*/
databaseFile = FileUtils.createTempFile("database", ".fa");
AlignmentI al = af.getViewport().getAlignment();
- deleteHmmSequences(al);
- exportFasta(al, databaseFile);
+ AlignmentI copy = new Alignment(al);
+ deleteHmmSequences(copy);
+ exportFasta(copy, databaseFile);
}
args.add(getFilePath(seqFile, true));