LocalIndexImpl.java

package GeDBIT.parallel.rmi;

import java.io.IOException;
import java.rmi.RemoteException;
import java.rmi.server.UnicastRemoteObject;
import java.util.logging.Level;

import GeDBIT.app.QueryVPIndex;
import GeDBIT.index.Index;
import GeDBIT.index.TableManager;
import GeDBIT.type.DNATable;
import GeDBIT.type.DoubleVectorTable;
import GeDBIT.type.ImageTable;
import GeDBIT.type.PeptideTable;
import GeDBIT.type.SpectraWithPrecursorMassTable;
import GeDBIT.type.Table;

public class LocalIndexImpl extends UnicastRemoteObject implements LocalIndex {
    private static final long serialVersionUID = 1061237826684535271L;

    public LocalIndexImpl() throws RemoteException {
	super();
    }

    public void query(String[] args) throws RemoteException {
	String indexName = "";
	String queryFileName = "";
	String forPrint = "";

	int firstQuery = 0;
	int lastQuery = 1;

	double minRadius = 0.0;
	double maxRadius = 10.0;
	double step = 1.0;

	boolean verify = false;
	Level debug = Level.OFF;

	int frag = 6;
	int dim = 2;

	int pathLength = 0;
	String dataType = "sequence";
	String resultsFileName = null;

	for (int i = 0; i < args.length; i = i + 2) {
	    if (args[i].equalsIgnoreCase("-d"))
		indexName = args[i + 1];

	    else if (args[i].equalsIgnoreCase("-q"))
		queryFileName = args[i + 1];

	    else if (args[i].equalsIgnoreCase("-t"))
		dataType = args[i + 1];

	    else if (args[i].equalsIgnoreCase("-forprint"))
		forPrint += args[i + 1] + ", ";

	    else if (args[i].equalsIgnoreCase("-f"))
		firstQuery = Integer.parseInt(args[i + 1]);

	    else if (args[i].equalsIgnoreCase("-l"))
		lastQuery = Integer.parseInt(args[i + 1]);

	    else if (args[i].equalsIgnoreCase("-p"))
		pathLength = Integer.parseInt(args[i + 1]);

	    else if (args[i].equalsIgnoreCase("-i"))
		minRadius = Double.parseDouble(args[i + 1]);

	    else if (args[i].equalsIgnoreCase("-a"))
		maxRadius = Double.parseDouble(args[i + 1]);

	    else if (args[i].equalsIgnoreCase("-s"))
		step = Double.parseDouble(args[i + 1]);

	    else if (args[i].equalsIgnoreCase("-g"))
		debug = Level.parse(args[i + 1]);

	    else if (args[i].equalsIgnoreCase("-frag"))
		frag = Integer.parseInt(args[i + 1]);

	    else if (args[i].equalsIgnoreCase("-dim"))
		dim = Integer.parseInt(args[i + 1]);

	    else if (args[i].equalsIgnoreCase("-v"))
		verify = (Integer.parseInt(args[i + 1]) == 1) ? true : false;

	    else if (args[i].equalsIgnoreCase("-res"))
		resultsFileName = args[i + 1];
	    else if (args[i].equalsIgnoreCase("-st")
		    || args[i].equalsIgnoreCase("-sv"))
		continue;
	    else
		throw new IllegalArgumentException("Invalid option " + args[i]);
	}

	if (indexName == "")
	    throw new IllegalArgumentException("Invalid Index file name!");

	if (queryFileName == "")
	    throw new IllegalArgumentException("Invalid Query file name!");

	if ((firstQuery < 0) || (lastQuery < 0) || (lastQuery < firstQuery))
	    throw new IllegalArgumentException(
		    "Invalid first query index or last query index!");

	if ((minRadius < 0) || (maxRadius < 0) || (maxRadius < minRadius)
		|| (step <= 0))
	    throw new IllegalArgumentException(
		    "Invalid min radius, max radius, or radius increasement unit!");

	Table dataTable = TableManager.getTableManager(indexName).getTable(
		indexName);
	Index index;
	if (dataTable != null)
	    index = dataTable.getIndex();
	else
	    throw new Error("index: " + indexName + " does not exist");

	Table queryTable = null;
	try {
	    if (dataType.equalsIgnoreCase("protein"))
		queryTable = new PeptideTable(queryFileName, "", lastQuery,
			frag);
	    else if (dataType.equalsIgnoreCase("vector"))
		queryTable = new DoubleVectorTable(queryFileName, "",
			lastQuery, dim);
	    else if (dataType.equalsIgnoreCase("dna"))
		queryTable = new DNATable(queryFileName, "", lastQuery, frag);
	    else if (dataType.equalsIgnoreCase("image"))
		queryTable = new ImageTable(queryFileName, "", lastQuery);
	    else if (dataType.equalsIgnoreCase("msms"))
		queryTable = new SpectraWithPrecursorMassTable(queryFileName,
			"", lastQuery);
	    else
		System.err.println("data type not supported! " + dataType);
	} catch (IOException e1) {
	    e1.printStackTrace();
	}
	QueryVPIndex evaluator = new QueryVPIndex(index, queryTable, minRadius,
		maxRadius, step, verify, debug, pathLength, frag,
		resultsFileName, firstQuery, lastQuery, forPrint);

	evaluator.evaluate();
    }

}