+\r
+ private static boolean compareClustalLines(File input, String[] reference) {\r
+ BufferedReader reader = null;\r
+ boolean status = true;\r
+ try {\r
+ reader = new BufferedReader(new FileReader(input));\r
+ // only compare first four lines of the file with reference\r
+ // because the reference length is only 4 lines\r
+ int i = 0;\r
+ String line;\r
+ while (null != (line = reader.readLine())) {\r
+ if (!Util.isEmpty(line)) {\r
+ line = line.trim();\r
+ if (!line.equals(reference[i].trim())) {\r
+ status = false;\r
+ break;\r
+ }\r
+ ++i;\r
+ }\r
+ }\r
+ reader.close();\r
+ } catch (IOException ioe) {\r
+ log.warn(ioe, ioe.getCause());\r
+ } finally {\r
+ FileUtil.closeSilently(reader);\r
+ }\r
+ return status;\r
+ }\r