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andreasprlicandreasprlic
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removing external dependency on log4j
1 parent 5654954 commit 879949e

6 files changed

Lines changed: 70 additions & 43 deletions

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‎biojava3-structure/pom.xml‎

Lines changed: 6 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
<?xml version="1.0" encoding="UTF-8"?>
2-
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
2+
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
3+
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
34
<modelVersion>4.0.0</modelVersion>
45
<parent>
56
<artifactId>biojava</artifactId>
@@ -8,7 +9,7 @@
89
</parent>
910
<artifactId>biojava3-structure</artifactId>
1011
<name>biojava3-structure</name>
11-
<description>The protein structure modules of BioJava.</description>
12+
<description>The protein structure modules of BioJava.</description>
1213
<dependencies>
1314
<dependency>
1415
<groupId>junit</groupId>
@@ -27,21 +28,15 @@
2728
<version>3.0.8-SNAPSHOT</version>
2829
<scope>compile</scope>
2930
</dependency>
30-
31-
<dependency>
32-
<groupId>org.apache.logging.log4j</groupId>
33-
<artifactId>log4j-core</artifactId>
34-
<version>2.0-beta7</version>
35-
</dependency>
36-
37-
<!-- <dependency> <groupId>org.biojava</groupId> <artifactId>biojava3-core</artifactId>
38-
<version>3.0.3-SNAPSHOT</version> <scope>test</scope> </dependency> -->
3931
<dependency>
4032
<groupId>xmlunit</groupId>
4133
<artifactId>xmlunit</artifactId>
4234
<version>1.4</version>
35+
<scope>test</scope>
4336
</dependency>
37+
4438
</dependencies>
39+
4540
<properties>
4641
<jdk.version>1.6</jdk.version>
4742
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>

‎biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBDescriptionFactory.java‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -22,9 +22,9 @@
2222
import java.io.IOException;
2323
import java.io.InputStream;
2424
import java.net.URL;
25+
import java.util.logging.Level;
26+
import java.util.logging.Logger;
2527

26-
import org.apache.logging.log4j.LogManager;
27-
import org.apache.logging.log4j.Logger;
2828
import org.w3c.dom.Element;
2929
import org.w3c.dom.NodeList;
3030

@@ -54,7 +54,7 @@
5454
*/
5555
public class RCSBDescriptionFactory {
5656

57-
private static final Logger logger = LogManager.getLogger(RCSBDescriptionFactory.class.getPackage().getName());
57+
private static final Logger logger = Logger.getLogger(RCSBDescriptionFactory.class.getPackage().getName());
5858

5959
private static final String URL_STUB = "http://www.rcsb.org/pdb/rest/describeMol?structureId=";
6060

@@ -69,7 +69,7 @@ public static RCSBDescription get(InputStream stream) {
6969
try {
7070
data = ReadUtils.getNodes(stream);
7171
} catch (IOException e) {
72-
logger.error("Couldn't parse XML", e);
72+
logger.log(Level.WARNING,"Couldn't parse XML", e);
7373
return null;
7474
}
7575

@@ -112,7 +112,7 @@ public static RCSBDescription get(String pdbId) {
112112
URL url = new URL(URL_STUB + pdbId);
113113
is = url.openConnection().getInputStream();
114114
} catch (IOException e) {
115-
logger.error("Couldn't open connection", e);
115+
logger.log(Level.WARNING,"Couldn't open connection", e);
116116
return null;
117117
}
118118
return get(is);
@@ -173,7 +173,7 @@ private static void parseChains(RCSBPolymer polymer, String string) {
173173
if (part.length() == 1) {
174174
polymer.addChain(part.charAt(0));
175175
} else {
176-
logger.error("Chain id contained more than one character");
176+
logger.log(Level.WARNING,"Chain id contained more than one character");
177177
}
178178
}
179179
}

‎biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/RCSBLigandsFactory.java‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -24,9 +24,9 @@
2424
import java.net.URL;
2525
import java.util.ArrayList;
2626
import java.util.List;
27+
import java.util.logging.Level;
28+
import java.util.logging.Logger;
2729

28-
import org.apache.logging.log4j.LogManager;
29-
import org.apache.logging.log4j.Logger;
3030
import org.w3c.dom.Element;
3131
import org.w3c.dom.NodeList;
3232

@@ -58,7 +58,7 @@ public class RCSBLigandsFactory {
5858

5959
private static final String HET_URL_STUB = "http://www.pdb.org/pdb/rest/describeHet?chemicalID=";
6060

61-
private static final Logger logger = LogManager.getLogger(RCSBLigandsFactory.class.getPackage().getName());
61+
private static final Logger logger = Logger.getLogger(RCSBLigandsFactory.class.getPackage().getName());
6262

6363
private static final String PDB_URL_STUB = "http://www.pdb.org/pdb/rest/ligandInfo?structureId=";
6464

