import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.Annotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.io.TCoffeeScoreFile;
import java.awt.Color;
import java.util.ArrayList;
import java.util.IdentityHashMap;
import jalview.datamodel.SequenceI;
import jalview.io.TCoffeeScoreFile;
import java.awt.Color;
import java.util.ArrayList;
import java.util.IdentityHashMap;
* @param alignment - annotated sequences to be searched
*/
public TCoffeeColourScheme(AnnotatedCollectionI alignment) {
* @param alignment - annotated sequences to be searched
*/
public TCoffeeColourScheme(AnnotatedCollectionI alignment) {
// assume only one set of TCOFFEE scores - but could have more than one potentially.
ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
// Search alignment to get all tcoffee annotation and pick one set of annotation to use to colour seqs.
// assume only one set of TCOFFEE scores - but could have more than one potentially.
ArrayList<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
// Search alignment to get all tcoffee annotation and pick one set of annotation to use to colour seqs.
}
@Override
public Color findColour(char c, int j, SequenceI seq) {
Color[] cols;
if( seqMap==null || (cols=seqMap.get(seq))==null) {
}
@Override
public Color findColour(char c, int j, SequenceI seq) {
Color[] cols;
if( seqMap==null || (cols=seqMap.get(seq))==null) {