+ if (serviceName.equalsIgnoreCase("JpredWS")) {\r
+ writer.close();\r
+ JpredAlignment jpred = (JpredAlignment)alignment;\r
+ if (outfile != null) {\r
+ FileOutputStream fout = new FileOutputStream(outfile);\r
+ SequenceUtil.writeFastaKeepTheStream(fout, jpred.getJpredSequences(), 60);\r
+ fout.close();\r
+ } else {\r
+ SequenceUtil.writeFasta(System.out, jpred.getJpredSequences());\r
+ }\r
+ } else {\r
+ IOHelper.writeOut(writer, alignment);\r
+ writer.close();\r
+ }\r
+ AlignmentMetadata md = alignment.getMetadata();\r
+ System.out.println("Output has been prepared with " + md.getProgram());\r