Vector headers;\r
long start;\r
long end;\r
+ boolean jvSuffix = true;\r
\r
/**\r
* Creates a new AlignFile object.\r
* Print out in alignment file format the Sequences in the seqs Vector.\r
*/\r
public abstract String print();\r
+\r
+ public void addJVSuffix(boolean b)\r
+ {\r
+ jvSuffix = b;\r
+ }\r
+\r
+ /**\r
+ * A general parser for ids.\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
+ Sequence parseId(String id)\r
+ {\r
+ Sequence seq = null;\r
+ id = id.trim();\r
+ int space = id.indexOf(" ");\r
+ if(space>-1)\r
+ {\r
+ seq = new Sequence(id.substring(0, space),"");\r
+ seq.setDescription(id.substring(space+1));\r
+ }\r
+ else\r
+ {\r
+ seq = new Sequence(id, "");\r
+ }\r
+\r
+ return seq;\r
+ }\r
+\r
+ /**\r
+ * Creates the output id.\r
+ * Adds prefix Uniprot format source|id\r
+ * And suffix Jalview /start-end\r
+ *\r
+ * @String id Id to be parsed\r
+ */\r
+ String printId(SequenceI seq)\r
+ {\r
+ return seq.getDisplayId(jvSuffix);\r
+ }\r
+\r
}\r