- public Alignment readFile(String inFile, String type, String format)
- throws java.io.IOException
- {
- Alignment al;
- if (format.equals(JSONFile.FILE_DESC))
- {
- afile = new JSONFile(inFile, type);
- al = new Alignment(afile.getSeqsAsArray());
- afile.addAnnotations(al);
- for (SequenceGroup sg : afile.getSeqGroups())
- {
- al.addGroup(sg);
- }
- }
- else
- {
- al = super.readFile(inFile, type, format);
- }
- return al;
- }
-
- public AlignmentI readFromFile(FileParse source, String format)
- throws java.io.IOException
- {
- Alignment al;
- if (format.equals(JSONFile.FILE_DESC))
- {
- afile = new JSONFile(source);
- al = new Alignment(afile.getSeqsAsArray());
- afile.addAnnotations(al);
- afile.addSeqGroups(al);
- }
- else
- {
- al = (Alignment) super.readFromFile(source, format);
- }
- return al;
- }
-