GenbankReader#process(int max) closes the underlying InputStream #663
Description
I tried to use the GenbankReader to read a Genbank file. I wanted to do this through repeated calls to the version of the process method that takes a number of records as the only parameter.
After the first call, the underlying inputstream is closed and the second call fails.
Here is an example :
import org.biojava.nbio.core.sequence.DNASequence;
import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.biojava.nbio.core.sequence.io.FileProxyDNASequenceCreator;
import org.biojava.nbio.core.sequence.io.GenbankReader;
import org.biojava.nbio.core.sequence.io.GenbankSequenceParser;
import org.biojava.nbio.core.sequence.io.GenericGenbankHeaderParser;
import org.biojava.nbio.core.sequence.template.AbstractSequence;
import java.io.File;
import java.io.FileInputStream;
import java.io.InputStream;
import java.util.LinkedHashMap;
class TestGBReading {
public static void main(String[] args) {
File file = new File("/tmp/gbpat100.seq");
LinkedHashMap<String, DNASequence> sequences = null;
GenbankReader<DNASequence, NucleotideCompound> gbReader = null;
try {
gbReader =
new GenbankReader<DNASequence, NucleotideCompound>(
file,
new GenericGenbankHeaderParser<DNASequence, NucleotideCompound>(),
new FileProxyDNASequenceCreator(
file,
DNACompoundSet.getDNACompoundSet(),
new GenbankSequenceParser<AbstractSequence<NucleotideCompound>,
NucleotideCompound>()
)
);
sequences = gbReader.process(10);
System.out.println("Reading first 10");
for (DNASequence seq : sequences.values()) {
System.out.println(" - " + seq.getAccession());
}
sequences = gbReader.process(10);
System.out.println("Reading next 10");
for (DNASequence seq : sequences.values()) {
System.out.println(" - " + seq.getAccession());
}
} catch (Exception e) {
e.printStackTrace();
}
}
}```