);
   }
 
-  protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn,
+  protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
           int selectedThresholdOption)
   {
 
@@ -445,7 +426,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 
-    av.setGlobalColourScheme(acg);
+    this.ap.alignFrame.changeColour(acg);
 
     if (av.getAlignment().getGroups() != null)
     {
@@ -456,25 +437,16 @@ public class AnnotationColourChooser extends AnnotationRowFilter
         {
           continue;
         }
-
-        if (useOriginalColours.isSelected())
-        {
-          sg.setColourScheme(new AnnotationColourGradient(currentAnn,
-                  sg.getColourScheme(), selectedThresholdOption));
-          ((AnnotationColourGradient) sg.cs)
-                  .setSeqAssociated(seqAssociated.isSelected());
-        }
-        else
-        {
-          sg.setColourScheme(new AnnotationColourGradient(currentAnn,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  selectedThresholdOption));
-          ((AnnotationColourGradient) sg.cs)
-                  .setSeqAssociated(seqAssociated.isSelected());
-        }
+        sg.setColourScheme(
+                acg.getInstance(av, sg));
       }
     }
-    return false;
   }
 
+  @Override
+  protected void sliderDragReleased()
+  {
+    super.sliderDragReleased();
+    ap.paintAlignment(true, true);
+  }
 }