- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param result DOCUMENT ME!\r
- * @param out DOCUMENT ME!\r
- * @param align DOCUMENT ME!\r
- */\r
- void ReadUniprotFile(String[] result, RandomAccessFile out, AlignmentI align)\r
- {\r
- SequenceI sequence = null;\r
- Vector features = null;\r
- String type;\r
- String description;\r
- String status;\r
- String start;\r
- String end;\r
- String pdb = null;\r
-\r
- for (int r = 0; r < result.length; r++)\r
- {\r
- if ((sequence == null) && (result[r].indexOf("<name>") > -1))\r
- {\r
- long filePointer = 0;\r
-\r
- if (out != null)\r
- {\r
- try\r
- {\r
- filePointer = out.getFilePointer();\r
- out.writeBytes("<entry>\n");\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- String seqName = parseElement(result[r], "<name>", out);\r
- sequence = align.findName(seqName);\r
-\r
- if (sequence == null)\r
- {\r
- sequence = align.findName(seqName.substring(0,\r
- seqName.indexOf('_')));\r
-\r
- if (sequence != null)\r
- {\r
- sbuffer.append("changing " + sequence.getName() +\r
- " to " + seqName + "\n");\r
- sequence.setName(seqName);\r
- }\r
- }\r
-\r
- if (sequence == null)\r
- {\r
- sbuffer.append("UNIPROT updated suggestion is " +\r
- result[r] + "\n");\r
- sequence = align.findName(result[r]);\r
-\r
- // this entry has been suggested by ebi.\r
- // doesn't match id in alignment file\r
- try\r
- {\r
- out.setLength(filePointer);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- // now skip to next entry\r
- while (result[r].indexOf("</entry>") == -1)\r
- r++;\r
- }\r
-\r
- features = new Vector();\r
- type = "";\r
- start = "0";\r
- end = "0";\r
- description = "";\r
- status = "";\r
- pdb = "";\r
- }\r