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paolopavanpaolopavan
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Changed logger to slf4j
1 parent f059f0e commit 9cbd9ee

3 files changed

Lines changed: 14 additions & 13 deletions

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‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/Hsp.java‎

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,8 +2,6 @@
22

33
import java.util.ArrayList;
44
import java.util.List;
5-
import java.util.logging.Level;
6-
import java.util.logging.Logger;
75
import org.biojava.nbio.core.alignment.SimpleAlignedSequence;
86
import org.biojava.nbio.core.alignment.SimpleSequencePair;
97
import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
@@ -16,6 +14,8 @@
1614
import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
1715
import org.biojava.nbio.core.sequence.template.Compound;
1816
import org.biojava.nbio.core.sequence.template.Sequence;
17+
import org.slf4j.Logger;
18+
import org.slf4j.LoggerFactory;
1919

2020
/**
2121
* This class models a search Hsp.
@@ -30,6 +30,7 @@
3030
*/
3131

3232
public abstract class Hsp <S extends Sequence<C>, C extends Compound> {
33+
private static final Logger logger = LoggerFactory.getLogger(Hsp.class);
3334
private Integer hspNum;
3435
private Double hspBitScore;
3536
private Integer hspScore;
@@ -118,7 +119,7 @@ else if (sequenceString.matches("^[ACUG]+$"))
118119
else
119120
returnSeq = new ProteinSequence(sequenceString, AminoAcidCompoundSet.getAminoAcidCompoundSet());
120121
} catch (CompoundNotFoundException ex) {
121-
Logger.getLogger(Hsp.class.getName()).log(Level.SEVERE, null, ex);
122+
logger.error("Unexpected error, could not find compound when creating Sequence object from Hsp", ex);
122123
}
123124
return returnSeq;
124125
}

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastTabularParser.java‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -41,6 +41,7 @@ private enum PARSING_CONSISTENCY {
4141
}
4242
private static final Logger log = Logger.getLogger(BlastTabularParser.class.getName());
4343

44+
4445
private File targetFile;
4546
private int fileLinesCount;
4647
private PARSING_CONSISTENCY parsingConsistency = PARSING_CONSISTENCY.IMPROVED;

‎biojava-core/src/main/java/org/biojava/nbio/core/search/io/blast/BlastXMLParser.java‎

Lines changed: 9 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -12,12 +12,11 @@
1212
import java.util.HashMap;
1313
import java.util.List;
1414
import java.util.Map;
15-
import java.util.logging.Level;
16-
import java.util.logging.Logger;
1715
import javax.xml.parsers.ParserConfigurationException;
1816
import javax.xml.xpath.XPathException;
1917
import org.biojava.nbio.core.sequence.template.Sequence;
2018
import org.biojava.nbio.core.util.XMLHelper;
19+
import org.slf4j.LoggerFactory;
2120
import org.w3c.dom.Document;
2221
import org.w3c.dom.Element;
2322
import org.xml.sax.SAXException;
@@ -34,7 +33,7 @@
3433
* @author Paolo Pavan
3534
*/
3635
public class BlastXMLParser implements ResultFactory {
37-
private static final Logger log = Logger.getLogger(BlastXMLParser.class.getName());
36+
private static final org.slf4j.Logger logger = LoggerFactory.getLogger(Hsp.class);
3837
Document blastDoc = null;
3938
private File targetFile;
4039
private List<Sequence> queryReferences, databaseReferences;
@@ -48,17 +47,17 @@ public void setFile(File f){
4847
}
4948

5049
private void readFile(String blastFile) throws IOException, ParseException{
51-
log.info("Start reading " + blastFile);
50+
logger.info("Start reading " + blastFile);
5251
try {
5352
blastDoc = XMLHelper.loadXML(blastFile);
5453
} catch (SAXException ex) {
55-
Logger.getLogger(BlastXMLParser.class.getName()).log(Level.SEVERE, null, ex);
54+
logger.error("A parsing error has occurred while reading XML blast file");
5655
throw new ParseException(ex.getMessage(),0);
5756
} catch (ParserConfigurationException ex) {
58-
Logger.getLogger(BlastXMLParser.class.getName()).log(Level.SEVERE, null, ex);
57+
logger.error("Internal XML parser non properly configured");
5958
throw new ParseException(ex.getMessage(),0);
6059
}
61-
log.info("Read finished");
60+
logger.info("Read finished");
6261
}
6362

6463
public List<Result> createObjects(double maxEScore) throws IOException, ParseException {
@@ -80,9 +79,9 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
8079
String reference = XMLHelper.selectSingleElement(blastDoc.getDocumentElement(),"BlastOutput_reference").getTextContent();
8180
String dbFile = XMLHelper.selectSingleElement(blastDoc.getDocumentElement(),"BlastOutput_db").getTextContent();
8281

83-
log.info("Query for hits in "+ targetFile);
82+
logger.info("Query for hits in "+ targetFile);
8483
ArrayList<Element> IterationsList = XMLHelper.selectElements(blastDoc.getDocumentElement(), "BlastOutput_iterations/Iteration[Iteration_hits]");
85-
log.info(IterationsList.size() + " results");
84+
logger.info(IterationsList.size() + " results");
8685

8786
resultsCollection = new ArrayList();
8887
for (Element element : IterationsList) {
@@ -167,7 +166,7 @@ public List<Result> createObjects(double maxEScore) throws IOException, ParseExc
167166
} catch (XPathException e) {
168167
throw new ParseException(e.getMessage(),0);
169168
}
170-
log.info("Parsing of "+targetFile+" finished.");
169+
logger.info("Parsing of "+targetFile+" finished.");
171170

172171
return resultsCollection;
173172
}

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