From bd3ef446b904569340cd106afa280faf8ea73001 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Sun, 6 Apr 2014 13:36:13 +0100
Subject: [PATCH] JAL-736 hack to show the conserved property values in the
 tooltip

---
 src/jalview/analysis/Conservation.java |   20 +++++++++++++++-----
 1 file changed, 15 insertions(+), 5 deletions(-)

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 8641629..0910f49 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -69,6 +69,8 @@ public class Conservation
 
   int[][] cons2;
 
+  private String[] consSymbs;
+
   /**
    * Creates a new Conservation object.
    * 
@@ -364,17 +366,17 @@ public class Conservation
     {
       consString.append('-');
     }
-
+    consSymbs = new String[end-start+1];
     for (int i = start; i <= end; i++)
     {
       gapcons = countConsNGaps(i);
       totGaps = gapcons[1];
       pgaps = ((float) totGaps * 100) / (float) sequences.length;
-
+      consSymbs[i-start]=new String();
+      
       if (percentageGaps > pgaps)
       {
         resultHash = total[i - start];
-
         // Now find the verdict
         count = 0;
         enumeration = resultHash.keys();
@@ -383,12 +385,12 @@ public class Conservation
         {
           type = (String) enumeration.nextElement();
           result = (Integer) resultHash.get(type);
-
           // Do we want to count +ve conservation or +ve and -ve cons.?
           if (consflag)
           {
             if (result.intValue() == 1)
             {
+              consSymbs[i-start] = type+" "+consSymbs[i-start];
               count++;
             }
           }
@@ -396,6 +398,14 @@ public class Conservation
           {
             if (result.intValue() != -1)
             {
+              { 
+                 if (result.intValue()==0) {
+                   consSymbs[i-start] = consSymbs[i-start]+ " !"+type;
+                 } else {
+                   consSymbs[i-start] = type+" "+consSymbs[i-start];
+                 }
+              }
+              
               count++;
             }
           }
@@ -681,7 +691,7 @@ public class Conservation
       float vprop = value - min;
       vprop /= max;
       conservation.annotations[i] = new Annotation(String.valueOf(c),
-              String.valueOf(value), ' ', value, new Color(minR
+              consSymbs[i-start], ' ', value, new Color(minR
                       + (maxR * vprop), minG + (maxG * vprop), minB
                       + (maxB * vprop)));
 
-- 
1.7.10.2