import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.util.StringUtils;
+import jalview.workers.InformationThread;
import java.util.ArrayList;
import java.util.Arrays;
private String vamsasId;
+ HiddenMarkovModel hmm;
+
+ boolean isHMMConsensusSequence = false;
private DBModList<DBRefEntry> dbrefs; // controlled access
/**
}
/**
+ * Create a new sequence object from a characters array using default values
+ * of 1 and -1 for start and end. The array used to create the sequence is
+ * copied and is not stored internally.
+ *
+ * @param name
+ * sequence name
+ * @param sequence
+ * list of residues
+ */
+ public Sequence(String name, char[] sequence)
+ {
+ this(name, Arrays.copyOf(sequence, sequence.length), 1, -1);
+ }
+
+ /**
* Creates a new Sequence object with new AlignmentAnnotations but inherits
* any existing dataset sequence reference. If non exists, everything is
* copied.
this.addPDBId(new PDBEntry(pdb));
}
}
+ if (seq.getHMM() != null)
+ {
+ this.hmm = new HiddenMarkovModel(seq.getHMM(), this);
+ }
}
@Override
}
/**
- * DOCUMENT ME!
+ * Answers the sequence name, with '/start-end' appended if jvsuffix is true
*
- * @return DOCUMENT ME!
+ * @return
*/
@Override
public String getDisplayId(boolean jvsuffix)
{
- StringBuffer result = new StringBuffer(name);
- if (jvsuffix)
+ if (!jvsuffix)
{
- result.append("/" + start + "-" + end);
+ return name;
}
+ StringBuilder result = new StringBuilder(name);
+ result.append("/").append(start).append("-").append(end);
return result.toString();
}
public void setStart(int start)
{
this.start = start;
+ sequenceChanged();
}
/**
@Override
public ContiguousI findPositions(int fromColumn, int toColumn)
{
- if (toColumn < fromColumn || fromColumn < 1)
+ fromColumn = Math.max(fromColumn, 1);
+ if (toColumn < fromColumn)
{
return null;
}
@Override
public void addDBRef(DBRefEntry entry)
{
+ // TODO JAL-3980 maintain as sorted list
if (datasetSequence != null)
{
datasetSequence.addDBRef(entry);
{
dbrefs = new DBModList<>();
}
+ // TODO JAL-3979 LOOK UP RATHER THAN SWEEP FOR EFFICIENCY
for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
{
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label)
{
+ return getAlignmentAnnotations(calcId, label, null, true);
+ }
+
+ @Override
+ public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description)
+ {
+ return getAlignmentAnnotations(calcId, label, description, false);
+ }
+
+ private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+ String label, String description, boolean ignoreDescription)
+ {
List<AlignmentAnnotation> result = new ArrayList<>();
if (this.annotation != null)
{
for (AlignmentAnnotation ann : annotation)
{
- if (ann.calcId != null && ann.calcId.equals(calcId)
- && ann.label != null && ann.label.equals(label))
+ String id = ann.getCalcId();
+ if ((id != null && id.equals(calcId))
+ && (ann.label != null && ann.label.equals(label))
+ && ((ignoreDescription && description == null)
+ || (ann.description != null
+ && ann.description.equals(description))))
{
result.add(ann);
}
}
}
+ @Override
+ public HiddenMarkovModel getHMM()
+ {
+ return hmm;
+ }
+
+ @Override
+ public void setHMM(HiddenMarkovModel hmm)
+ {
+ this.hmm = hmm;
+ }
+
+ @Override
+ public boolean hasHMMAnnotation()
+ {
+ if (this.annotation == null) {
+ return false;
+ }
+ for (AlignmentAnnotation ann : annotation)
+ {
+ if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
/**
* {@inheritDoc}
*/
List<SequenceFeature> result = getFeatures().findFeatures(startPos,
endPos, types);
- if (datasetSequence != null)
- {
- result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
- types);
- }
- else
- {
- result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
- }
/*
* if end column is gapped, endPos may be to the right,
// otherwise, sequence was completely hidden
return 0;
}
+
+ @Override
+ public boolean hasHMMProfile()
+ {
+ return hmm != null;
+ }
}