com.philiphubbard.sabe.MRMerVertex.java Source code

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Here is the source code for com.philiphubbard.sabe.MRMerVertex.java

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// Copyright (c) 2014 Philip M. Hubbard
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
// 
// http://opensource.org/licenses/MIT

package com.philiphubbard.sabe;

import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.io.BytesWritable;

import com.philiphubbard.digraph.MRVertex;

// A version of MRVertex that stores MerString instances.  Thus, on the
// assumption that the IDs of the vertices encode (k-1)-mers via the
// Mer class, this class can specialize chain compression to keep
// track of the resulting merged MerString.

public class MRMerVertex extends MRVertex {

    // Use this property with hadoop.conf.Configuration.setInt() to set the
    // length of the mers (the (k-1) for the (k-1)-mers) associated with
    // each vertex.

    public static final String CONFIG_MER_LENGTH = "CONFIG_MER_LENGTH";

    // Construct a vertex with an ID that encodes a (k-1)-mer via the
    // Mer class.  The Configuration is used to get the (k-1) length.

    public MRMerVertex(int id, Configuration config) {
        super(id, config);
        merString = new MerString(id, config.getInt(CONFIG_MER_LENGTH, 1));
    }

    // Construct a vertex from the hadoop.io.BytesWritable, assumed to
    // have the format produced by MRVertex.toWritable().

    public MRMerVertex(BytesWritable writable, Configuration config) {
        super(writable, config);
    }

    // Get the MerString associated with this vertex.

    public MerString getMerString() {
        return merString;
    }

    // Returns true if the values (not the references) of this vertex and
    // the other vertex are equivalent.

    public boolean equals(MRMerVertex other) {
        if (!super.equals(other))
            return false;
        return (merString.equals(other.merString));
    }

    // Returns a displayable (human readable) string representation of
    // this vertex.

    public String toDisplayString(Configuration config) {
        StringBuilder s = new StringBuilder();

        s.append("MRMerVertex ");
        s.append(getId());

        s.append(" (");
        int merLength = config.getInt(CONFIG_MER_LENGTH, 1);
        s.append(Mer.fromInt(getId(), merLength));
        s.append(") ");

        MRVertex.AdjacencyIterator toIt = createToAdjacencyIterator();
        if (toIt.begin() != NO_VERTEX) {
            s.append("; to: ");
            for (int to = toIt.begin(); !toIt.done(); to = toIt.next()) {
                s.append(to);
                s.append(" ");
            }
        }

        MRVertex.AdjacencyIterator fromIt = createFromAdjacencyIterator();
        if (fromIt.begin() != NO_VERTEX) {
            s.append("; from: ");
            for (int from = fromIt.begin(); !fromIt.done(); from = fromIt.next()) {
                s.append(from);
                s.append(" ");
            }
        }

        if (merString != null) {
            s.append("; mer ");
            s.append(merString.toDisplayString());
        }

        return s.toString();
    }

    //

    // Specializes the virtual function from MRVertex, to merge this vertex's
    // MerString with that of the other vertex during chain compression.

    @Override
    protected void compressChainInternal(MRVertex other, Configuration config) {
        if (other instanceof MRMerVertex) {
            MRMerVertex otherMer = (MRMerVertex) other;

            int merLength = config.getInt(CONFIG_MER_LENGTH, 1);

            if (merString == null)
                merString = new MerString(getId(), merLength);
            MerString otherMerString = otherMer.merString;
            if (otherMerString == null)
                otherMerString = new MerString(other.getId(), merLength);

            merString.merge(otherMerString, merLength - 1);
        }
    }

    // Specializes the virtual function from MRVertex to write out this vertex's
    // MerString.

    @Override
    protected byte[] toWritableInternal() {
        if (merString != null)
            return merString.toBytes();
        else
            return null;
    }

    // Specializes the virtual function from MRVertex to read in this vertex's
    // MerString from the byte array, starting at index i and assuming length n.

    @Override
    protected void fromWritableInternal(byte[] array, int i, int n) {
        merString = new MerString(array, i, n);
    }

    //

    private MerString merString;

}