import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
-import jalview.analysis.Profile;
import jalview.schemes.ColourSchemeI;
import java.awt.Color;
boolean upd = false;
try
{
- Profile[] cnsns = AAFrequency.calculate(sequences, startRes,
+ ProfilesI cnsns = AAFrequency.calculate(sequences, startRes,
endRes + 1, showSequenceLogo);
if (consensus != null)
{
if ((conservation != null)
|| (cs != null && cs.conservationApplied()))
{
- Conservation c = new Conservation(groupName, 3, sequences,
- startRes, endRes + 1);
+ Conservation c = new Conservation(groupName, sequences, startRes,
+ endRes + 1);
c.calculate();
c.verdict(false, consPercGaps);
if (conservation != null)
c.completeAnnotations(conservation, null, startRes, endRes + 1);
}
- public Profile[] consensusData = null;
+ public ProfilesI consensusData = null;
- private void _updateConsensusRow(Profile[] cnsns, long nseq)
+ private void _updateConsensusRow(ProfilesI cnsns, long nseq)
{
if (consensus == null)
{
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ if (calcId == null)
+ {
+ return aa;
+ }
for (AlignmentAnnotation a : getAlignmentAnnotation())
{
- if (a.getCalcId() == calcId)
+ if (calcId.equals(a.getCalcId()))
{
aa.add(a);
}