private boolean isNa = false;
/**
+ * reference to the complementary CDS/Protein alignment for this alignment, if available
+ */
+ private AlignmentView complementView=null;
+
+ /**
+ * setter for
+ * @param complementView
+ */
+ public void setComplement(AlignmentView complementView)
+ {
+ this.complementView = complementView;
+
+ }
+ /**
+ *
+ * @return true if a complement is available
+ */
+ public boolean hasComplementView()
+ {
+ return complementView!=null;
+ }
+ /**
+ *
+ * @return the complement view or null
+ */
+ public AlignmentView getComplementView()
+ {
+ return complementView;
+ }
+
+ /**
* false if the view concerns peptides
*
* @return
ScGroup()
{
- seqs = new ArrayList<SeqCigar>();
+ seqs = new ArrayList<>();
}
/**
SequenceI[] selseqs;
if (selection != null && selection.getSize() > 0)
{
- List<SequenceI> sel = selection.getSequences(null);
this.selected = new ScGroup();
selseqs = selection.getSequencesInOrder(alignment,
selectedRegionOnly);
selseqs = alignment.getSequencesArray();
}
- List<List<SequenceI>> seqsets = new ArrayList<List<SequenceI>>();
+ List<List<SequenceI>> seqsets = new ArrayList<>();
// get the alignment's group list and make a copy
- List<SequenceGroup> grps = new ArrayList<SequenceGroup>();
+ List<SequenceGroup> grps = new ArrayList<>();
List<SequenceGroup> gg = alignment.getGroups();
grps.addAll(gg);
ScGroup[] sgrps = null;
// strip out any groups that do not actually intersect with the
// visible and selected region
int ssel = selection.getStartRes(), esel = selection.getEndRes();
- List<SequenceGroup> isg = new ArrayList<SequenceGroup>();
+ List<SequenceGroup> isg = new ArrayList<>();
for (SequenceGroup sg : grps)
{
if (!(sg.getStartRes() > esel || sg.getEndRes() < ssel))
{
if (scGroups == null)
{
- scGroups = new ArrayList<ScGroup>();
+ scGroups = new ArrayList<>();
}
addedgps[sg] = true;
scGroups.add(sgrps[sg]);