/*
* Found a sequence mapping. Locate the start/end mapped residues.
*/
- List<AlignedCodonFrame> mapping = Arrays.asList(new AlignedCodonFrame[] { acf });
+ List<AlignedCodonFrame> mapping = Arrays
+ .asList(new AlignedCodonFrame[] { acf });
SearchResults sr = buildSearchResults(selected,
startResiduePos, mapping);
for (Match m : sr.getResults())
* @param fromGapChar
*/
protected static void mapHiddenColumns(int[] hidden,
- List<AlignedCodonFrame> mappings,
- ColumnSelection mappedColumns, List<SequenceI> fromSequences,
- List<SequenceI> toSequences, char fromGapChar)
+ List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
+ List<SequenceI> fromSequences, List<SequenceI> toSequences,
+ char fromGapChar)
{
for (int col = hidden[0]; col <= hidden[1]; col++)
{
* @param fromGapChar
*/
protected static void mapColumn(int col,
- List<AlignedCodonFrame> mappings,
- ColumnSelection mappedColumns, List<SequenceI> fromSequences,
- List<SequenceI> toSequences, char fromGapChar)
+ List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
+ List<SequenceI> fromSequences, List<SequenceI> toSequences,
+ char fromGapChar)
{
int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
toSequences, fromGapChar);
* Get the residue position and find the mapped position.
*/
int residuePos = fromSeq.findPosition(col);
- SearchResults sr = buildSearchResults(fromSeq, residuePos,
- mappings);
+ SearchResults sr = buildSearchResults(fromSeq, residuePos, mappings);
for (Match m : sr.getResults())
{
int mappedStartResidue = m.getStart();
{
return ranges;
}
-
+
int[] copy = Arrays.copyOf(ranges, ranges.length);
int sxpos = -1;
int cdspos = 0;
break;
}
}
-
+
if (sxpos > 0)
{
/*