Plugin.java

package net.sourceforge.seqware.pipeline.plugin;

import java.io.IOException;
import java.util.List;
import java.util.Map;
import joptsimple.BuiltinHelpFormatter;
import joptsimple.OptionException;
import joptsimple.OptionParser;
import joptsimple.OptionSet;
import net.sourceforge.seqware.common.metadata.Metadata;
import net.sourceforge.seqware.common.module.ReturnValue;
import net.sourceforge.seqware.common.util.Log;

/**
 * <p>
 * Abstract Plugin class.
 * </p>
 * 
 * @author boconnor
 * @version $Id: $Id
 */
public abstract class Plugin implements PluginInterface {

    protected OptionParser parser = new OptionParser();
    protected OptionSet options = null;
    protected String[] params = null;
    protected Metadata metadata = null;
    protected Map<String, String> config = null;

    /**
     * <p>
     * Constructor for Plugin.
     * </p>
     */
    public Plugin() {
        super();
    }

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

    /*
     * (non-Javadoc)
     * 
     * @see net.sourceforge.seqware.pipeline.plugin.PluginInterface#setParams(java.util.List)
     */
    /** {@inheritDoc} */
    @Override
    public void setParams(List<String> params) {
        Log.info("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} */
    @Override
    public void setMetadata(Metadata metadata) {
        Log.info("Setting Metadata: " + metadata);
        this.metadata = metadata;
    }

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

        try {
            parser.formatHelpWith(new BuiltinHelpFormatter(160, 2));
            parser.printHelpOn(System.out);
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        return ("");
    }

    /** {@inheritDoc} */
    @Override
    public String get_description() {
        return ("");
    }

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

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

    /**
     * <p>
     * print.
     * </p>
     * 
     * @param output
     *            a {@link java.lang.String} object.
     */
    public void print(String output) {

        // FIXME: Yong, do something cleaver here, for now I'm using System.out
        System.out.print(output);

    }

    /**
     * <p>
     * println.
     * </p>
     * 
     * @param output
     *            a {@link java.lang.String} object.
     */
    public void println(String output) {

        // FIXME: Yong, do something cleaver here, for now I'm using System.out
        Log.stdout(output);

    }

}