/usr/share/doc/libbiojava-java-demos/examples/ssaha/SSAHASeqLarge.java is in libbiojava-java-demos 1:1.7.1-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | package ssaha;
import java.io.*;
import java.util.*;
import org.biojava.bio.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.program.ssaha.*;
public class SSAHASeqLarge {
public static void main(String[] args)
throws Throwable {
File dataStoreFile = new File(args[0]);
String seqStr = args[1];
final DataStore ds = new NIODataStoreFactory().getDataStore(
dataStoreFile
);
SearchListener listener = new HitMerger(
new ResultPrinter(ds),
20
);
//System.out.println("Searching:");
SymbolList symList = new SimpleSymbolList(
DNATools.getDNA().getTokenization("token"),
seqStr
);
ds.search("Sequence", symList, listener);
}
}
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