import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
StockholmFile file = new StockholmFile(new FileParse(
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
StockholmFile file = new StockholmFile(new FileParse(
inputAlignmentTemp.getAbsolutePath(), DataSourceType.FILE));
seqs = file.getSeqsAsArray();
// look for PP cons and ref seq in alignment only annotation
AlignmentAnnotation modelpos = null, ppcons = null;
for (AlignmentAnnotation aa : file.getAnnotations())
// look for PP cons and ref seq in alignment only annotation
AlignmentAnnotation modelpos = null, ppcons = null;
for (AlignmentAnnotation aa : file.getAnnotations())