{
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))
{
// 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);
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));
}
}
* <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.
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
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)
for (int col = 0; col < cols; col++)
{
// todo would prefer a Java bean for consensus data
- Hashtable<String, int[]> columnHash = new Hashtable<String, int[]>();
+ Hashtable<String, int[]> columnHash = new Hashtable<>();
// #seqs, #ungapped seqs, counts indexed by (codon encoded + 1)
int[] codonCounts = new int[66];
codonCounts[0] = alignment.getSequences().size();
{
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);
{
codonCounts[codonEncoded + 2]++;
ungappedCount++;
+ break;
}
}
}
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
{
if (samePercent.length() > 0)
{
- mouseOver.append(samePercent).append(": ")
- .append(lastPercent).append("% ");
+ mouseOver.append(samePercent).append(": ").append(lastPercent)
+ .append("% ");
}
samePercent.setLength(0);
samePercent.append(codon);