JAL-1807 disambiguated method signatures with numeric primitive args

[jalview.git] / src / jalview / analysis / AAFrequency.java

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 50045dc..6dd3a97 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -327,7 +327,7 @@ public class AAFrequency
                     .append(((c == 0) ? "" : "; "))
                     .append(alphabet[c])
                     .append(" ")
-                    .append(((fmt != null) ? fmt.form(tval) : ((int) tval)))
+                    .append(((fmt != null) ? fmt.formDouble(tval) : ((int) tval)))
                     .append("%");
           }
         }
@@ -344,7 +344,7 @@ public class AAFrequency
             // { (char) c };
             vl[c] = profile[0][c];
           }
-          QuickSort.sort(vl, ca);
+          QuickSort.sortFloat(vl, ca);
           for (int p = 0, c = ca.length - 1; profile[0][ca[c]] > 0; c--)
           {
             final char residue = ca[c];
@@ -355,7 +355,7 @@ public class AAFrequency
                       .append((((p == 0) ? "" : "; ")))
                       .append(residue)
                       .append(" ")
-                      .append(((fmt != null) ? fmt.form(tval)
+                      .append(((fmt != null) ? fmt.formDouble(tval)
                               : ((int) tval))).append("%");
               p++;
             }
@@ -365,7 +365,7 @@ public class AAFrequency
       else
       {
         mouseOver.append(
-                (((fmt != null) ? fmt.form(value) : ((int) value))))
+                (((fmt != null) ? fmt.formDouble(value) : ((int) value))))
                 .append("%");
       }
       consensus.annotations[i] = new Annotation(maxRes,
@@ -425,7 +425,7 @@ public class AAFrequency
       ca[c] = (char) c;
       vl[c] = profile[0][c];
     }
-    QuickSort.sort(vl, ca);
+    QuickSort.sortFloat(vl, ca);
     int nextArrayPos = 2;
     int totalPercentage = 0;
     int distinctValuesCount = 0;
@@ -480,7 +480,7 @@ public class AAFrequency
     {
       codons[i] = (char) i;
     }
-    QuickSort.sort(sortedCounts, codons);
+    QuickSort.sortInt(sortedCounts, codons);
     int totalPercentage = 0;
     int distinctValuesCount = 0;
     int j = 3;
@@ -615,7 +615,7 @@ public class AAFrequency
       int[] sortedCodonCounts = new int[codonCounts.length - 2];
       System.arraycopy(codonCounts, 2, sortedCodonCounts, 0,
               codonCounts.length - 2);
-      QuickSort.sort(sortedCodonCounts, codons);
+      QuickSort.sortInt(sortedCodonCounts, codons);
 
       int modalCodonEncoded = codons[codons.length - 1];
       int modalCodonCount = sortedCodonCounts[codons.length - 1];
@@ -665,7 +665,7 @@ public class AAFrequency
         String codon = String
                 .valueOf(CodingUtils.decodeCodon(codonEncoded));
         percent = fmt == null ? Integer.toString(pct) : fmt
-                .form(pct);
+                .formLong(pct);
         if (showProfileLogo || codonCount == modalCodonCount)
         {
           if (percent.equals(lastPercent) && j > 0)