X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=e4f2dfa01a9e41cc2b945dbe5c6e573e85ed0818;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=b806355bf949de713b78068b9aee7ef70da075c9;hpb=136c0793b90b72b928c4d77dc109dd5c644e00d3;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
*
* - the full profile (percentages of all residues present), if
* showSequenceLogo is true, or
- * - just the modal (most common) residue(s), if showSequenceLogo is false
+ * - just the modal (most common) residue(s), if showSequenceLogo is
+ * false
*
* 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 codons = MappingUtils
- .findCodonsFor(seq, col, mappings);
+ List 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);