}
pid = pid / (aseq1.length - count) * 100;
- output.append(new Format("Percentage ID = %3.2f\n").form(pid));
- output.append(NEWLINE);
+ output.append(new Format("Percentage ID = %3.2f").form(pid));
+ output.append(NEWLINE).append(NEWLINE);
try
{
os.print(output.toString());
*/
public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
{
- ArrayList<Integer> as1 = new ArrayList<Integer>(),
- as2 = new ArrayList<Integer>();
+ ArrayList<Integer> as1 = new ArrayList<>(),
+ as2 = new ArrayList<>();
int pdbpos = s2.getStart() + getSeq2Start() - 2;
int alignpos = s1.getStart() + getSeq1Start() - 2;
int lp2 = pdbpos - 3, lp1 = alignpos - 3;
{
mapseq1[i++] = ip;
}
- ;
i = 0;
for (Integer ip : as2)
{
mapseq2[i++] = ip;
}
- ;
if (lastmatch)
{
mapseq1[mapseq1.length - 1] = alignpos;
List<SequenceI> ochains, AlignmentI al, String dnaOrProtein,
boolean removeOldAnnots)
{
- List<SequenceI> orig = new ArrayList<SequenceI>(),
- repl = new ArrayList<SequenceI>();
- List<AlignSeq> aligs = new ArrayList<AlignSeq>();
+ List<SequenceI> orig = new ArrayList<>(),
+ repl = new ArrayList<>();
+ List<AlignSeq> aligs = new ArrayList<>();
if (al != null && al.getHeight() > 0)
{
- ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
- ArrayList<AlignSeq> aligns = new ArrayList<AlignSeq>();
+ ArrayList<SequenceI> matches = new ArrayList<>();
+ ArrayList<AlignSeq> aligns = new ArrayList<>();
for (SequenceI sq : ochains)
{