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Merged
josemduarte merged 2 commits into from
Jun 2, 2017
Merged

Fix for #663 #666

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5e52308
Fix for #663 and some code cleanup.
psoares May 31, 2017
5e4eb1d
Removed unused import.
psoares May 31, 2017
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66 changes: 42 additions & 24 deletions biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,8 @@
import org.biojava.nbio.core.sequence.io.template.SequenceHeaderParserInterface;
import org.biojava.nbio.core.sequence.template.AbstractSequence;
import org.biojava.nbio.core.sequence.template.Compound;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.*;
import java.util.ArrayList;
Expand All @@ -55,20 +57,28 @@ public class GenbankReader<S extends AbstractSequence<C>, C extends Compound> {

private SequenceCreatorInterface<C> sequenceCreator;
private GenbankSequenceParser<S,C> genbankParser;
private InputStream inputStream;
private BufferedReader bufferedReader;
private boolean closed;
private final Logger logger = LoggerFactory.getLogger(this.getClass());

public boolean isClosed() {
return closed;
}

/**
* If you are going to use FileProxyProteinSequenceCreator then do not use this constructor because we need details about
* local file offsets for quick reads. InputStreams does not give you the name of the stream to access quickly via file seek. A seek in
* an inputstream is forced to read all the data so you don't gain anything.
* @param br
* @param is
* @param headerParser
* @param sequenceCreator
*/
public GenbankReader(InputStream is, SequenceHeaderParserInterface<S,C> headerParser, SequenceCreatorInterface<C> sequenceCreator) {
public GenbankReader(final InputStream is, final SequenceHeaderParserInterface<S,C> headerParser,
final SequenceCreatorInterface<C> sequenceCreator) {
this.sequenceCreator = sequenceCreator;
this.inputStream = is;
genbankParser = new GenbankSequenceParser<S,C>();
bufferedReader = new BufferedReader(new InputStreamReader(is));
genbankParser = new GenbankSequenceParser<>();
closed = false;
}

/**
Expand All @@ -85,14 +95,14 @@ public GenbankReader(InputStream is, SequenceHeaderParserInterface<S,C> headerPa
* method denies read access to the file.
*/
public GenbankReader(
File file,
SequenceHeaderParserInterface<S,C> headerParser,
SequenceCreatorInterface<C> sequenceCreator
final File file,
final SequenceHeaderParserInterface<S,C> headerParser,
final SequenceCreatorInterface<C> sequenceCreator
) throws FileNotFoundException {

inputStream = new FileInputStream(file);
this.bufferedReader = new BufferedReader(new FileReader(file));
this.sequenceCreator = sequenceCreator;
genbankParser = new GenbankSequenceParser<S,C>();
genbankParser = new GenbankSequenceParser<>();
}

/**
Expand All @@ -108,8 +118,7 @@ public GenbankReader(
* @throws CompoundNotFoundException
*/
public LinkedHashMap<String,S> process() throws IOException, CompoundNotFoundException {
LinkedHashMap<String,S> sequences = process(-1);
return sequences;
return process(-1);
}

/**
Expand All @@ -122,7 +131,7 @@ public LinkedHashMap<String,S> process() throws IOException, CompoundNotFoundExc
* time before the first result is available.<br>
* <b>N.B.</b>
* <ul>
* <li>This method ca't be called after calling its NO-ARGUMENT twin.</li>
* <li>This method can't be called after calling its NO-ARGUMENT twin.</li>
* <li>remember to close the underlying resource when you are done.</li>
* </ul>
* @see #process()
Expand All @@ -134,17 +143,17 @@ public LinkedHashMap<String,S> process() throws IOException, CompoundNotFoundExc
* @throws IOException
* @throws CompoundNotFoundException
*/
public LinkedHashMap<String,S> process(int max) throws IOException, CompoundNotFoundException {
LinkedHashMap<String,S> sequences = new LinkedHashMap<String,S>();
public LinkedHashMap<String,S> process(final int max) throws IOException, CompoundNotFoundException {
LinkedHashMap<String,S> sequences = new LinkedHashMap<>();
@SuppressWarnings("unchecked")
int i=0;
BufferedReader br = new BufferedReader(new InputStreamReader(inputStream));
while(true) {
if(max>0 && i>=max) break;
i++;
String seqString = genbankParser.getSequence(br, 0);
String seqString = genbankParser.getSequence(bufferedReader, 0);
//reached end of file?
if(seqString==null) break;
@SuppressWarnings("unchecked")
S sequence = (S) sequenceCreator.getSequence(seqString, 0);
genbankParser.getSequenceHeaderParser().parseHeader(genbankParser.getHeader(), sequence);

