* Cache a copy of the target sequences so we can mimic successive edits on
* them. This lets us compute mappings for all edits in the set.
*/
- Map<SequenceI, SequenceI> targetCopies = new HashMap<SequenceI, SequenceI>();
+ Map<SequenceI, SequenceI> targetCopies = new HashMap<>();
for (SequenceI seq : mapTo.getSequences())
{
SequenceI ds = seq.getDatasetSequence();
boolean undo, AlignmentI mapTo, List<AlignedCodonFrame> mappings)
{
SequenceI[] sortOrder = command.getSequenceOrder(undo);
- List<SequenceI> mappedOrder = new ArrayList<SequenceI>();
+ List<SequenceI> mappedOrder = new ArrayList<>();
int j = 0;
/*
toSequences, fromGapChar);
}
- for (int[] hidden : hiddencols.getHiddenRegions())
+ for (int[] hidden : hiddencols)
{
mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences,
toSequences, fromGapChar);
public static List<char[]> findCodonsFor(SequenceI seq, int col,
List<AlignedCodonFrame> mappings)
{
- List<char[]> result = new ArrayList<char[]>();
+ List<char[]> result = new ArrayList<>();
int dsPos = seq.findPosition(col);
for (AlignedCodonFrame mapping : mappings)
{
SequenceI sequence, List<AlignedCodonFrame> mappings,
List<SequenceI> filterList)
{
- List<AlignedCodonFrame> result = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> result = new ArrayList<>();
if (sequence == null || mappings == null)
{
return result;