From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 8 Feb 2006 15:22:23 +0000 (+0000)
Subject: Colour above or below threshold
X-Git-Tag: Root_VamJalview_2_07b+~163
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=df227ed4042d4c9fa2affb391fa09b662f3b8a2a;p=jalview.git

Colour above or below threshold
---

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index c3e30fb..06040a6 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -69,6 +69,10 @@ public class AnnotationColourChooser
         annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
     }
 
+    threshold.addItem("No Threshold");
+    threshold.addItem("Above Threshold");
+    threshold.addItem("Below Threshold");
+
   }
 
   public AnnotationColourChooser()
@@ -107,19 +111,6 @@ public class AnnotationColourChooser
         maxColour_actionPerformed(e);
       }
     });
-    thresholdCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    thresholdCheck.setOpaque(false);
-    thresholdCheck.setHorizontalTextPosition(SwingConstants.LEADING);
-    thresholdCheck.setSelectedIcon(null);
-    thresholdCheck.setText("Above Threshold");
-    thresholdCheck.setBounds(new Rectangle(329, 6, 126, 23));
-    thresholdCheck.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        thresholdCheck_actionPerformed(e);
-      }
-    });
     ok.setOpaque(false);
     ok.setText("OK");
     ok.addActionListener(new ActionListener()
@@ -150,12 +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);
   }
@@ -163,13 +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)
   {
@@ -195,6 +193,10 @@ public class AnnotationColourChooser
 
   void changeColour()
   {
+    // Check if combobox is still adjusting
+    if(threshold.getSelectedIndex()==-1)
+          return;
+
     // We removed the non-graph annotations when filling the combobox
     // so allow for them again here
     int nograph = 0, graph = -1;
@@ -212,16 +214,26 @@ public class AnnotationColourChooser
     jalview.datamodel.AlignmentAnnotation aa
         = av.alignment.getAlignmentAnnotation()[graph+nograph];
 
-    AnnotationColourGradient acg = new AnnotationColourGradient(aa,
-     minColour.getBackground(),
-     maxColour.getBackground(),
-     thresholdCheck.isSelected());
 
-   if(thresholdCheck.isSelected() && aa.graphLines==null)
+    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();
 
@@ -253,4 +265,9 @@ public class AnnotationColourChooser
     changeColour();
   }
 
+  public void threshold_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+  }
+
 }
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index bc44559..5825612 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -24,8 +24,14 @@ import jalview.datamodel.*;
 
 public class AnnotationColourGradient extends ResidueColourScheme
 {
+    public static int NO_THRESHOLD = -1;
+    public static int BELOW_THRESHOLD = 0;
+    public static int ABOVE_THRESHOLD = 1;
+
     AlignmentAnnotation annotation;
-    boolean aboveAnnotationThreshold = false;
+    int aboveAnnotationThreshold = -1;
+
+    GraphLine annotationThreshold;
 
     float r1, g1, b1, rr, gg, bb, dr, dg, db;
     float range;
@@ -34,12 +40,15 @@ public class AnnotationColourGradient extends ResidueColourScheme
      * Creates a new AnnotationColourGradient object.
      */
     public AnnotationColourGradient(AlignmentAnnotation annotation,
-        Color minColour, Color maxColour, boolean aboveThreshold)
+        Color minColour, Color maxColour, int aboveThreshold)
     {
       this.annotation = annotation;
 
       aboveAnnotationThreshold = aboveThreshold;
 
+      if(aboveThreshold!=NO_THRESHOLD && annotation.graphLines!=null)
+        annotationThreshold = annotation.getGraphLine(0);
+
       r1 = minColour.getRed();
       g1 = minColour.getGreen();
       b1 = minColour.getBlue();
@@ -91,8 +100,9 @@ public class AnnotationColourGradient extends ResidueColourScheme
             currentColour = Color.white;
           else
           {
-            if(!aboveAnnotationThreshold || (annotation.graphLines!=null
-               && annotation.annotations[j].value>=annotation.getGraphLine(0).value))
+            if(  aboveAnnotationThreshold==NO_THRESHOLD
+               || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)
+               || (annotationThreshold!=null && aboveAnnotationThreshold==BELOW_THRESHOLD && annotation.annotations[j].value<=annotationThreshold.value))
             {
                 dr = rr *
                      ((annotation.annotations[j].value-annotation.graphMin) / range )