Expand All @@ -165,32 +174,41 @@ public LinkedHashMap<String,S> process(int max) throws IOException, CompoundNotF

sequences.put(sequence.getAccession().getID(), sequence);
}
br.close();
close();

if (max < 0) {
close();
}

return sequences;
}

public void close() throws IOException {
inputStream.close();
public void close() {
try {
bufferedReader.close();
this.closed = true;
} catch (IOException e) {
logger.error("Couldn't close the reader. {}", e.getMessage());
this.closed = false;
}
}

public static void main(String[] args) throws Exception {
String proteinFile = "src/test/resources/BondFeature.gb";
FileInputStream is = new FileInputStream(proteinFile);

GenbankReader<ProteinSequence, AminoAcidCompound> proteinReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(is, new GenericGenbankHeaderParser<ProteinSequence,AminoAcidCompound>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
GenbankReader<ProteinSequence, AminoAcidCompound> proteinReader = new GenbankReader<>(is, new GenericGenbankHeaderParser<>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
LinkedHashMap<String,ProteinSequence> proteinSequences = proteinReader.process();
System.out.println(proteinSequences);

String inputFile = "src/test/resources/NM_000266.gb";
is = new FileInputStream(inputFile);
GenbankReader<DNASequence, NucleotideCompound> dnaReader = new GenbankReader<DNASequence, NucleotideCompound>(is, new GenericGenbankHeaderParser<DNASequence,NucleotideCompound>(), new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
GenbankReader<DNASequence, NucleotideCompound> dnaReader = new GenbankReader<>(is, new GenericGenbankHeaderParser<>(), new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
LinkedHashMap<String,DNASequence> dnaSequences = dnaReader.process();
System.out.println(dnaSequences);

String crazyFile = "src/test/resources/CraftedFeature.gb";
is = new FileInputStream(crazyFile);
GenbankReader<DNASequence, NucleotideCompound> crazyReader = new GenbankReader<DNASequence, NucleotideCompound>(is, new GenericGenbankHeaderParser<DNASequence,NucleotideCompound>(), new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
GenbankReader<DNASequence, NucleotideCompound> crazyReader = new GenbankReader<>(is, new GenericGenbankHeaderParser<>(), new DNASequenceCreator(DNACompoundSet.getDNACompoundSet()));
LinkedHashMap<String,DNASequence> crazyAnnotatedSequences = crazyReader.process();

is.close();
Expand Down
93 changes: 74 additions & 19 deletions biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankReaderTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,14 +20,14 @@
*/
package org.biojava.nbio.core.sequence.io;

import static org.junit.Assert.assertNotNull;

import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;

import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.DNASequence;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
Expand All @@ -46,10 +46,13 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import static org.junit.Assert.*;

/**
*
* @author Scooter Willis <willishf at gmail dot com>
* @author Jacek Grzebyta
* @author Philippe Soares
*/
public class GenbankReaderTest {

Expand Down Expand Up @@ -84,31 +87,83 @@ public void testProcess() throws Exception {
InputStream inStream = this.getClass().getResourceAsStream("/BondFeature.gb");
assertNotNull(inStream);

GenbankReader<ProteinSequence, AminoAcidCompound> GenbankProtein
= new GenbankReader<ProteinSequence, AminoAcidCompound>(
GenbankReader<ProteinSequence, AminoAcidCompound> genbankProtein
= new GenbankReader<>(
inStream,
new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
new GenericGenbankHeaderParser<>(),
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())
);
@SuppressWarnings("unused")
LinkedHashMap<String, ProteinSequence> proteinSequences = GenbankProtein.process();
inStream.close();

LinkedHashMap<String, ProteinSequence> proteinSequences = genbankProtein.process();

assertNotNull(proteinSequences);
assertEquals(1, proteinSequences.size());

