+ // Only purpose is to replace "analize" with "fold" method \r
+ // so that a clustal input file and not fasta will be generated\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public String customAnalize(List<FastaSequence> sequences,\r
+ List<Option<RNAalifold>> options) throws UnsupportedRuntimeException,\r
+ LimitExceededException, JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<RNAalifold> confRNAalifold = init(sequences);\r
+ List<String> params = WSUtil.getCommands(options, RNAalifold.KEY_VALUE_SEPARATOR);\r
+ confRNAalifold.addParameters(params);\r
+ return WSUtil.fold(sequences, confRNAalifold, log, "customAnalize", getLimit(""));\r
+ }\r
+ \r
+ \r