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