*/
public class IdentifyFile
{
- public static final String FeaturesFile = "GFF or Jalview features";
-
/**
* Identify a datasource's file content.
*
// preserves original behaviour prior to version 2.3
}
+ public FileFormatI identify(AlignmentFileReaderI file, boolean closeSource)
+ throws IOException
+ {
+ FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType());
+ return identify(fp, closeSource);
+ }
+
/**
* Identify contents of source, closing it or resetting source to start
* afterwards.
}
int lessThan = data.indexOf("<");
if ((lessThan > -1)) // possible Markup Language data i.e HTML,
- // RNAML, XML
+ // RNAML, XML
{
String upper = data.toUpperCase();
if (upper.substring(lessThan).startsWith("<HTML"))
.println("File Identification failed! - Empty file was read.");
throw new FileFormatException("EMPTY DATA FILE");
}
+ System.out.println("File format identified as " + reply.toString());
return reply;
}
}
/**
- * Returns true if the data has at least 6 tab-delimited fields _and_
- * fields 4 and 5 are integer (start/end)
+ * Returns true if the data has at least 6 tab-delimited fields _and_ fields 4
+ * and 5 are integer (start/end)
+ *
* @param data
* @return
*/
return false;
}
String[] columns = data.split("\t");
- if (columns.length < 6) {
+ if (columns.length < 6)
+ {
return false;
}
for (int col = 3; col < 5; col++)
{
- try {
+ try
+ {
Integer.parseInt(columns[col]);
- } catch (NumberFormatException e) {
+ } catch (NumberFormatException e)
+ {
return false;
}
}