I have a problem getting BioJava to work in a Netbeans RCP application, built using Maven. I've created a Maven module as a wrapper, including org.biojava.* and org.forester.* packages as public in the POM. Then, from another module I set the wrapper as a dependency, and use some of the basic examples from the BioJava cookbook for testing.
Whenever I try to instantiate some object of a class from BioJava, the application freezes and I have to kill it using the Windows task manager.
Here's the wrapper's pom file:
<?xml version="1.0" encoding="UTF-8"?>
<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/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>nl.hecklab.bioinformatics</groupId>
<artifactId>Spider-parent</artifactId>
<version>1.0.0</version>
</parent>
<artifactId>BiojavaWrapper</artifactId>
<version>4.1.0</version>
<packaging>nbm</packaging>
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>nbm-maven-plugin</artifactId>
<extensions>true</extensions>
<configuration>
<useOSGiDependencies>true</useOSGiDependencies>
<publicPackages>
<publicPackage>org.biojava.*</publicPackage>
<publicPackage>org.forester.*</publicPackage>
</publicPackages>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<configuration>
<useDefaultManifestFile>true</useDefaultManifestFile>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-alignment</artifactId>
<version>4.1.0</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.12</version>
</dependency>
</dependencies>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
</project>
Here's some code I try to get to work. This is just a very coarse example, called from a button in a TopComponent. Input and output are just text fields.
private void jButton1ActionPerformed(java.awt.event.ActionEvent evt) {
Reader r = new Reader(new File("D:\\current\\fastafile.fasta"));
for (ProteinSequence a : r.getSequences()) {
input.append(a.toString());
}
Profile<ProteinSequence, AminoAcidCompound> profile = Alignments.getMultipleSequenceAlignment(r.sequences);
output.setText(String.format("Clustalw:%n%s%n", profile));
ConcurrencyTools.shutdown();
}
Here's the reader class:
public class Reader {
List<ProteinSequence> sequences = new ArrayList<>();
public Reader(File fastaFile) {
try {
FileInputStream inStream = new FileInputStream(fastaFile);
FastaReader<ProteinSequence, AminoAcidCompound> fastaReader
= new FastaReader<>(
inStream,
new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(),
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));
LinkedHashMap<String, ProteinSequence> b = fastaReader.process();
sequences.addAll(b.values());
} catch (IOException ex) {
Logger.getLogger(Reader.class.getName()).log(Level.SEVERE, null, ex);
}
}
public List<ProteinSequence> getSequences() {
return sequences;
}
}
In the (Netbeans) IDE, the classes are found and used in autocompletion, and the project builds successfully, in each case indicating that principally the dependencies are set up correctly.
