* @throws IOException
* DOCUMENT ME!
*/
- public MSFfile(String inFile, String type) throws IOException
+ public MSFfile(String inFile, DataSourceType type) throws IOException
{
super(inFile, type);
}
*
* @return DOCUMENT ME!
*/
- public String print(SequenceI[] sqs)
+ @Override
+ public String print(SequenceI[] sqs, boolean jvSuffix)
{
boolean is_NA = Comparison.isNucleotide(sqs);
while ((i < s.length) && (s[i] != null))
{
- nameBlock[i] = new String(" Name: " + printId(s[i]) + " ");
+ nameBlock[i] = new String(" Name: " + printId(s[i], jvSuffix) + " ");
idBlock[i] = new String("Len: "
+ maxLenpad.form(s[i].getSequence().length) + " Check: "
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 + " "));
return out.toString();
}
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public String print()
- {
- return print(getSeqsAsArray());
- }
}