JAL-1807 explicit imports (jalview.bin)

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

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index d6088e4..6dd3a97 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -311,12 +311,12 @@ public class AAFrequency
         mouseOver.append(hci.get(AAFrequency.MAXRESIDUE) + " ");
       }
       int[][] profile = (int[][]) hci.get(AAFrequency.PROFILE);
-      int sequenceCount = profile[1][0];
-      int nonGappedCount = profile[1][1];
-      int normalisedBy = ignoreGapsInConsensusCalculation ? nonGappedCount
-              : sequenceCount;
       if (profile != null && includeAllConsSymbols)
       {
+        int sequenceCount = profile[1][0];
+        int nonGappedCount = profile[1][1];
+        int normalisedBy = ignoreGapsInConsensusCalculation ? nonGappedCount
+                : sequenceCount;
         mouseOver.setLength(0);
         if (alphabet != null)
         {
@@ -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;
@@ -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
@@ -616,7 +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];
@@ -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
-                .form(pct);
+        percent = fmt == null ? Integer.toString(pct) : fmt
+                .formLong(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;
         }
       }