X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=06040a696199444f6135ae262cf244096e7cc0c8;hb=cc6f7ebe59c148e62cd9f1947d9ba30638db2980;hp=71582e593da9e1af0ec440d90fd84dc682faa71d;hpb=452198e86b03d40c83d0492ab04ab2f6d52e8f5e;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 71582e5..06040a6 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -42,7 +42,7 @@ public class AnnotationColourChooser
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Colour by Annotation", 470, 110, false);
+    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 110, false);
 
     try{
       jbInit();
@@ -65,9 +65,14 @@ public class AnnotationColourChooser
 
     for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
     {
-      annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
+      if(av.alignment.getAlignmentAnnotation()[i].graph>0)
+        annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
     }
 
+    threshold.addItem("No Threshold");
+    threshold.addItem("Above Threshold");
+    threshold.addItem("Below Threshold");
+
   }
 
   public AnnotationColourChooser()
@@ -106,18 +111,6 @@ public class AnnotationColourChooser
         maxColour_actionPerformed(e);
       }
     });
-    thresholdCheck.setOpaque(false);
-    thresholdCheck.setHorizontalTextPosition(SwingConstants.LEADING);
-    thresholdCheck.setSelectedIcon(null);
-    thresholdCheck.setText("Above Threshold");
-    thresholdCheck.setBounds(new Rectangle(329, 6, 109, 23));
-    thresholdCheck.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        thresholdCheck_actionPerformed(e);
-      }
-    });
     ok.setOpaque(false);
     ok.setText("OK");
     ok.addActionListener(new ActionListener()
@@ -148,12 +141,20 @@ public class AnnotationColourChooser
     });
     jPanel1.setBackground(Color.white);
     jPanel2.setBackground(Color.white);
+    threshold.setBounds(new Rectangle(328, 6, 125, 22));
+    threshold.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        threshold_actionPerformed(e);
+      }
+    });
     jPanel1.add(ok);
     jPanel1.add(cancel);
     jPanel2.add(annotations);
     jPanel2.add(minColour);
     jPanel2.add(maxColour);
-    jPanel2.add(thresholdCheck);
+    jPanel2.add(threshold);
     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
     this.add(jPanel2, java.awt.BorderLayout.CENTER);
   }
@@ -161,13 +162,12 @@ public class AnnotationColourChooser
   JComboBox annotations = new JComboBox();
   JButton minColour = new JButton();
   JButton maxColour = new JButton();
-  JCheckBox thresholdCheck = new JCheckBox();
   JButton ok = new JButton();
   JButton cancel = new JButton();
   JPanel jPanel1 = new JPanel();
   JPanel jPanel2 = new JPanel();
   BorderLayout borderLayout1 = new BorderLayout();
-
+  JComboBox threshold = new JComboBox();
 
   public void minColour_actionPerformed(ActionEvent e)
   {
@@ -193,18 +193,47 @@ public class AnnotationColourChooser
 
   void changeColour()
   {
-    jalview.datamodel.AlignmentAnnotation aa = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];
+    // Check if combobox is still adjusting
+    if(threshold.getSelectedIndex()==-1)
+          return;
 
-    AnnotationColourGradient acg = new AnnotationColourGradient(aa,
-     minColour.getBackground(),
-     maxColour.getBackground(),
-     thresholdCheck.isSelected());
+    // 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(thresholdCheck.isSelected() && aa.graphLines==null)
+      if(graph==annotations.getSelectedIndex())
+        break;
+    }
+
+    jalview.datamodel.AlignmentAnnotation aa
+        = av.alignment.getAlignmentAnnotation()[graph+nograph];
+
+
+    int aboveThreshold = -1;
+    if(threshold.getSelectedItem().equals("Above Threshold"))
+      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+    else if(threshold.getSelectedItem().equals("Below Threshold"))
+      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+
+    if(aboveThreshold!=AnnotationColourGradient.NO_THRESHOLD && aa.graphLines==null)
    {
      aa.addGraphLine(new jalview.datamodel.GraphLine((aa.graphMax-aa.graphMin)/2f, "Threshold", Color.black));
    }
 
+    AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+     minColour.getBackground(),
+     maxColour.getBackground(),
+     aboveThreshold );
+
+
+
+
    av.setGlobalColourScheme(acg);
    ap.repaint();
 
@@ -236,4 +265,9 @@ public class AnnotationColourChooser
     changeColour();
   }
 
+  public void threshold_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
 }