*/
Vector<AlignmentAnnotation> annotation;
- /**
- * The index of the sequence in a MSA
- */
- int index = -1;
-
private SequenceFeaturesI sequenceFeatureStore;
/*
}
}
- /**
- * @return The index (zero-based) on this sequence in the MSA. It returns
- * {@code -1} if this information is not available.
- */
- @Override
- public int getIndex()
- {
- return index;
- }
-
- /**
- * Defines the position of this sequence in the MSA. Use the value {@code -1}
- * if this information is undefined.
- *
- * @param The
- * position for this sequence. This value is zero-based (zero for
- * this first sequence)
- */
- @Override
- public void setIndex(int value)
- {
- index = value;
- }
-
@Override
public void setRNA(RNA r)
{
public void transferAnnotation(SequenceI entry, Mapping mp);
/**
- * @param index
- * The sequence index in the MSA
- */
- public void setIndex(int index);
-
- /**
- * @return The index of the sequence in the alignment
- */
- public int getIndex();
-
- /**
* @return The RNA of the sequence in the alignment
*/
return "EnsemblGenomes";
}
- private String Wrong[];
@Override
public String getTestQuery()
{
- return "DDB_G0283883";
+ /*
+ * Salmonella gene, Uniprot Q8Z9G6, EMBLCDS CAD01290
+ */
+ return "CAD01290";
}
@Override
}
parseCalled = true;
parse();
- // sets the index of each sequence in the alignment
- for (int i = 0, c = seqs.size(); i < c; i++)
- {
- seqs.get(i).setIndex(i);
- }
}
/**