- AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
- FormatAdapter.FILE, "FASTA");
+ AlignmentI al;
+ if (format == FileFormat.HMMER3)
+ {
+ al = new FormatAdapter().readFile("examples/uniref50.hmm",
+ DataSourceType.FILE, FileFormat.HMMER3);
+ }
+ else
+ {
+ al = new FormatAdapter().readFile("examples/uniref50.fa",
+ DataSourceType.FILE, FileFormat.Fasta);
+ }