import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
import jalview.datamodel.ProfilesI;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.IdColumns;
import jalview.viewmodel.styles.ViewStyle;
import jalview.workers.AlignCalcManager;
import jalview.workers.ComplementConsensusThread;
return searchResults;
}
+ @Override
+ public ContactListI getContactList(AlignmentAnnotation _aa, int column)
+ {
+ return alignment.getContactListFor(_aa, column);
+ }
+
+ @Override
+ public ContactMatrixI getContactMatrix(
+ AlignmentAnnotation alignmentAnnotation)
+ {
+ return alignment.getContactMatrixFor(alignmentAnnotation);
+ }
+
+
/**
* get the consensus sequence as displayed under the PID consensus annotation
* row.
false));
}
+ /**
+ * ordered list of annotation values displayed per sequence in ID panel
+ */
+ private IdColumns id_columns = null;
+
+ /**
+ * available and currently visible columns for this view
+ */
+ @Override
+ public IdColumns getIdColumns()
+ {
+ if (alignment == null)
+ {
+ return null;
+ }
+ if (id_columns == null)
+ {
+ id_columns = new IdColumns(alignment);
+ }
+ return id_columns;
+ }
+
public void setSavedUpToDate(boolean s)
{
setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES);