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paolopavanpaolopavan
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Completed procedure for SearchIO constructor with Factory guess. This will allow auto selection of the appropriate parser based on file extension. Tests added.
1 parent 24fab31 commit 9080b37

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4 files changed

+150
-69
lines changed

4 files changed

+150
-69
lines changed

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

Lines changed: 53 additions & 68 deletions
Original file line numberDiff line numberDiff line change
@@ -7,18 +7,20 @@
77
package org.biojava.nbio.core.search.io;
88

99
import java.io.File;
10-
import java.net.URL;
11-
import java.util.ArrayList;
1210
import java.util.HashMap;
1311
import java.util.Iterator;
1412
import java.util.List;
13+
import java.util.ServiceLoader;
1514

1615
/**
1716
*
1817
* @author pavanpa
1918
*/
2019
public class SearchIO implements Iterable<Result>{
21-
private HashMap<String,ResultFactory> extensionFactoryAssociation;
20+
static private HashMap<String,ResultFactory> extensionFactoryAssociation;
21+
22+
private ResultFactory factory;
23+
private File file;
2224

2325
/**
2426
* this threshold applies in retrieving hsp. Those having e-value below this
@@ -31,32 +33,68 @@ public class SearchIO implements Iterable<Result>{
3133
*/
3234
private List<Result> results;
3335

34-
private final String NOT_SUPPORTED_FILE_EXCEPTION = "This extension is not associated with any parser.";
36+
private final String NOT_SUPPORTED_FILE_EXCEPTION =
37+
"This extension is not associated with any parser. You can try to specify a ResultFactory object.";
3538

39+
/**
40+
* Build a SearchIO reader and tries to select the appropriate parser inspecting
41+
* file extension.
42+
*
43+
* @param f
44+
* @throws Exception
45+
*/
3646
public SearchIO (File f) throws Exception{
37-
//this(f,getFactory(f));
47+
factory = guessFactory(f);
48+
file = f;
49+
process();
3850
}
3951

52+
/**
53+
* Build a SearchIO reader and specify a ResultFactory object to be used
54+
* for parsing
55+
*
56+
* @param f
57+
* @param factory
58+
* @throws Exception
59+
*/
4060
public SearchIO (File f, ResultFactory factory) throws Exception{
41-
factory.setFile(f);
42-
results = factory.createObjects(evalueThreshold);
61+
file = f;
62+
this.factory = factory;
63+
process();
4364
}
44-
65+
/**
66+
* Build a SearchIO reader, specify a ResultFactory object to be used for parsing
67+
* and filter hsp retrieved by a e-value threshold.
68+
* This usually increase parsing speed
69+
* @param f
70+
* @param factory
71+
* @param maxEvalue
72+
* @throws Exception
73+
*/
4574
public SearchIO(File f, ResultFactory factory, double maxEvalue) throws Exception{
75+
file = f;
76+
this.factory = factory;
4677
this.evalueThreshold = maxEvalue;
47-
factory.setFile(f);
78+
process();
79+
}
80+
81+
private void process() throws Exception {
82+
factory.setFile(file);
4883
results = factory.createObjects(evalueThreshold);
4984
}
5085

5186
private ResultFactory guessFactory(File f){
52-
List<Class<?>> classes = FactoryLoader.find("Bio.SearchIO.ConcreteFactories");
53-
87+
if (extensionFactoryAssociation == null){
88+
extensionFactoryAssociation = new HashMap<String, ResultFactory>();
89+
ServiceLoader<ResultFactory> impl = ServiceLoader.load(ResultFactory.class);
90+
for (ResultFactory loadedImpl : impl) {
91+
List<String> fileExtensions = loadedImpl.getFileExtensions();
92+
for (String ext: fileExtensions) extensionFactoryAssociation.put(ext, loadedImpl);
93+
}
94+
}
95+
5496
String filename = f.getAbsolutePath();
5597
int extensionPos = filename.lastIndexOf(".");
56-
/*
57-
int lastSeparator = indexOfLastSeparator(filename);
58-
return (lastSeparator > extensionPos ? -1 : extensionPos);
59-
*/
6098
String extension = filename.substring(extensionPos + 1);
6199
if (extensionFactoryAssociation.get(extension) == null)
62100
throw new UnsupportedOperationException(NOT_SUPPORTED_FILE_EXCEPTION
@@ -89,57 +127,4 @@ public void remove() {
89127
}
90128
};
91129
}
92-
93-
94-
95-
96130
}
97-
/**
98-
* da :
99-
* http://stackoverflow.com/questions/15519626/how-to-get-all-classes-names-in-a-package
100-
* @author pavanpa
101-
*/
102-
class FactoryLoader {
103-
private static final char DOT = '.';
104-
105-
private static final char SLASH = '/';
106-
107-
private static final String CLASS_SUFFIX = ".class";
108-
109-
private static final String BAD_PACKAGE_ERROR = "Unable to get resources from path '%s'. Are you sure the package '%s' exists?";
110-
111-
public static List<Class<?>> find(String scannedPackage) {
112-
String scannedPath = scannedPackage.replace(DOT, SLASH);
113-
URL scannedUrl = Thread.currentThread().getContextClassLoader().getResource(scannedPath);
114-
115-
if (scannedUrl == null) {
116-
throw new IllegalArgumentException(String.format(BAD_PACKAGE_ERROR, scannedPath, scannedPackage));
117-
}
118-
File scannedDir = new File(scannedUrl.getFile());
119-
List<Class<?>> classes = new ArrayList<Class<?>>();
120-
for (File file : scannedDir.listFiles()) {
121-
classes.addAll(find(file, scannedPackage));
122-
}
123-
return classes;
124-
}
125-
126-
private static List<Class<?>> find(File file, String scannedPackage) {
127-
List<Class<?>> classes = new ArrayList<Class<?>>();
128-
String resource = scannedPackage + DOT + file.getName();
129-
if (file.isDirectory()) {
130-
for (File child : file.listFiles()) {
131-
classes.addAll(find(child, resource));
132-
}
133-
} else if (resource.endsWith(CLASS_SUFFIX)) {
134-
int endIndex = resource.length() - CLASS_SUFFIX.length();
135-
String className = resource.substring(0, endIndex);
136-
try {
137-
classes.add(Class.forName(className));
138-
} catch (ClassNotFoundException ignore) {
139-
}
140-
}
141-
return classes;
142-
}
143-
144-
}
145-

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

Lines changed: 4 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -68,7 +68,10 @@ private enum PARSING_CONSISTENCY {
6868

6969
@Override
7070
public List<String> getFileExtensions() {
71-
throw new UnsupportedOperationException("Not supported yet."); //To change body of generated methods, choose Tools | Templates.
71+
List l = new ArrayList();
72+
l.add("blasttabular");
73+
l.add("blasttxt");
74+
return l;
7275
}
7376

7477
@Override

‎biojava-core/src/main/resources/META-INF/services/org.biojava.nbio.core.search.io.ResultFactory‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,2 @@
1+
org.biojava.nbio.core.search.io.blast.BlastXMLQuery
2+
org.biojava.nbio.core.search.io.blast.BlastTabularParser

‎biojava-core/src/test/java/org/biojava/nbio/core/search/io/SearchIOTest.java‎

Lines changed: 91 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,91 @@
1+
/*
2+
* To change this license header, choose License Headers in Project Properties.
3+
* To change this template file, choose Tools | Templates
4+
* and open the template in the editor.
5+
*/
6+
package org.biojava.nbio.core.search.io;
7+
8+
import java.io.File;
9+
import java.net.URL;
10+
import java.util.Iterator;
11+
import org.biojava.nbio.core.search.io.blast.BlastXMLQuery;
12+
import org.junit.After;
13+
import org.junit.AfterClass;
14+
import org.junit.Before;
15+
import org.junit.BeforeClass;
16+
import org.junit.Test;
17+
import static org.junit.Assert.*;
18+
import org.junit.Ignore;
19+
20+
/**
21+
*
22+
* @author pavanpa
23+
*/
24+
public class SearchIOTest {
25+
26+
public SearchIOTest() {
27+
}
28+
29+
@BeforeClass
30+
public static void setUpClass() {
31+
}
32+
33+
@AfterClass
34+
public static void tearDownClass() {
35+
}
36+
37+
@Before
38+
public void setUp() {
39+
}
40+
41+
@After
42+
public void tearDown() {
43+
}
44+
45+
@Test
46+
public void testConstructorWithFactoryGuess() {
47+
System.out.println("Constructor test with GuessFactory");
48+
String resource = "/org/biojava/nbio/core/search/io/blast/test.two-query.blasttxt";
49+
URL resourceURL = getClass().getResource(resource);
50+
File file = new File(resourceURL.getFile());
51+
52+
final SearchIO instance;
53+
try {
54+
instance = new SearchIO(file);
55+
} catch (Exception e) {
56+
fail("test failed:\n"+e.getMessage());
57+
}
58+
}
59+
60+
@Test
61+
public void testConstructorWithoutFactoryGuess() {
62+
System.out.println("Constructor test specifying Factory");
63+
String resource = "/org/biojava/nbio/core/search/io/blast/testBlastReport.xml";
64+
URL resourceURL = getClass().getResource(resource);
65+
File file = new File(resourceURL.getFile());
66+
67+
ResultFactory blastResultFactory = new BlastXMLQuery();
68+
final SearchIO instance;
69+
try {
70+
instance = new SearchIO(file, blastResultFactory);
71+
} catch (Exception e) {
72+
fail("test failed:\n"+e.getMessage());
73+
}
74+
}
75+
76+
@Test
77+
public void testConstructorWithEvalueHspFilter() {
78+
System.out.println("Constructor test specifying Factory");
79+
String resource = "/org/biojava/nbio/core/search/io/blast/testBlastReport.xml";
80+
URL resourceURL = getClass().getResource(resource);
81+
File file = new File(resourceURL.getFile());
82+
83+
ResultFactory blastResultFactory = new BlastXMLQuery();
84+
final SearchIO instance;
85+
try {
86+
instance = new SearchIO(file, blastResultFactory, 10e-10);
87+
} catch (Exception e) {
88+
fail("test failed:\n"+e.getMessage());
89+
}
90+
}
91+
}

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