+ \r
+ /**\r
+ * Return RNA secondary structure from a file using FoldWS\r
+ * \r
+ * @param <T>\r
+ * web service type e.g. Clustal\r
+ * @param file\r
+ * to read the results from\r
+ * @param foldws\r
+ * FoldWS required\r
+ * @param preset\r
+ * Preset to use optional\r
+ * @param customOptions\r
+ * file which contains new line separated list of options\r
+ * @return String\r
+ */\r
+ \r
+ static <T> String fold(File file, FoldWS<T> foldws, Preset<T> preset,\r
+ List<Option<T>> customOptions) {\r
+ FileInputStream instream = null;\r
+ Alignment alignment = null;\r
+ String rnastruct = null;\r
+ try {\r
+ instream = new FileInputStream(file);\r
+ alignment = ClustalAlignmentUtil.readClustalFile(instream);\r
+ instream.close();\r
+ String jobId = null;\r
+ if (customOptions != null && preset != null) {\r
+ System.out.println("WARN: Parameters (-f) are defined together"\r
+ + "with a preset (-r), ignoring preset! ");\r
+ }\r
+ if (customOptions != null) {\r
+ jobId = foldws.customFold(alignment, customOptions);\r
+ } else if (preset != null) {\r
+ jobId = foldws.presetFold(alignment, preset);\r
+ } else {\r
+ jobId = foldws.fold(alignment);\r
+ }\r
+ System.out.println("\n\ncalling fold.........");\r
+ Thread.sleep(1000);\r
+ rnastruct = foldws.getResult(jobId);\r
+ \r
+ } catch (IOException e) {\r
+ System.err.println("Exception while reading the input file. Exception details: ");\r
+ e.printStackTrace();\r
+ } catch (UnknownFileFormatException e) {\r
+ System.err.println("Exception while reading input file. Doesnt look like a Clustal format file");\r
+ e.printStackTrace();\r
+ } catch (JobSubmissionException e) {\r
+ System.err.println("Exception while submitting job to the web server. ");\r
+ e.printStackTrace();\r
+ } catch (ResultNotAvailableException e) {\r
+ System.err.println("Exception while waiting for results. Exception details: ");\r
+ e.printStackTrace();\r
+ } catch (InterruptedException ignored) {\r
+ // ignore and propagate an interruption\r
+ Thread.currentThread().interrupt();\r
+ } catch (WrongParameterException e) {\r
+ e.printStackTrace();\r
+ } finally {\r
+ if (instream != null) {\r
+ try {\r
+ instream.close();\r
+ } catch (IOException ignored) {\r
+ // ignore\r
+ }\r
+ }\r
+ }\r
+ return rnastruct;\r
+ }\r
+ \r