From b35507f7bb2af382a19ba88a005ccbb27ffaa802 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 27 Apr 2007 08:50:06 +0000
Subject: [PATCH] Annotation gradient will use direct colours if no graph
 exists

---
 src/jalview/gui/AnnotationColourChooser.java      |   77 ++++++++++++---------
 src/jalview/schemes/AnnotationColourGradient.java |    2 +-
 2 files changed, 45 insertions(+), 34 deletions(-)

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 31c7ba7..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
@@ -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()
     {
@@ -107,18 +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();
@@ -217,9 +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);
@@ -231,6 +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);
@@ -241,11 +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();
@@ -260,6 +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()
   {
@@ -295,27 +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"))
@@ -379,6 +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)
@@ -503,4 +509,9 @@ public class AnnotationColourChooser
     changeColour();
   }
 
+  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+  {
+    changeColour();
+  }
+
 }
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index ff6673a..6a7a3cf 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -160,7 +160,7 @@ public class AnnotationColourGradient
           && !jalview.util.Comparison.isGap(c))
       {
 
-        if (predefinedColours)
+       if (predefinedColours)
         {
           if(annotation.annotations[j].colour != null)
               return annotation.annotations[j].colour;
-- 
1.7.10.2