@@ -92,7 +92,7 @@ public static List<RCSBLigand> getFromHeteroAtomIds(InputStream stream) {
9292
try {
9393
data = ReadUtils.getNodes(stream);
9494
} catch (IOException e) {
95-
logger.error("Couldn't parse XML", e);
95+
logger.log(Level.WARNING,"Couldn't parse XML", e);
9696
return null;
9797
}
9898

@@ -153,7 +153,7 @@ public static List<RCSBLigand> getFromHeteroAtomIds(String... heteroAtomIds) {
153153
URL url = new URL(HET_URL_STUB + sb.toString());
154154
is = url.openConnection().getInputStream();
155155
} catch (IOException e) {
156-
logger.error("Couldn't open connection", e);
156+
logger.log(Level.WARNING,"Couldn't open connection", e);
157157
return null;
158158
}
159159
return getFromHeteroAtomIds(is);
@@ -170,7 +170,7 @@ public static RCSBLigands getFromPdbId(InputStream stream) {
170170
try {
171171
data = ReadUtils.getNodes(stream);
172172
} catch (IOException e) {
173-
logger.error("Couldn't parse XML", e);
173+
logger.log(Level.WARNING,"Couldn't parse XML", e);
174174
return null;
175175
}
176176

@@ -216,7 +216,7 @@ public static RCSBLigands getFromPdbId(String pdbId) {
216216
URL url = new URL(PDB_URL_STUB + pdbId);
217217
is = url.openConnection().getInputStream();
218218
} catch (IOException e) {
219-
logger.error("Couldn't open connection", e);
219+
logger.log(Level.WARNING,"Couldn't open connection", e);
220220
return null;
221221
}
222222
return getFromPdbId(is);
@@ -233,7 +233,7 @@ public static List<RCSBLigands> getFromPdbIds(InputStream stream) {
233233
try {
234234
dataaa = ReadUtils.getNodes(stream);
235235
} catch (IOException e) {
236-
logger.error("Couldn't parse XML", e);
236+
logger.log(Level.WARNING,"Couldn't parse XML", e);
237237
return null;
238238
}
239239

@@ -309,7 +309,7 @@ public static RCSBLigands getFromPdbIds(String pdbId) {
309309
URL url = new URL(PDB_URL_STUB + pdbId);
310310
is = url.openConnection().getInputStream();
311311
} catch (IOException e) {
312-
logger.error("Couldn't open connection", e);
312+
logger.log(Level.WARNING,"Couldn't open connection", e);
313313
return null;
314314
}
315315
return getFromPdbId(is);
@@ -332,7 +332,7 @@ public static List<RCSBLigands> getFromPdbIds(String... pdbIds) {
332332
URL url = new URL(PDB_URL_STUB + sb.toString());
333333
is = url.openConnection().getInputStream();
334334
} catch (IOException e) {
335-
logger.error("Couldn't open connection", e);
335+
logger.log(Level.WARNING,"Couldn't open connection", e);
336336
return null;
337337
}
338338
return getFromPdbIds(is);

‎biojava3-structure/src/main/java/org/biojava/bio/structure/rcsb/ReadUtils.java‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -26,13 +26,13 @@
2626

2727
import java.io.IOException;
2828
import java.io.InputStream;
29+
import java.util.logging.Level;
30+
import java.util.logging.Logger;
2931

3032
import javax.xml.parsers.DocumentBuilder;
3133
import javax.xml.parsers.DocumentBuilderFactory;
3234
import javax.xml.parsers.ParserConfigurationException;
3335

34-
import org.apache.logging.log4j.LogManager;
35-
import org.apache.logging.log4j.Logger;
3636
import org.w3c.dom.Document;
3737
import org.w3c.dom.Node;
3838
import org.w3c.dom.NodeList;
@@ -44,7 +44,7 @@
4444
*/
4545
public class ReadUtils {
4646

47-
private static final Logger logger = LogManager.getLogger(ReadUtils.class.getPackage().getName());
47+
private static final Logger logger = Logger.getLogger(ReadUtils.class.getPackage().getName());
4848

4949
// this IS needed
5050
private static boolean documentBuilderFactorySet = false;
@@ -76,15 +76,15 @@ static NodeList getNodes(InputStream stream) throws IOException {
7676
try {
7777
builder = builderFactory.newDocumentBuilder();
7878
} catch (ParserConfigurationException e) {
79-
logger.error("Couldn't configure parser", e);
79+
logger.log(Level.WARNING,"Couldn't configure parser", e);
8080
stream.close();
8181
throw new IOException(e);
8282
}
8383
try {
8484
document = builder.parse(stream);
8585
} catch (SAXException e) {
8686
System.out.println(e.getMessage());
87-
logger.error("Couldn't parse stream", e);
87+
logger.log(Level.WARNING,"Couldn't parse stream", e);
8888
stream.close();
8989
throw new IOException(e);
9090
}
@@ -97,7 +97,7 @@ static Double toDouble(String s) {
9797
try {
9898
return Double.parseDouble(s);
9999
} catch (NumberFormatException e) {
100-
logger.error(s + " is not a floating-point number", e);
100+
logger.log(Level.WARNING,s + " is not a floating-point number", e);
101101
}
102102
return null;
103103
}
@@ -107,7 +107,7 @@ static Integer toInt(String s) {
107107
try {
108108
return Integer.parseInt(s);
109109
} catch (NumberFormatException e) {
110-
logger.error(s + " is not an integer", e);
110+
logger.log(Level.WARNING,s + " is not an integer", e);
111111
}
112112
return null;
113113
}