ProteinSequence proteinSequence = proteinSequences.get("NP_000257");
assertNotNull(proteinSequences.get("NP_000257"));
assertEquals("NP_000257", proteinSequence.getAccession().getID());
assertEquals("4557789", proteinSequence.getAccession().getIdentifier());
assertEquals("GENBANK", proteinSequence.getAccession().getDataSource().name());
assertEquals(1, proteinSequence.getAccession().getVersion().intValue());
assertTrue(genbankProtein.isClosed());

logger.info("process DNA");
inStream = this.getClass().getResourceAsStream("/NM_000266.gb");
assertNotNull(inStream);

GenbankReader<DNASequence, NucleotideCompound> GenbankDNA
= new GenbankReader<DNASequence, NucleotideCompound>(
GenbankReader<DNASequence, NucleotideCompound> genbankDNA
= new GenbankReader<>(
inStream,
new GenericGenbankHeaderParser<DNASequence, NucleotideCompound>(),
new GenericGenbankHeaderParser<>(),
new DNASequenceCreator(DNACompoundSet.getDNACompoundSet())
);
@SuppressWarnings("unused")
LinkedHashMap<String, DNASequence> dnaSequences = GenbankDNA.process();
inStream.close();
LinkedHashMap<String, DNASequence> dnaSequences = genbankDNA.process();

assertNotNull(dnaSequences);
assertEquals(1, dnaSequences.size());

DNASequence dnaSequence = dnaSequences.get("NM_000266");
assertNotNull(dnaSequences.get("NM_000266"));
assertEquals("NM_000266", dnaSequence.getAccession().getID());
assertEquals("223671892", dnaSequence.getAccession().getIdentifier());
assertEquals("GENBANK", dnaSequence.getAccession().getDataSource().name());
assertEquals(3, dnaSequence.getAccession().getVersion().intValue());
assertTrue(genbankDNA.isClosed());
}

/**
* Test the process method with a number of sequences to be read at each call.
* The underlying {@link InputStream} should remain open until the last call.
*/
@Test
public void testPartialProcess() throws IOException, CompoundNotFoundException, NoSuchFieldException {
InputStream inStream = this.getClass().getResourceAsStream("/two-dnaseqs.gb");

GenbankReader<DNASequence, NucleotideCompound> genbankDNA
= new GenbankReader<>(
inStream,
new GenericGenbankHeaderParser<>(),
new DNASequenceCreator(DNACompoundSet.getDNACompoundSet())
);

// First call to process(1) returns the first sequence
LinkedHashMap<String, DNASequence> dnaSequences = genbankDNA.process(1);

assertNotNull(dnaSequences);
assertEquals(1, dnaSequences.size());
assertNotNull(dnaSequences.get("vPetite"));

// Second call to process(1) returns the second sequence
dnaSequences = genbankDNA.process(1);
assertNotNull(dnaSequences);
assertEquals(1, dnaSequences.size());
assertNotNull(dnaSequences.get("sbFDR"));

assertFalse(genbankDNA.isClosed());
genbankDNA.close();
assertTrue(genbankDNA.isClosed());

}

@Test
public void CDStest() throws Exception {
Expand All @@ -118,9 +173,9 @@ public void CDStest() throws Exception {
assertNotNull(inStream);

GenbankReader<ProteinSequence, AminoAcidCompound> GenbankProtein
= new GenbankReader<ProteinSequence, AminoAcidCompound>(
= new GenbankReader<>(
inStream,
new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
new GenericGenbankHeaderParser<>(),
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())
);
LinkedHashMap<String, ProteinSequence> proteinSequences = GenbankProtein.process();
Expand All @@ -130,7 +185,7 @@ public void CDStest() throws Exception {
Assert.assertTrue(proteinSequences.size() == 1);
logger.debug("protein sequences: {}", proteinSequences);

ProteinSequence protein = new ArrayList<ProteinSequence>(proteinSequences.values()).get(0);
ProteinSequence protein = new ArrayList<>(proteinSequences.values()).get(0);

FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound> cdsFeature = protein.getFeaturesByType("CDS").get(0);
String codedBy = cdsFeature.getQualifiers().get("coded_by").get(0).getValue();
Expand All @@ -139,8 +194,8 @@ public void CDStest() throws Exception {

Assert.assertNotNull(codedBy);
Assert.assertTrue(!codedBy.isEmpty());
Assert.assertEquals(codedBy, "NM_000266.2:503..904");
Assert.assertEquals(5, dbrefs.size());
assertEquals(codedBy, "NM_000266.2:503..904");
assertEquals(5, dbrefs.size());

}

Expand Down