-
- try
- {
- AlignFile afile = null;
-
- if (format.equalsIgnoreCase("FASTA"))
- {
- afile = new FastaFile();
- afile.addJVSuffix(
- jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));
- }
- else if (format.equalsIgnoreCase("MSF"))
- {
- afile = new MSFfile();
- afile.addJVSuffix(
- jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true));
- }
- else if (format.equalsIgnoreCase("PileUp"))
- {
- afile = new PileUpfile();
- afile.addJVSuffix(
- jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true));
- }
- else if (format.equalsIgnoreCase("CLUSTAL"))
- {
- afile = new ClustalFile();
- afile.addJVSuffix(
- jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));
- }
- else if (format.equalsIgnoreCase("BLC"))
- {
- afile = new BLCFile();
- afile.addJVSuffix(
- jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));
- }
- else if (format.equalsIgnoreCase("PIR"))
- {
- afile = new PIRFile();
- afile.addJVSuffix(
- jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true));
- }
- else if (format.equalsIgnoreCase("PFAM"))
- {
- afile = new PfamFile();
- afile.addJVSuffix(
- jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));
- }
-
- afile.setSeqs(seqs);
-
- return afile.print();
- }
- catch (Exception e)
- {
- System.err.println("Failed to write alignment as a '" + format +
- "' file\n");
- e.printStackTrace();
- }
-
- return null;