X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=83a8a12b0cb1733abe1abc44c00fe9b14d483ccc;hb=60f2d6c034560415fd0139c8bc7df0c19cae1186;hp=ba76858d39d049f526df041f1b5393585365fa8b;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index ba76858..83a8a12 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -27,6 +27,7 @@ import javax.swing.event.*;
 
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import java.awt.Dimension;
 
 public class AnnotationColourChooser
     extends JPanel
@@ -39,7 +40,7 @@ public class AnnotationColourChooser
   jalview.datamodel.AlignmentAnnotation currentAnnotation;
   boolean adjusting = false;
 
-  public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
+  public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
   {
     oldcs = av.getGlobalColourScheme();
     if (av.alignment.getGroups() != null)
@@ -63,12 +64,6 @@ public class AnnotationColourChooser
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
     Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
 
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {}
 
     slider.addChangeListener(new ChangeListener()
     {
@@ -81,6 +76,13 @@ public class AnnotationColourChooser
         }
       }
     });
+    slider.addMouseListener(new MouseAdapter()
+        {
+          public void mouseReleased(MouseEvent evt)
+          {
+            ap.paintAlignment(true);
+          }
+        });
 
     if (av.alignment.getAlignmentAnnotation() == null)
     {
@@ -100,18 +102,30 @@ public class AnnotationColourChooser
     }
 
     adjusting = true;
+    Vector list = new Vector();
+    int index = 1;
     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
     {
-      if (av.alignment.getAlignmentAnnotation()[i].graph > 0)
-      {
-        annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
-      }
+      String label = av.alignment.getAlignmentAnnotation()[i].label;
+      if (!list.contains(label))
+        list.addElement(label);
+      else
+        list.addElement(label+"_"+(index++));
     }
 
+    annotations = new JComboBox(list);
+
     threshold.addItem("No Threshold");
     threshold.addItem("Above Threshold");
     threshold.addItem("Below Threshold");
 
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {}
+
     adjusting = false;
 
     changeColour();
@@ -210,9 +224,9 @@ public class AnnotationColourChooser
     slider.setBackground(Color.white);
     slider.setEnabled(false);
     slider.setOpaque(false);
-    slider.setPreferredSize(new Dimension(150, 32));
+    slider.setPreferredSize(new Dimension(100, 32));
     thresholdValue.setEnabled(false);
-    thresholdValue.setColumns(10);
+    thresholdValue.setColumns(7);
     jPanel3.setBackground(Color.white);
     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     currentColours.setOpaque(false);
@@ -224,6 +238,15 @@ public class AnnotationColourChooser
         currentColours_actionPerformed(e);
       }
     });
+    thresholdIsMin.setBackground(Color.white);
+    thresholdIsMin.setText("Threshold is Min/Max");
+    thresholdIsMin.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        thresholdIsMin_actionPerformed(actionEvent);
+      }
+    });
     jPanel1.add(ok);
     jPanel1.add(cancel);
     jPanel2.add(annotations);
@@ -234,11 +257,12 @@ public class AnnotationColourChooser
     jPanel3.add(threshold);
     jPanel3.add(slider);
     jPanel3.add(thresholdValue);
+    jPanel3.add(thresholdIsMin);
     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
     this.add(jPanel2, java.awt.BorderLayout.NORTH);
   }
 
-  JComboBox annotations = new JComboBox();
+  JComboBox annotations;
   JPanel minColour = new JPanel();
   JPanel maxColour = new JPanel();
   JButton ok = new JButton();
@@ -253,6 +277,7 @@ public class AnnotationColourChooser
   JSlider slider = new JSlider();
   JTextField thresholdValue = new JTextField(20);
   JCheckBox currentColours = new JCheckBox();
+  JCheckBox thresholdIsMin = new JCheckBox();
 
   public void minColour_actionPerformed()
   {
@@ -288,27 +313,8 @@ public class AnnotationColourChooser
       return;
     }
 
-    // We removed the non-graph annotations when filling the combobox
-    // so allow for them again here
-    int nograph = 0, graph = -1;
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
-    {
-      if (av.alignment.getAlignmentAnnotation()[i].graph == 0)
-      {
-        nograph++;
-      }
-      else
-      {
-        graph++;
-      }
-
-      if (graph == annotations.getSelectedIndex())
-      {
-        break;
-      }
-    }
 
-    currentAnnotation = av.alignment.getAlignmentAnnotation()[graph + nograph];
+    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];
 
     int aboveThreshold = -1;
     if (threshold.getSelectedItem().equals("Above Threshold"))
@@ -372,6 +378,13 @@ public class AnnotationColourChooser
               aboveThreshold);
     }
 
+    if(currentAnnotation.graphMin==0f&& currentAnnotation.graphMax==0f)
+    {
+      acg.predefinedColours = true;
+    }
+
+    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+
     av.setGlobalColourScheme(acg);
 
     if (av.alignment.getGroups() != null)
@@ -405,7 +418,7 @@ public class AnnotationColourChooser
       }
     }
 
-    ap.repaint();
+    ap.paintAlignment(false);
   }
 
   public void ok_actionPerformed(ActionEvent e)
@@ -480,7 +493,7 @@ public class AnnotationColourChooser
     }
 
     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
-    ap.repaint();
+    ap.paintAlignment(false);
   }
 
   public void currentColours_actionPerformed(ActionEvent e)
@@ -496,4 +509,9 @@ public class AnnotationColourChooser
     changeColour();
   }
 
+  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+  {
+    changeColour();
+  }
+
 }