al.setProperty(key,value);\r
}\r
}\r
+\r
+ /**\r
+ * Write annotations as a CSV file of the form 'label, value, value, ...' for each row.\r
+ * @param annotations\r
+ * @return CSV file as a string.\r
+ */\r
+ public String printCSVAnnotations(AlignmentAnnotation[] annotations)\r
+ {\r
+ StringBuffer sp = new StringBuffer();\r
+ for (int i=0; i<annotations.length; i++)\r
+ {\r
+ String atos = annotations[i].toString();\r
+ int p = 0;\r
+ do {\r
+ int cp = atos.indexOf("\n", p);\r
+ sp.append(annotations[i].label);\r
+ sp.append(",");\r
+ if (cp>p)\r
+ {\r
+ sp.append(atos.substring(p, cp+1));\r
+ } else {\r
+ sp.append(atos.substring(p));\r
+ sp.append("\n");\r
+ }\r
+ p = cp+1;\r
+ } while (p>0);\r
+ }\r
+ return sp.toString();\r
+ }\r
}\r