java

Java implementation of Tracker Commons WCON data format

This project contains a Java interface to the WCON data format from OpenWorm's Tracker Commons.

This is not a stand-alone implementation. Rather, the Java implementation calls the Scala implementation, as that also runs on the Java Virtual Machine. This project supplies a few high-level routines that ease usage from Java.

Requirements

You need to have Java 8 running on your machine. Additionally, you need to be able to compile the Scala implementation: follow the instructions there. When you can type sbt package there and have it complete successfully, you're ready to begin here.

Since you already need to have SBT running on your machine to build the Scala version, SBT is also used to build the Java version (instead of more traditional tools like Ant or Maven). Again, you already have it, so you shouldn't have to worry about it any more than you already did.

Building the Java implementation

In the src/java directory, enter

sbt assembly

at the command-line. This will compile the Scala project if it needs to, then compile the files for this project. It produces a single .jar file that contains the Scala runtime, the class files from the Scala implementation, any additional class files needed, and the routines in this package. You can then include this single jar on your classpath. (It is in the target directory.)

Example usage

Here is an example of reading WCON data using the Java WCON reader.

import org.openworm.trackercommons.compatibility.*;
import org.openworm.trackercommons.javawcon.*;

public class ReadWconExample {
  public static void main(String args[]) throws java.io.IOException {
    java.io.File f = new java.io.File("../../tests/intermediate.wcon");
    Wcon w = Wcons.read(f);
    System.out.println("There are " + w.datas().length + " records");
    System.out.println("The first record has ID " + w.datas()[0].id());
    System.out.println("The first timepoint for that ID is " + w.datas()[0].t(0));
    System.out.println("The third x coordinate for that timepoint is " + w.datas()[0].x(0, 2));
  }
}

You can compile this with javac -cp target/JavaWcon-0.1.jar ReadWconExample.java and run it with java -cp target/JavaWcon-0.1.jar ReadWconExample (if you place this file in the Java Tracker Commons directory, which is probably not a great idea in general).

Documentation

You mostly want to view the Scaladocs for the org.openworm.trackercommons.compatibility library to see what you can do with the main classes here (Wcon, Metadata, Data, etc.). Run sbt doc inside the Scala project to generate documentation and point your browser there (at target/scala-2.11/api).