+ 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;
+ }
+