From 136cfe6c2bede95a91ee16bd4093e71848a97be5 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 27 Apr 2007 09:54:58 +0000
Subject: [PATCH] ThresholdIsMin available in applet

---
 src/jalview/appletgui/AnnotationColourChooser.java |   61 +++++++++++---------
 1 file changed, 33 insertions(+), 28 deletions(-)

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 430bf65..2853b6b 100755
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -25,6 +25,7 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import java.awt.Rectangle;
 
 public class AnnotationColourChooser
     extends Panel implements ActionListener,
@@ -83,12 +84,21 @@ 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++));
+    }
+
+    for (int i = 0; i < list.size(); i++)
+    {
+        annotations.addItem(list.elementAt(i).toString());
     }
 
     threshold.addItem("No Threshold");
@@ -128,6 +138,7 @@ public class AnnotationColourChooser
     maxColour.setLabel("Max Colour");
     maxColour.addActionListener(this);
 
+    thresholdIsMin.addItemListener(this);
     ok.setLabel("OK");
     ok.addActionListener(this);
 
@@ -146,16 +157,19 @@ public class AnnotationColourChooser
 
     slider.setBackground(Color.white);
     slider.setEnabled(false);
-    slider.setBounds(new Rectangle(172, 7, 120, 16));
+    slider.setBounds(new Rectangle(125, 6, 82, 16));
     thresholdValue.setEnabled(false);
-    thresholdValue.setBounds(new Rectangle(295, 4, 83, 22));
-    thresholdValue.setColumns(10);
+    thresholdValue.setBounds(new Rectangle(211, 4, 56, 22));
+    thresholdValue.setColumns(5);
     jPanel3.setBackground(Color.white);
     currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
     currentColours.setLabel("Use Original Colours");
     currentColours.addItemListener(this);
 
-    threshold.setBounds(new Rectangle(19, 4, 141, 22));
+    threshold.setBounds(new Rectangle(11, 3, 113, 22));
+    thresholdIsMin.setBackground(Color.white);
+    thresholdIsMin.setLabel("Threshold is min/max");
+    thresholdIsMin.setBounds(new Rectangle(270, 3, 135, 23));
     jPanel1.add(ok);
     jPanel1.add(cancel);
     jPanel2.add(annotations);
@@ -165,6 +179,7 @@ public class AnnotationColourChooser
     jPanel3.add(threshold);
     jPanel3.add(slider);
     jPanel3.add(thresholdValue);
+    jPanel3.add(thresholdIsMin);
     this.add(jPanel2, java.awt.BorderLayout.NORTH);
     this.add(jPanel3, java.awt.BorderLayout.CENTER);
     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
@@ -184,6 +199,7 @@ public class AnnotationColourChooser
   TextField thresholdValue = new TextField(20);
   Checkbox currentColours = new Checkbox();
   BorderLayout borderLayout1 = new BorderLayout();
+  Checkbox thresholdIsMin = new Checkbox();
 
   public void actionPerformed(ActionEvent evt)
   {
@@ -297,27 +313,9 @@ 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"))
@@ -378,6 +376,13 @@ public class AnnotationColourChooser
               aboveThreshold);
     }
 
+    if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f)
+    {
+      acg.predefinedColours = true;
+    }
+
+    acg.thresholdIsMinMax = thresholdIsMin.getState();
+
     av.setGlobalColourScheme(acg);
 
     if (av.alignment.getGroups() != null)
-- 
1.7.10.2