- if (format.equals("FASTA"))
- {
- alignFile = new FastaFile(inFile, type);
- }
- else if (format.equals("MSF"))
- {
- alignFile = new MSFfile(inFile, type);
- }
- else if (format.equals("PileUp"))
- {
- alignFile = new PileUpfile(inFile, type);
- }
- else if (format.equals("CLUSTAL"))
- {
- alignFile = new ClustalFile(inFile, type);
- }
- else if (format.equals("BLC"))
- {
- alignFile = new BLCFile(inFile, type);
- }
- else if (format.equals("PIR"))
- {
- alignFile = new PIRFile(inFile, type);
- }
- else if (format.equals("PFAM"))
- {
- alignFile = new PfamFile(inFile, type);
- }
- else if (format.equals("JnetFile"))
- {
- alignFile = new JPredFile(inFile, type);
- ((JPredFile) alignFile).removeNonSequences();
- }
- else if (format.equals("PDB"))
- {
-
- StructureImportSettings.addSettings(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile,
- type);
- ((StructureFile) alignFile).setDbRefType(format);
- }
- else if (format.equalsIgnoreCase("mmCIF"))