X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;fp=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=e4f2dfa01a9e41cc2b945dbe5c6e573e85ed0818;hb=2dd39c36211f947fda099c550e711ef5905efefd;hp=b806355bf949de713b78068b9aee7ef70da075c9;hpb=4dd40d33a5becefd51c31a426f2501b21029f82c;p=jalview.git

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index b806355..e4f2dfa 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -147,14 +147,13 @@ public class AAFrequency
       {
         if (sequences[row] == null)
         {
-          System.err
-                  .println("WARNING: Consensus skipping null sequence - possible race condition.");
+          System.err.println(
+                  "WARNING: Consensus skipping null sequence - possible race condition.");
           continue;
         }
-        char[] seq = sequences[row].getSequence();
-        if (seq.length > column)
+        if (sequences[row].getLength() > column)
         {
-          char c = seq[column];
+          char c = sequences[row].getCharAt(column);
           residueCounts.add(c);
           if (Comparison.isNucleotide(c))
           {
@@ -316,7 +315,7 @@ public class AAFrequency
     // always set ranges again
     gaprow.graphMax = nseq;
     gaprow.graphMin = 0;
-    double scale = 0.8/nseq;
+    double scale = 0.8 / nseq;
     for (int i = startCol; i < endCol; i++)
     {
       ProfileI profile = profiles.get(i);
@@ -334,9 +333,9 @@ public class AAFrequency
 
       String description = "" + gapped;
 
-      gaprow.annotations[i] = new Annotation("", description,
-              '\0', gapped, jalview.util.ColorUtils.bleachColour(
-                      Color.DARK_GRAY, (float) scale * gapped));
+      gaprow.annotations[i] = new Annotation("", description, '\0', gapped,
+              jalview.util.ColorUtils.bleachColour(Color.DARK_GRAY,
+                      (float) scale * gapped));
     }
   }
 
@@ -345,7 +344,8 @@ public class AAFrequency
    * <ul>
    * <li>the full profile (percentages of all residues present), if
    * showSequenceLogo is true, or</li>
-   * <li>just the modal (most common) residue(s), if showSequenceLogo is false</li>
+   * <li>just the modal (most common) residue(s), if showSequenceLogo is
+   * false</li>
    * </ul>
    * Percentages are as a fraction of all sequence, or only ungapped sequences
    * if ignoreGaps is true.
@@ -366,8 +366,8 @@ public class AAFrequency
     String description = null;
     if (counts != null && showSequenceLogo)
     {
-      int normaliseBy = ignoreGaps ? profile.getNonGapped() : profile
-              .getHeight();
+      int normaliseBy = ignoreGaps ? profile.getNonGapped()
+              : profile.getHeight();
       description = counts.getTooltip(normaliseBy, dp);
     }
     else
@@ -424,8 +424,8 @@ public class AAFrequency
     QuickSort.sort(values, symbols);
     int nextArrayPos = 2;
     int totalPercentage = 0;
-    final int divisor = ignoreGaps ? profile.getNonGapped() : profile
-            .getHeight();
+    final int divisor = ignoreGaps ? profile.getNonGapped()
+            : profile.getHeight();
 
     /*
      * traverse the arrays in reverse order (highest counts first)
@@ -542,8 +542,8 @@ public class AAFrequency
         {
           continue;
         }
-        List<char[]> codons = MappingUtils
-                .findCodonsFor(seq, col, mappings);
+        List<char[]> codons = MappingUtils.findCodonsFor(seq, col,
+                mappings);
         for (char[] codon : codons)
         {
           int codonEncoded = CodingUtils.encodeCodon(codon);
@@ -623,10 +623,10 @@ public class AAFrequency
 
       int modalCodonEncoded = codons[codons.length - 1];
       int modalCodonCount = sortedCodonCounts[codons.length - 1];
-      String modalCodon = String.valueOf(CodingUtils
-              .decodeCodon(modalCodonEncoded));
-      if (sortedCodonCounts.length > 1
-              && sortedCodonCounts[codons.length - 2] == sortedCodonCounts[codons.length - 1])
+      String modalCodon = String
+              .valueOf(CodingUtils.decodeCodon(modalCodonEncoded));
+      if (sortedCodonCounts.length > 1 && sortedCodonCounts[codons.length
+              - 2] == sortedCodonCounts[codons.length - 1])
       {
         /*
          * two or more codons share the modal count
@@ -685,8 +685,8 @@ public class AAFrequency
           {
             if (samePercent.length() > 0)
             {
-              mouseOver.append(samePercent).append(": ")
-                      .append(lastPercent).append("% ");
+              mouseOver.append(samePercent).append(": ").append(lastPercent)
+                      .append("% ");
             }
             samePercent.setLength(0);
             samePercent.append(codon);