import jalview.schemes.*;\r
\r
/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
+ * Parse and create Jalview Features files\r
+ * Detects GFF format features files and parses.\r
+ * Does not implement standard print() - call specific printFeatures or printGFF.\r
+ * Uses AlignmentI.findSequence(String id) to find the sequence object for the features annotation - this normally works on an exact match.\r
+ * @author AMW\r
* @version $Revision$\r
*/\r
public class FeaturesFile\r
{\r
desc = st.nextToken();\r
type = st.nextToken();\r
+ try {\r
start = Integer.parseInt(st.nextToken());\r
- end = Integer.parseInt(st.nextToken());\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ start=0;\r
+ }\r
+ try {\r
+ end = Integer.parseInt(st.nextToken());\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {\r
+ end=-1;\r
+ } \r
try\r
{\r
score = new Float(st.nextToken()).floatValue();\r
{\r
System.out.println(line);\r
System.out.println("Error parsing feature file: " + ex + "\n" + line);\r
+ ex.printStackTrace(System.err);\r
return false;\r
}\r
\r