+ /*\r
+ * delete intervals in scontigs which are not translated.\r
+ * 1. map skip into sequence position intervals\r
+ * 2. truncate existing ranges and add new ranges to exclude untranslated regions.\r
+ if (skip.size()>0)\r
+ {\r
+ Vector narange = new Vector();\r
+ for (vc=0; vc<scontigs.length; vc++)\r
+ {\r
+ narange.addElement(new int[] {scontigs[vc]});\r
+ }\r
+ int sint=0,iv[];\r
+ vc = 0;\r
+ while (sint<skip.size())\r
+ {\r
+ skipint = (int[]) skip.elementAt(sint);\r
+ do {\r
+ iv = (int[]) narange.elementAt(vc);\r
+ if (iv[0]>=skipint[0] && iv[0]<=skipint[1])\r
+ {\r
+ if (iv[0]==skipint[0])\r
+ {\r
+ // delete beginning of range\r
+ } else {\r
+ // truncate range and create new one if necessary\r
+ iv = (int[]) narange.elementAt(vc+1);\r
+ if (iv[0]<=skipint[1])\r
+ {\r
+ // truncate range\r
+ iv[0] = skipint[1];\r
+ } else {\r
+ \r
+ }\r
+ }\r
+ } else\r
+ if (iv[0]<skipint[0])\r
+ {\r
+ iv = (int[]) narange.elementAt(vc+1);\r
+ }\r
+ } while (iv[0])\r
+ }\r
+ }*/\r