return;
}
- String rslt="JOB NOT DEFINED";
+ String rslt = "JOB NOT DEFINED";
try
{
calcMan.workerCannotRun(this);
} catch (ResultNotAvailableException x)
{
- System.err.println("collection error:\nJob ID: "+rslt);
+ System.err.println("collection error:\nJob ID: " + rslt);
x.printStackTrace();
calcMan.workerCannotRun(this);
if (alignment == null || alignment.getWidth() <= 0
|| alignment.getSequences() == null
-// || (alignedSeqs && !alignment.isAligned() && !submitGaps)
+ // || (alignedSeqs && !alignment.isAligned() && !submitGaps)
|| alignment.isNucleotide() ? !nucleotidesAllowed
: !proteinAllowed)
{
List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
int minlen = 10;
- int ln=-1;
+ int ln = -1;
if (bySequence)
{
seqNames = new HashMap<String, SequenceI>();
seqNames.put(newname, sq);
}
FastaSequence seq;
- seqs.add(seq=new compbio.data.sequence.FastaSequence(newname,
+ seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
(submitGaps) ? sq.getSequenceAsString() : AlignSeq
.extractGaps(jalview.util.Comparison.GapChars,
sq.getSequenceAsString())));
- if (seq.getSequence().length()>ln)
+ if (seq.getSequence().length() > ln)
{
ln = seq.getSequence().length();
}
if (alignedSeqs && submitGaps)
{
// try real hard to return something submittable
- // TODO: some of AAcons measures need a minimum of two or three amino acids at each position, and aacons doesn't gracefully degrade.
- for (int p=0; p<seqs.size();p++)
+ // TODO: some of AAcons measures need a minimum of two or three amino
+ // acids at each position, and aacons doesn't gracefully degrade.
+ for (int p = 0; p < seqs.size(); p++)
{
- FastaSequence sq=seqs.get(p);
- int l=sq.getSequence().length();
- if (l<ln)
+ FastaSequence sq = seqs.get(p);
+ int l = sq.getSequence().length();
+ if (l < ln)
{
- char[] padded=new char[ln];
- System.arraycopy(sq.getSequence().toCharArray(),0,padded,0,sq.getSequence().length());
- while (l<ln)
+ char[] padded = new char[ln];
+ System.arraycopy(sq.getSequence().toCharArray(), 0, padded, 0, sq
+ .getSequence().length());
+ while (l < ln)
{
- padded[l++]='-';
+ padded[l++] = '-';
}
- seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(), new String(padded)));
+ seqs.set(p, new compbio.data.sequence.FastaSequence(sq.getId(),
+ new String(padded)));
}
}