*/
package jalview.datamodel;
-import java.util.ArrayList;
-import java.util.List;
-
import jalview.util.MapList;
import jalview.util.MappingUtils;
+import java.util.ArrayList;
+import java.util.List;
+
/**
* Stores mapping between the columns of a protein alignment and a DNA alignment
* and a list of individual codon to amino acid mappings between sequences.
public class AlignedCodonFrame
{
- /*
+ /**
* tied array of na Sequence objects.
*/
private SequenceI[] dnaSeqs = null;
- /*
+ /**
* tied array of Mappings to protein sequence Objects and SequenceI[]
* aaSeqs=null; MapLists where each maps from the corresponding dnaSeqs
* element to corresponding aaSeqs element
if (dnaSeqs[mi] == targetDs && dnaToProt[mi].to == sourceDs)
{
int[] codon = dnaToProt[mi].map.locateInFrom(pos, pos);
- if (codon != null) {
+ if (codon != null)
+ {
return codon;
}
}
* Read off the mapped nucleotides (converting to position base 0)
*/
codonPos = MappingUtils.flattenRanges(codonPos);
- return new char[]
- { dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1],
+ return new char[] { dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1],
dnaSeq[codonPos[2] - 1] };
}
List<SequenceI> related = new ArrayList<SequenceI>();
SequenceI seqDs = seq.getDatasetSequence();
seqDs = seqDs != null ? seqDs : seq;
-
+
for (int ds = 0; ds < dnaSeqs.length; ds++)
{
final Mapping mapping = dnaToProt[ds];