*/
package jalview.analysis;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.TreeMap;
-
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeMap;
+
/**
* grab bag of useful alignment manipulation operations Expect these to be
* refactored elsewhere at some point.
s.setStart(s.getStart() - ustream_ds);
s.setEnd(s_end + downstream.length);
}
- AlignmentI newAl = new jalview.datamodel.Alignment(
- sq.toArray(new SequenceI[0]));
+ AlignmentI newAl = new Alignment(sq.toArray(new SequenceI[0]));
for (SequenceI s : sq)
{
if (s.getAnnotation() != null)
* name. For use in mapping between different alignment views of the same
* sequences.
*
- * @see jalview.datamodel.AlignmentI#getSequencesByName()
+ * @see AlignmentI#getSequencesByName()
*/
public static Map<String, List<SequenceI>> getSequencesByName(
AlignmentI al)