import java.util.Collection;
import java.util.Collections;
import java.util.Iterator;
+import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import eu.etaxonomy.cdm.model.molecular.SequenceString;
import eu.etaxonomy.cdm.model.molecular.SingleRead;
import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
+import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment.Shift;
import eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.ToggleInsertOverwriteHandler;
import eu.etaxonomy.taxeditor.editor.handler.alignmenteditor.ToggleLeftRightInsertionHandler;
import eu.etaxonomy.taxeditor.model.MessagingUtils;
private SingleReadAlignment.Shift[] convertToCDMShifts(PherogramAreaModel model) {
- SingleReadAlignment.Shift[] result = new SingleReadAlignment.Shift[model.getShiftChangeCount()];
Iterator<ShiftChange> iterator = model.shiftChangeIterator();
- int pos = 0;
+ List<Shift> shifts = new ArrayList<SingleReadAlignment.Shift>();
while (iterator.hasNext()) {
ShiftChange shiftChange = iterator.next();
- result[pos] = new SingleReadAlignment.Shift(shiftChange.getBaseCallIndex(), shiftChange.getShiftChange());
+ shifts.add(new SingleReadAlignment.Shift(shiftChange.getBaseCallIndex(), shiftChange.getShiftChange()));
}
- return result;
+ return shifts.toArray(new Shift[]{});
}