import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.renderer.ResidueShader;
}
}
- /**
- * get the consensus sequence as displayed under the PID consensus annotation
- * row.
- *
- * @return consensus sequence as a new sequence object
- */
- public SequenceI getConsensusSeq()
- {
- if (consensus == null)
- {
- updateConsensus(null);
- }
- if (consensus == null)
- {
- return null;
- }
- StringBuffer seqs = new StringBuffer();
- for (int i = 0; i < consensus.annotations.length; i++)
- {
- Annotation annotation = consensus.annotations[i];
- if (annotation != null)
- {
- String description = annotation.description;
- if (description != null && description.startsWith("["))
- {
- // consensus is a tie - just pick the first one
- seqs.append(description.charAt(1));
- }
- else
- {
- seqs.append(annotation.displayCharacter);
- }
- }
- }
-
- SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus "
- + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
- return sq;
- }
-
boolean validCharWidth;
/**