*/
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
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("HMMER3"))
+ {
+ reply = FileFormat.HMMER3;
+ break;
+ }
if (data.startsWith("H ") && !aaIndexHeaderRead)
{
aaIndexHeaderRead = true;
reply = FileFormat.Rnaml;
break;
}
+ if (upper.substring(lessThan).startsWith("<BSML"))
+ {
+ reply = FileFormat.BSML;
+ break;
+ }
}
if ((data.length() < 1) || (data.indexOf("#") == 0))
return true;
}
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
public static void main(String[] args)
{
for (int i = 0; args != null && i < args.length; i++)
}
}
+
}