HelloWorld.java

/**
 * 
 */
package net.sourceforge.seqware.pipeline.plugins;

import java.io.IOException;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
import joptsimple.OptionException;
import net.sourceforge.seqware.common.metadata.Metadata;
import net.sourceforge.seqware.common.module.ReturnValue;
import net.sourceforge.seqware.pipeline.plugin.Plugin;
import net.sourceforge.seqware.pipeline.plugin.PluginInterface;
import org.openide.util.lookup.ServiceProvider;

/**
 * <p>
 * HelloWorld class.
 * </p>
 * 
 * @author boconnor ProviderFor(PluginInterface.class)
 * @version $Id: $Id
 */
@ServiceProvider(service = PluginInterface.class)
public class HelloWorld extends Plugin {

    ReturnValue ret = new ReturnValue();

    /**
     * <p>
     * Constructor for HelloWorld.
     * </p>
     */
    public HelloWorld() {
        super();
        parser.acceptsAll(Arrays.asList("help", "h", "?"), "Provides this help message.");
        ret.setExitStatus(ReturnValue.SUCCESS);
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#setConfig(java.util.Map)
     */
    /**
     * {@inheritDoc}
     * 
     * @param config
     */
    @Override
    public void setConfig(Map<String, String> config) {
        println("Setting Config");
        println("Config File Contents:");
        for (String key : config.keySet()) {
            println("  " + key + " " + config.get(key));
        }
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#setParams(java.util.List)
     */
    /**
     * {@inheritDoc}
     * 
     * @param params
     */
    @Override
    public void setParams(List<String> params) {
        println("Setting Params: " + params);
        this.params = params.toArray(new String[params.size()]);
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#setMetadata(net.sourceforge.seqware.pipeline.metadata.Metadata)
     */
    /**
     * {@inheritDoc}
     * 
     * @param metadata
     */
    @Override
    public void setMetadata(Metadata metadata) {
        println("Setting Metadata: " + metadata);
        this.metadata = metadata;
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#get_syntax()
     */
    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public String get_syntax() {

        try {
            parser.printHelpOn(System.err);
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return ("");
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#parse_parameters()
     */
    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue parse_parameters() {

        try {
            options = parser.parse(params);
        } catch (OptionException e) {
            get_syntax();
            ret.setExitStatus(ReturnValue.INVALIDARGUMENT);
        }
        return ret;
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#init()
     */
    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue init() {
        return ret;
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#do_test()
     */
    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue do_test() {
        // TODO Auto-generated method stub
        return ret;
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#do_run()
     */
    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue do_run() {
        // TODO Auto-generated method stub
        println("  Hello");
        return ret;
    }

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#clean_up()
     */
    /**
     * {@inheritDoc}
     * 
     * @return
     */
    @Override
    public ReturnValue clean_up() {
        // TODO Auto-generated method stub
        return ret;
    }

    /**
     * <p>
     * get_description.
     * </p>
     * 
     * @return a {@link java.lang.String} object.
     */
    @Override
    public String get_description() {
        return ("A very simple HelloWorld to show how to make plugins.");
    }

}