super(source);
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public String print()
- {
- return print(getSeqsAsArray());
- }
-
@Override
- public String print(SequenceI[] s)
+ public String print(SequenceI[] s, boolean jvsuffix)
{
StringBuffer out = new StringBuffer("PileUp");
out.append(newline);
i++;
}
- out.append(" MSF: " + s[0].getSequence().length
+ out.append(" MSF: " + s[0].getLength()
+ " Type: P Check: " + bigChecksum % 10000 + " ..");
out.append(newline);
out.append(newline);
while ((i < s.length) && (s[i] != null))
{
String seq = s[i].getSequenceAsString();
- out.append(" Name: " + printId(s[i]) + " oo Len: " + seq.length()
- + " Check: " + checksums[i] + " Weight: 1.00");
+ out.append(" Name: " + printId(s[i], jvsuffix) + " oo Len: "
+ + seq.length() + " Check: " + checksums[i]
+ + " Weight: 1.00");
out.append(newline);
if (seq.length() > max)
while ((j < s.length) && (s[j] != null))
{
- String name = printId(s[j]);
+ String name = printId(s[j], jvsuffix);
out.append(new Format("%-" + maxid + "s").form(name + " "));
int start = (i * 50) + (k * 10);
int end = start + 10;
- if ((end < s[j].getSequence().length)
- && (start < s[j].getSequence().length))
+ int length = s[j].getLength();
+ if ((end < length) && (start < length))
{
out.append(s[j].getSequence(start, end));
}
else
{
- if (start < s[j].getSequence().length)
+ if (start < length)
{
out.append(s[j].getSequenceAsString().substring(start));
out.append(newline);