- else\r
- return null;\r
- }\r
-\r
- public static SequenceI[] read(String format,String inStr) {\r
- if (FormatProperties.contains(format)) {\r
- AlignFile afile = FormatFactory.get(format,inStr);\r
- return afile.getSeqsAsArray();\r
- } else {\r
- // Should throw exception\r
- return null;\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ * @param format DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public static SequenceI[] readFile(String inFile, String type, String format)\r
+ {\r
+ try\r
+ {\r
+ AlignFile afile = null;\r
+\r
+ if (format.equals("FASTA"))\r
+ {\r
+ afile = new FastaFile(inFile, type);\r
+ }\r
+ else if (format.equals("MSF"))\r
+ {\r
+ afile = new MSFfile(inFile, type);\r
+ }\r
+ else if (format.equals("PileUp"))\r
+ {\r
+ afile = new PileUpfile(inFile, type);\r
+ }\r
+ else if (format.equals("CLUSTAL"))\r
+ {\r
+ afile = new ClustalFile(inFile, type);\r
+ }\r
+ else if (format.equals("BLC"))\r
+ {\r
+ afile = new BLCFile(inFile, type);\r
+ }\r
+ else if (format.equals("PIR"))\r
+ {\r
+ afile = new PIRFile(inFile, type);\r
+ }\r
+ else if (format.equals("PFAM"))\r
+ {\r
+ afile = new PfamFile(inFile, type);\r
+ }\r
+\r
+ return afile.getSeqsAsArray();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ System.err.println("Failed to read alignment using the '" + format +\r
+ "' reader.");\r
+ e.printStackTrace();\r
+ }\r
+\r
+ return null;\r