- rt = Runtime.getRuntime();\r
- SeqInit(s1, s2, type);\r
+ SeqInit(s1, s1.getSequence(), s2, s2.getSequence(), type);\r
+ }\r
+\r
+ /**\r
+ * Creates a new AlignSeq object.\r
+ *\r
+ * @param s1 DOCUMENT ME!\r
+ * @param s2 DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ */\r
+ public AlignSeq(SequenceI s1,\r
+ String string1,\r
+ SequenceI s2,\r
+ String string2,\r
+ String type)\r
+ {\r
+ SeqInit(s1, string1, s2, string2, type);\r