‎biojava3-structure/src/main/java/org/biojava/bio/structure/scop/Astral.java‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -27,9 +27,9 @@
2727
import java.util.Map;
2828
import java.util.Set;
2929
import java.util.TreeSet;
30+
import java.util.logging.Level;
31+
import java.util.logging.Logger;
3032

31-
import org.apache.logging.log4j.LogManager;
32-
import org.apache.logging.log4j.Logger;
3333

3434
/**
3535
* Provides programmatic access to ASTRAL representative sets. See the paper by <a
@@ -99,7 +99,7 @@ public String toString() {
9999

100100
private static Map<String, SoftReference<Astral>> instances = new HashMap<String, SoftReference<Astral>>();
101101

102-
private static final Logger logger = LogManager.getLogger(Astral.class.getName());
102+
private static final Logger logger = Logger.getLogger(Astral.class.getName());
103103

104104
private Set<String> names;
105105

@@ -208,11 +208,11 @@ private void init(Reader reader) {
208208
String scopId = line.split("\\s")[0].substring(1);
209209
names.add(scopId);
210210
if (i % 1000 == 0) {
211-
logger.debug("Reading ASTRAL line for " + scopId);
211+
logger.log(Level.FINE,"Reading ASTRAL line for " + scopId);
212212
}
213213
i++;
214214
} catch (RuntimeException e) {
215-
logger.error("Couldn't read line " + line, e);
215+
logger.log(Level.WARNING,"Couldn't read line " + line, e);
216216
}
217217
}
218218
}
@@ -226,7 +226,7 @@ private void init(Reader reader) {
226226
try {
227227
br.close();
228228
} catch (IOException e) {
229-
logger.warn("Could not close stream", e);
229+
logger.log(Level.WARNING,"Could not close stream", e);
230230
}
231231
}
232232
}

‎biojava3-structure/src/test/java/org/biojava/bio/structure/TestAltLocs.java‎

Lines changed: 35 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@
88
import org.biojava.bio.structure.io.mmcif.chem.PolymerType;
99
import org.biojava.bio.structure.io.mmcif.chem.ResidueType;
1010
import org.biojava.bio.structure.io.mmcif.model.ChemComp;
11+
import org.biojava3.structure.StructureIO;
1112

1213
public class TestAltLocs extends TestCase {
1314

@@ -144,7 +145,7 @@ public void test1JXX(){
144145
for ( Group altGroup : g.getAltLocs() ) {
145146
ensureAllAtomsSameInsCode(altGroup);
146147
}
147-
148+
148149
} catch(Exception e){
149150
e.printStackTrace();
150151
fail(e.getMessage());
@@ -156,19 +157,50 @@ public void test1JXX(){
156157

157158
private void ensureAllAtomsSameInsCode(Group g) {
158159

159-
// System.out.println(String.format("Group size: %d", g.getAtoms().size()));
160+
// System.out.println(String.format("Group size: %d", g.getAtoms().size()));
160161

161162
Character defaultAltLoc = null;
162163
for (Atom atom : g.getAtoms()) {
163164
if ( defaultAltLoc == null) {
164165
defaultAltLoc = atom.getAltLoc();
165166
continue;
166167
}
167-
// System.out.print(atom.toPDB());
168+
// System.out.print(atom.toPDB());
168169
Character altLoc = atom.getAltLoc();
169170

170171
assertEquals(defaultAltLoc,altLoc);
171172
}
172173
}
173174

175+
public void test1AAC(){
176+
try {
177+
Structure s = StructureIO.getStructure("1AAC");
178+
179+
Chain a = s.getChainByPDB("A");
180+
181+
Group g = a.getGroupByPDB( ResidueNumber.fromString("27"));
182+
183+
System.out.println(g);
184+
for (Atom atom : g.getAtoms()) {
185+
System.out.print(atom.toPDB());
186+
}
187+
188+
189+
int pos = 0;
190+
for (Group alt: g.getAltLocs()) {
191+
pos++;
192+
System.out.println("altLoc: " + pos + " " + alt);
193+
for (Atom atom : alt.getAtoms()) {
194+
System.out.print(atom.toPDB());
195+
}
196+
}
197+
198+
} catch (Exception e){
199+
e.printStackTrace();
200+
fail(e.getMessage());
201+
}
202+
203+
204+
}
205+
174206
}

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