From e5c9a94fcd7765b981e73640626989217276a46a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 1 Jul 2015 15:53:27 +0100
Subject: [PATCH] JAL-1681 more condensed tooltip where codons share same
 percentage

---
 src/jalview/analysis/AAFrequency.java |   41 ++++++++++++++++++++++++++++-----
 1 file changed, 35 insertions(+), 6 deletions(-)

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 69c39df..50045dc 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -596,7 +596,6 @@ public class AAFrequency
       // array holds #seqs, #ungapped, then codon counts indexed by codon
       final int[] codonCounts = (int[]) hci.get(PROFILE);
       int totalCount = 0;
-      StringBuilder mouseOver = new StringBuilder(32);
 
       /*
        * First pass - get total count and find the highest
@@ -636,26 +635,56 @@ public class AAFrequency
        */
 
       /*
-       * Scan sorted array backwards for most frequent values first.
+       * Scan sorted array backwards for most frequent values first. Show
+       * repeated values compactly.
        */
+      StringBuilder mouseOver = new StringBuilder(32);
+      StringBuilder samePercent = new StringBuilder();
+      String percent = null;
+      String lastPercent = null;
+      Format fmt = getPercentageFormat(nseqs);
+
       for (int j = codons.length - 1; j >= 0; j--)
       {
         int codonCount = sortedCodonCounts[j];
         if (codonCount == 0)
         {
+          /*
+           * remaining codons are 0% - ignore, but finish off the last one if
+           * necessary
+           */
+          if (samePercent.length() > 0)
+          {
+            mouseOver.append(samePercent).append(": ").append(percent)
+                    .append("% ");
+          }
           break;
         }
         int codonEncoded = codons[j];
         final int pct = codonCount * 100 / totalCount;
         String codon = String
                 .valueOf(CodingUtils.decodeCodon(codonEncoded));
-        Format fmt = getPercentageFormat(nseqs);
-        String formatted = fmt == null ? Integer.toString(pct) : fmt
+        percent = fmt == null ? Integer.toString(pct) : fmt
                 .form(pct);
         if (showProfileLogo || codonCount == modalCodonCount)
         {
-          mouseOver.append(codon).append(": ").append(formatted)
-                  .append("% ");
+          if (percent.equals(lastPercent) && j > 0)
+          {
+            samePercent.append(samePercent.length() == 0 ? "" : ", ");
+            samePercent.append(codon);
+          }
+          else
+          {
+            if (samePercent.length() > 0)
+            {
+              mouseOver.append(samePercent).append(": ")
+                      .append(lastPercent)
+                      .append("% ");
+            }
+            samePercent.setLength(0);
+            samePercent.append(codon);
+          }
+          lastPercent = percent;
         }
       }
 
-- 
1.7.10.2