*/
package jalview.io;
-import java.io.IOException;
import java.util.Locale;
+import java.io.File;
+import java.io.IOException;
+
/**
* DOCUMENT ME!
*
*/
public class IdentifyFile
{
+
+ public FileFormatI identify(Object file, DataSourceType protocol)
+ throws FileFormatException
+ {
+ // BH 2018
+ return (file instanceof File ? identify((File) file, protocol)
+ : identify((String) file, protocol));
+
+ }
+
+ public FileFormatI identify(File file, DataSourceType sourceType)
+ throws FileFormatException
+ {
+ // BH 2018
+ String emessage = "UNIDENTIFIED FILE PARSING ERROR";
+ FileParse parser = null;
+ try
+ {
+ parser = new FileParse(file, sourceType);
+ if (parser.isValid())
+ {
+ return identify(parser);
+ }
+ } catch (Exception e)
+ {
+ System.err.println("Error whilst identifying " + file);
+ e.printStackTrace(System.err);
+ emessage = e.getMessage();
+ }
+ if (parser != null)
+ {
+ throw new FileFormatException(parser.errormessage);
+ }
+ throw new FileFormatException(emessage);
+ }
+
/**
* Identify a datasource's file content.
*
}
} catch (Exception e)
{
- System.err.println("Error whilst identifying");
+ System.err.println("Error whilst identifying " + file);
e.printStackTrace(System.err);
emessage = e.getMessage();
}
if (source.inFile != null)
{
String fileStr = source.inFile.getName();
- // possibly a Jalview archive.
- if (fileStr.lastIndexOf(".jar") > -1
- || fileStr.lastIndexOf(".zip") > -1)
+ if (fileStr.contains(".jar") || fileStr.contains(".zip")
+ || fileStr.contains(".jvp"))
{
+ // possibly a Jalview archive (but check further)
reply = FileFormat.Jalview;
}
}
if (!lineswereskipped && data.startsWith("PK"))
{
- reply = FileFormat.Jalview; // archive.
+ reply = FileFormat.Jalview; // archive
break;
}
}
reply = FileFormat.ScoreMatrix;
break;
}
+ if (data.startsWith("LOCUS"))
+ {
+ reply = FileFormat.GenBank;
+ break;
+ }
+ if (data.startsWith("ID "))
+ {
+ if (data.substring(2).trim().split(";").length == 7)
+ {
+ reply = FileFormat.Embl;
+ break;
+ }
+ }
if (data.startsWith("H ") && !aaIndexHeaderRead)
{
aaIndexHeaderRead = true;
reply = FileFormat.Phylip;
break;
}
- else
+ else if (!lineswereskipped && looksLikeJnetData(data))
{
- if (!lineswereskipped && looksLikeJnetData(data))
- {
reply = FileFormat.Jnet;
break;
- }
+
}
+ else // phylogenetic file
+ {
+ String identifier = data.toLowerCase();
+ String secondLine = source.nextLine().toLowerCase();
+ if (identifier.startsWith("<phyloxml")
+ || secondLine.startsWith("<phyloxml"))
+ {
+ reply = FileFormat.PhyloXML;
+ break;
+ }
+ // commented out, nexus parser is troublesome
+ // else if (((identifier.startsWith("nexus"))
+ // || (identifier.startsWith("#nexus"))
+ // || (identifier.startsWith("# nexus"))
+ // || (identifier.startsWith("begin"))))
+ // {
+ // reply = FileFormat.Nexus;
+ // break;
+ // }
+ }
lineswereskipped = true; // this means there was some junk before any
// key file signature
}
return true;
}
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
public static void main(String[] args)
{
for (int i = 0; args != null && i < args.length; i++)
System.err.println("Usage: <Filename> [<Filename> ...]");
}
}
+
}