+ public String getAlignment(String format)\r
+ {\r
+ return getAlignment(format, "true");\r
+ }\r
+\r
+ public String getAlignment(String format, String suffix)\r
+ {\r
+ try\r
+ {\r
+ boolean seqlimits = suffix.equalsIgnoreCase("true");\r
+\r
+ String reply = new AppletFormatAdapter().formatSequences(format,\r
+ currentAlignFrame.viewport.getAlignment().getSequences(), seqlimits);\r
+ return reply;\r
+ }\r
+ catch (Exception ex)\r
+ {ex.printStackTrace();\r
+ return "Error retrieving alignment in " + format + " format. ";\r
+\r
+ }\r
+ }\r
+\r