- * @param s1 first sequence for alignment
- * @param s2 second sequence for alignment
- * @param type molecule type, either AlignSeq.PEP or AlignSeq.DNA
+ * @param s1
+ * first sequence for alignment
+ * @param s2
+ * second sequence for alignment
+ * @param type
+ * molecule type, either AlignSeq.PEP or AlignSeq.DNA
SequenceI alSeq1 = new Sequence(s1.getName(), getAStr1());
alSeq1.setStart(s1.getStart() + getSeq1Start() - 1);
alSeq1.setEnd(s1.getStart() + getSeq1End() - 1);
SequenceI alSeq1 = new Sequence(s1.getName(), getAStr1());
alSeq1.setStart(s1.getStart() + getSeq1Start() - 1);
alSeq1.setEnd(s1.getStart() + getSeq1End() - 1);
SequenceI alSeq2 = new Sequence(s2.getName(), getAStr2());
alSeq2.setStart(s2.getStart() + getSeq2Start() - 1);
alSeq2.setEnd(s2.getStart() + getSeq2End() - 1);
SequenceI alSeq2 = new Sequence(s2.getName(), getAStr2());
alSeq2.setStart(s2.getStart() + getSeq2Start() - 1);
alSeq2.setEnd(s2.getStart() + getSeq2End() - 1);
- output.append("ALL GAPS: "
- + (s1str.length() == 0 ? s1.getName() : " ")
- + (s2str.length() == 0 ? s2.getName() : ""));
+ output.append(
+ "ALL GAPS: " + (s1str.length() == 0 ? s1.getName() : " ")
+ + (s2str.length() == 0 ? s2.getName() : ""));
if (!PEP.equals(moleculeType) && !DNA.equals(moleculeType))
{
output.append("Wrong type = dna or pep only");
if (!PEP.equals(moleculeType) && !DNA.equals(moleculeType))
{
output.append("Wrong type = dna or pep only");
- throw new Error(MessageManager.formatMessage(
- "error.unknown_type_dna_or_pep",
- new String[] { moleculeType }));
+ throw new Error(MessageManager
+ .formatMessage("error.unknown_type_dna_or_pep", new String[]
+ { moleculeType }));
- score[i][j] = max(score[i - 1][j - 1]
- + (pairwiseScore * 10), E[i][j], F[i][j]);
+ score[i][j] = max(score[i - 1][j - 1] + (pairwiseScore * 10),
+ E[i][j], F[i][j]);
int pdbpos = s2.getStart() + getSeq2Start() - 2;
int alignpos = s1.getStart() + getSeq1Start() - 2;
int lp2 = pdbpos - 3, lp1 = alignpos - 3;
int pdbpos = s2.getStart() + getSeq2Start() - 2;
int alignpos = s1.getStart() + getSeq1Start() - 2;
int lp2 = pdbpos - 3, lp1 = alignpos - 3;
- int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2
- .size() + (lastmatch ? 1 : 0)];
+ int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)],
+ mapseq2 = new int[as2.size() + (lastmatch ? 1 : 0)];
List<SequenceI> ochains, AlignmentI al, String dnaOrProtein,
boolean removeOldAnnots)
{
List<SequenceI> ochains, AlignmentI al, String dnaOrProtein,
boolean removeOldAnnots)
{