Fragment.java

/**
 * edu.utexas.GeDBIT.type.Fragment 2006.05.24
 *
 * Copyright Information:
 *
 * Change Log:
 * 2006.05.24: Created, by Willard
 */
package GeDBIT.type;

import java.io.IOException;
import java.io.ObjectInput;
import java.io.ObjectOutput;

import GeDBIT.index.TableManager;

/**
 * @author Willard
 * 
 */
public class Fragment extends IndexObject {
    /**
     * 
     */
    private static final long serialVersionUID = -7087849259510041868L;

    /**
     * 
     */
    private SequenceTable sTable;

    /**
     * 
     */
    public Fragment() {
    }

    /**
     * @param table
     * @param rowID
     */
    public Fragment(SequenceTable table, int rowID) {
	super(rowID);
	this.sTable = table;
    }

    /**
     * @param i
     * @return
     */
    public Symbol get(int i) {
	return sTable.alphabet
		.get(sTable.sequences[sTable.originalRowIDs[rowIDStart]].data[sTable.fragmentOffsets[rowIDStart]
			+ i]);
    }

    /*
     * (non-Javadoc)
     * 
     * @see GeDBIT.type.IndexObject#size()
     */
    public int size() {
	return sTable.fragmentLength;
    }

    /*
     * (non-Javadoc)
     * 
     * @see GeDBIT.type.IndexObject#expand()
     */
    public IndexObject[] expand() {
	IndexObject[] dbO = new IndexObject[rowIDLength];
	for (int i = 0; i < rowIDLength; i++) {
	    dbO[i] = new Fragment(sTable, rowIDStart + i);
	}
	return dbO;
    }

    /*
     * (non-Javadoc)
     * 
     * @see GeDBIT.type.IndexObject#compareTo(GeDBIT.type.IndexObject)
     */
    public int compareTo(IndexObject oThat) {
	if (!(oThat instanceof Fragment))
	    throw new Error("not compatible");
	Fragment that = (Fragment) oThat;
	if (this == that)
	    return 0;

	if (this.size() < that.size())
	    return -1;
	else if (this.size() > that.size())
	    return 1;
	else {
	    for (int i = 0; i < sTable.fragmentLength; i++) {
		byte byte1 = sTable.sequences[sTable.originalRowIDs[rowIDStart]].data[sTable.fragmentOffsets[rowIDStart]
			+ i];
		byte byte2 = that.sTable.sequences[that.sTable.originalRowIDs[that.rowIDStart]].data[that.sTable.fragmentOffsets[that.rowIDStart]
			+ i];
		if (byte1 < byte2)
		    return -1;
		else if (byte1 > byte2)
		    return 1;
	    }
	    return 0;
	}

    }

    /*
     * (non-Javadoc)
     * 
     * @see java.lang.Object#equals(java.lang.Object)
     */
    public final boolean equals(Object object) {
	if (object == null)
	    return false;

	if (!(object instanceof Fragment))
	    return false;

	Fragment that = (Fragment) object;

	if (this.size() != that.size())
	    return false;

	if (!this.sTable.alphabet.equals(that.sTable.alphabet))
	    return false;

	for (int i = 0; i < size(); ++i)
	    if (this.get(i) != that.get(i))
		return false;
	return true;
    }

    // taken from Joshua Bloch's Effective Java
    public int hashCode() {
	int result = super.hashCode();
	result = 37 * result + size();
	result = 37 * result + sTable.alphabet.hashCode();
	for (int i = 0; i < size(); ++i) {
	    result = 37 * result + get(i).hashCode();
	}
	return result;
    }

    /*
     * (non-Javadoc)
     * 
     * @see java.lang.Object#toString()
     */
    public String toString() {
	StringBuffer sourceSequence = new StringBuffer(rowIDLength);
	for (int i = 0; i < rowIDLength; i++) {
	    sourceSequence
		    .append(sTable.sequences[sTable.getOriginalRowID(rowIDStart
			    + i)].sequenceID).append(", offset: ")
		    .append(sTable.getFragmentOffset(rowIDStart + i))
		    .append(" ");
	}
	StringBuffer fragment = new StringBuffer(sTable.fragmentLength);
	for (int i = 0; i < sTable.fragmentLength; i++) {
	    fragment.append(get(i));
	}
	return "fragment: " + fragment.toString() + " source: "
		+ sourceSequence.toString();
    }

    /*
     * (non-Javadoc)
     * 
     * @see GeDBIT.type.IndexObject#readExternal(java.io.ObjectInput)
     */
    public void readExternal(ObjectInput in) throws IOException,
	    ClassNotFoundException {
	super.readExternal(in);
	String indexPrefix = (String) in.readObject();
	sTable = (SequenceTable) TableManager.getTableManager(indexPrefix)
		.getTable(in.readInt());
    }

    /*
     * (non-Javadoc)
     * 
     * @see GeDBIT.type.IndexObject#writeExternal(java.io.ObjectOutput)
     */
    public void writeExternal(ObjectOutput out) throws IOException {
	super.writeExternal(out);
	out.writeObject(sTable.getIndexPrefix());
	out.writeInt(sTable.getTableLocation());
    }
}