X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=5ee69f2d21f84a83f863f01c5c5c9b63baf2d75b;hb=6fb502e4a8749d1d98f5442c3b8156ab47996b77;hp=599cf0b201ad6d885b49a7df079011139e45636f;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
old mode 100755
new mode 100644
index 599cf0b..5ee69f2
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -30,6 +30,8 @@ import net.miginfocom.swing.MigLayout;
 import jalview.bin.Cache;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.util.MessageManager;
+
 import java.awt.Dimension;
 
 public class AnnotationColourChooser extends JPanel
@@ -47,6 +49,10 @@ public class AnnotationColourChooser extends JPanel
   jalview.datamodel.AlignmentAnnotation currentAnnotation;
 
   boolean adjusting = false;
+  /**
+   * enabled if the user is dragging the slider - try to keep updates to a minimun
+   */
+  boolean sliderDragging = false;
 
   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
   {
@@ -76,14 +82,32 @@ public class AnnotationColourChooser extends JPanel
         if (!adjusting)
         {
           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
-          valueChanged();
+          valueChanged(!sliderDragging);
         }
       }
     });
     slider.addMouseListener(new MouseAdapter()
     {
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        sliderDragging=true;
+        super.mousePressed(e);
+      }
+
+      @Override
+      public void mouseDragged(MouseEvent e)
+      {
+        sliderDragging=true;
+        super.mouseDragged(e);
+      }
       public void mouseReleased(MouseEvent evt)
       {
+        if (sliderDragging)
+        {
+          sliderDragging=false;
+          valueChanged(true);
+        }
         ap.paintAlignment(true);
       }
     });
@@ -96,18 +120,19 @@ public class AnnotationColourChooser extends JPanel
     // Always get default shading from preferences.
     setDefaultMinMax();
 
+    adjusting = true;
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setSelected(acg.predefinedColours);
-      if (!acg.predefinedColours)
+      currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
+      if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
       {
         minColour.setBackground(acg.getMinColour());
         maxColour.setBackground(acg.getMaxColour());
       }
       seqAssociated.setSelected(acg.isSeqAssociated());
+      
     }
-    adjusting = true;
     annotations = new JComboBox(
             getAnnotationItems(seqAssociated.isSelected()));
 
@@ -193,7 +218,6 @@ public class AnnotationColourChooser extends JPanel
     System.arraycopy(anmap, 0, annmap, 0, annmap.length);
     return list;
   }
-
   private void setDefaultMinMax()
   {
     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
@@ -244,7 +268,7 @@ public class AnnotationColourChooser extends JPanel
       }
     });
     ok.setOpaque(false);
-    ok.setText("OK");
+    ok.setText(MessageManager.getString("action.ok"));
     ok.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -253,7 +277,7 @@ public class AnnotationColourChooser extends JPanel
       }
     });
     cancel.setOpaque(false);
-    cancel.setText("Cancel");
+    cancel.setText(MessageManager.getString("action.cancel"));
     cancel.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -262,7 +286,7 @@ public class AnnotationColourChooser extends JPanel
       }
     });
     defColours.setOpaque(false);
-    defColours.setText("Defaults");
+    defColours.setText(MessageManager.getString("action.set_defaults"));
     defColours
             .setToolTipText("Reset min and max colours to defaults from user preferences.");
     defColours.addActionListener(new ActionListener()
@@ -306,7 +330,7 @@ public class AnnotationColourChooser extends JPanel
     thresholdValue.setColumns(7);
     currentColours.setFont(JvSwingUtils.getLabelFont());
     currentColours.setOpaque(false);
-    currentColours.setText("Use Original Colours");
+    currentColours.setText(MessageManager.getString("label.use_original_colours"));
     currentColours.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -316,7 +340,7 @@ public class AnnotationColourChooser extends JPanel
     });
     thresholdIsMin.setBackground(Color.white);
     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
-    thresholdIsMin.setText("Threshold is Min/Max");
+    thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
     thresholdIsMin.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
@@ -326,7 +350,7 @@ public class AnnotationColourChooser extends JPanel
     });
     seqAssociated.setBackground(Color.white);
     seqAssociated.setFont(JvSwingUtils.getLabelFont());
-    seqAssociated.setText("Per-sequence only");
+    seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
     seqAssociated.addActionListener(new ActionListener()
     {
 
@@ -527,7 +551,7 @@ public class AnnotationColourChooser extends JPanel
     if (currentAnnotation.graphMin == 0f
             && currentAnnotation.graphMax == 0f)
     {
-      acg.predefinedColours = true;
+      acg.setPredefinedColours(true);
     }
 
     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
@@ -632,18 +656,38 @@ public class AnnotationColourChooser extends JPanel
     }
   }
 
-  public void valueChanged()
+  public void valueChanged(boolean updateAllAnnotation)
   {
     if (currentColours.isSelected()
             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
     {
       changeColour();
     }
-
     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+    propagateSeqAssociatedThreshold(updateAllAnnotation);
     ap.paintAlignment(false);
   }
 
+  private void propagateSeqAssociatedThreshold(boolean allAnnotation)
+  {
+    if (currentAnnotation.sequenceRef == null
+            || currentAnnotation.threshold == null)
+    {
+      return;
+    }
+    // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
+
+    float thr = currentAnnotation.threshold.value;
+    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    {
+      AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
+      if (aa.label.equals(currentAnnotation.label))
+      {
+        aa.threshold.value = thr;
+      }
+    }
+  }
+
   public void currentColours_actionPerformed(ActionEvent e)
   {
     if (currentColours.isSelected())