*/
package jalview.analysis;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Map;
+
import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
import jalview.datamodel.AlignedCodon;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.util.MapList;
import jalview.util.ShiftList;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
-
public class Dna
{
private static final String STOP_X = "X";
if (rf != 0)
{
final String errMsg = "trimming contigs for incomplete terminal codon.";
- if (Cache.log != null)
- {
- Cache.log.debug(errMsg);
- }
- else
- {
- System.err.println(errMsg);
- }
+ System.err.println(errMsg);
// map and trim contigs to ORF region
vc = scontigs.length - 1;
lastnpos = vismapping.shift(lastnpos); // place npos in context of