/**
* by default, we filter out non-standard residues before submission
*/
- private boolean filterNonStandardResidues = true;
+ protected boolean filterNonStandardResidues = true;
/**
* Recover any existing parameters for this service
((jalview.gui.AlignViewport) alignViewport).setCalcIdSettingsFor(
getCalcId(),
new AAConSettings(true, service, this.preset,
- (arguments != null) ? JabaParamStore
- .getJwsArgsfromJaba(arguments) : null), true);
+ (arguments != null)
+ ? JabaParamStore.getJwsArgsfromJaba(arguments)
+ : null),
+ true);
}
}
super(alignViewport, alignPanel);
}
- public AbstractJabaCalcWorker(Jws2Instance service,
- AlignFrame alignFrame, WsParamSetI preset, List<Argument> paramset)
+ public AbstractJabaCalcWorker(Jws2Instance service, AlignFrame alignFrame,
+ WsParamSetI preset, List<Argument> paramset)
{
this(alignFrame.getCurrentView(), alignFrame.alignPanel);
this.guiProgress = alignFrame;
}
if (collectAnnotationResultsFor(rslt))
{
- jalview.bin.Cache.log
- .debug("Updating result annotation from Job " + rslt
- + " at " + service.getUri());
+ jalview.bin.Cache.log.debug("Updating result annotation from Job "
+ + rslt + " at " + service.getUri());
updateResultAnnotation(true);
ap.adjustAnnotationHeight();
}
catch (JobSubmissionException x)
{
- System.err.println("submission error with " + getServiceActionText()
- + " :");
+ System.err.println(
+ "submission error with " + getServiceActionText() + " :");
x.printStackTrace();
calcMan.disableWorker(this);
} catch (ResultNotAvailableException x)
AnnotatedCollectionI inputSeqs)
{
if (alignment == null || alignment.getWidth() <= 0
- || alignment.getSequences() == null || alignment.isNucleotide() ? !nucleotidesAllowed
- : !proteinAllowed)
+ || alignment.getSequences() == null || alignment.isNucleotide()
+ ? !nucleotidesAllowed
+ : !proteinAllowed)
{
return null;
}
for (SequenceI sq : (inputSeqs.getSequences()))
{
- if (bySequence ? sq.findPosition(end + 1)
- - sq.findPosition(start + 1) > minlen - 1 : sq.getEnd()
- - sq.getStart() > minlen - 1)
+ if (bySequence
+ ? sq.findPosition(end + 1)
+ - sq.findPosition(start + 1) > minlen - 1
+ : sq.getEnd() - sq.getStart() > minlen - 1)
{
String newname = SeqsetUtils.unique_name(seqs.size() + 1);
// make new input sequence with or without gaps
}
for (int apos : sq.gapMap())
{
+ char sqc = sq.getCharAt(apos);
if (!filterNonStandardResidues
- || ResidueProperties.aaIndex[sq.getCharAt(apos)] < 20)
+ || (sq.isProtein() ? ResidueProperties.aaIndex[sqc] < 20
+ : ResidueProperties.nucleotideIndex[sqc] < 5))
{
gapMap[apos] = true; // aligned and real amino acid residue
}
FastaSequence sq = seqs.get(p);
int l = sq.getSequence().length();
// strip gapped columns
- char[] padded = new char[realw], orig = sq.getSequence()
- .toCharArray();
+ char[] padded = new char[realw],
+ orig = sq.getSequence().toCharArray();
for (int i = 0, pp = 0; i < realw; pp++)
{
if (gapMap[pp])