- public static SequenceI[] readFile(String inFile, String type, String format) {\r
- try {\r
- AlignFile afile = null;\r
-\r
- if (format.equals("FASTA")) {\r
- afile = new FastaFile(inFile, type);\r
- } else if (format.equals("MSF")) {\r
- afile = new MSFfile(inFile, type);\r
- } else if (format.equals("PileUp")) {\r
- afile = new PileUpfile(inFile, type);\r
- } else if (format.equals("CLUSTAL")) {\r
- afile = new ClustalFile(inFile, type);\r
- } else if (format.equals("BLC")) {\r
- afile = new BLCFile(inFile, type);\r
- } else if (format.equals("PIR")) {\r
- afile = new PIRFile(inFile, type);\r
- } else if (format.equals("PFAM")) {\r
- afile = new PfamFile(inFile, type);\r
- }\r
-\r
- return afile.getSeqsAsArray();\r
- } catch (Exception e) {\r
- System.err.println("Failed to read alignment using the '" + format +\r
- "' reader.");\r
- e.printStackTrace();\r
- }\r
-\r
- return null;\r
+ return formatSequences(format, seqs);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param format DOCUMENT ME!\r
+ * @param seqs DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String formatSequences(String format,\r
+ SequenceI[] seqs)\r
+ {\r
+\r
+ try\r
+ {\r
+ AlignFile afile = null;\r
+\r
+ if (format.equalsIgnoreCase("FASTA"))\r
+ {\r
+ afile = new FastaFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("FASTA_JVSUFFIX", true));\r
+ }\r
+ else if (format.equalsIgnoreCase("MSF"))\r
+ {\r
+ afile = new MSFfile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("MSF_JVSUFFIX", true));\r
+ }\r
+ else if (format.equalsIgnoreCase("PileUp"))\r
+ {\r
+ afile = new PileUpfile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PILEUP_JVSUFFIX", true));\r
+ }\r
+ else if (format.equalsIgnoreCase("CLUSTAL"))\r
+ {\r
+ afile = new ClustalFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("CLUSTAL_JVSUFFIX", true));\r
+ }\r
+ else if (format.equalsIgnoreCase("BLC"))\r
+ {\r
+ afile = new BLCFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("BLC_JVSUFFIX", true));\r
+ }\r
+ else if (format.equalsIgnoreCase("PIR"))\r
+ {\r
+ afile = new PIRFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PIR_JVSUFFIX", true));\r
+ }\r
+ else if (format.equalsIgnoreCase("PFAM"))\r
+ {\r
+ afile = new PfamFile();\r
+ afile.addJVSuffix(\r
+ jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));\r
+ }\r
+\r
+ afile.setSeqs(seqs);\r
+\r
+ return afile.print();\r