edu.berkeley.compbio.sequtils.sequencefragmentiterator.StubSFI.java Source code

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Here is the source code for edu.berkeley.compbio.sequtils.sequencefragmentiterator.StubSFI.java

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/*
 * Copyright (c) 2007-2013  David Soergel  <dev@davidsoergel.com>
 * Licensed under the Apache License, Version 2.0
 * http://www.apache.org/licenses/LICENSE-2.0
 */

package edu.berkeley.compbio.sequtils.sequencefragmentiterator;

import com.davidsoergel.dsutils.GenericFactory;
import com.davidsoergel.dsutils.GenericFactoryException;
import edu.berkeley.compbio.sequtils.ByteArraySequenceReader;
import edu.berkeley.compbio.sequtils.NotEnoughSequenceException;
import edu.berkeley.compbio.sequtils.SequenceException;
import edu.berkeley.compbio.sequtils.strings.SequenceFragment;
import org.apache.commons.lang.NotImplementedException;
import org.apache.log4j.Logger;
import org.jetbrains.annotations.NotNull;

import java.util.LinkedList;
import java.util.List;
import java.util.NoSuchElementException;

/**
 * @version 1.0
 */
public class StubSFI extends ScanningSFI {
    // ------------------------------ FIELDS ------------------------------

    private static final Logger logger = Logger.getLogger(StubSFI.class);

    boolean initialized = false;
    List<ByteArraySequenceReader> sections;// = new LinkedList<SectionFragment>();

    private int charactersRead = 0;
    //List<SequenceFragmentMetadata> metadatas;

    //private Iterator<SequenceReader> it;
    private int pos = 0;

    private GenericFactory<ByteArraySequenceReader> byteArraySequenceReaderFactory;

    // --------------------------- CONSTRUCTORS ---------------------------

    //KcountScanner theScanner;

    public StubSFI() throws SequenceException, GenericFactoryException//Initialize the sequence provider with the correct input file or directory
    {
        super();
        initialized = true;
        sections = new LinkedList<ByteArraySequenceReader>();
        //metadatas = new LinkedList<SequenceFragmentMetadata>();
        //spectrumScanner = new ExactKcountScanner();

        sections.add(new ByteArraySequenceReader("ATGGTGCGAGCTAGACCAGATTTAGACAAGAACTTGGCCTCGTAAGCTAT"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq1", 0));

        sections.add(new ByteArraySequenceReader("ATCGTGCGGGCTAGACAAGATATAGACCAGAACTCGGCCTCGTAAGCTAT"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq2", 0)); // just a few mutations

        sections.add(new ByteArraySequenceReader("CGTTATGCCGATAGACGTACAGATCGGTGTCACGTGCCGTCAACAGCACG"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq3", 0));
        sections.add(new ByteArraySequenceReader("CGTAATCCCGACAGATGTACAGATCGGTCTCACGTCCCGTCCACATCACG"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq4", 0)); // just a few mutations

        sections.add(new ByteArraySequenceReader("GCGTGAGTCCCCGGTTTGTCCAAACAGATTTGTTGGAAACCCAAGGTTGG"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq5", 0));
        sections.add(new ByteArraySequenceReader("GCCTGACTCCCTGGTTCGTCCAAACTGATTTGATGGAAACCTAAGGTTGG"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq6", 0)); // just a few mutations

        sections.add(new ByteArraySequenceReader("TCGCGAATCGACTGCCGATCGACTACATCGGCAATACCGCATCGACATCG"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq7", 0)); // just a few mutations
        sections.add(new ByteArraySequenceReader("CTCGCCTCGCTCCCGCTCGCCCTCGCTCCGCTCCGCTCGACGCTCCGCTC"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq8", 0)); // just a few mutations

        sections.add(new ByteArraySequenceReader("ATACTAATCATATATTCCTATCAGATCATAATTCTATTATCAATGATTAT"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq9", 0)); // just a few mutations
        sections.add(new ByteArraySequenceReader("ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq10", 0)); // just a few mutations

        sections.add(new ByteArraySequenceReader("CGTTATACCGATAGACGTACAAATCGGTGTCACGTGCCGTCAACAGCACG"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq11", 0));
        sections.add(new ByteArraySequenceReader("CGTAATACCGACAGATGTACATATCGGTCTCACGTCCCGTCCACATCACG"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq12", 0)); // just a few mutations

        sections.add(new ByteArraySequenceReader("CGTTATTCCGATAGACGTACATATCGGTGTCACGTGCCGTCAACAGCACG"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq13", 0));
        sections.add(new ByteArraySequenceReader("CGTAATTCCGACAGATGTACAAATCGGTCTCACGTCCCGTCCACATCACG"));
        //metadatas.add(new SequenceFragmentMetadata(null, "Seq14", 0)); // just a few mutations

        //it = sections.iterator();
        //return this;
    }

    // --------------------- GETTER / SETTER METHODS ---------------------

    public long getCharactersRead() {
        return charactersRead;
    }

    // ------------------------ INTERFACE METHODS ------------------------

    // --------------------- Interface Iterator ---------------------

    public boolean hasNext() {
        return pos < 14;
    }

    public SequenceFragment peek() {
        throw new NotImplementedException();
    }

    @NotNull
    public SequenceFragment next()//Supplies the next read
    {
        //assert length == 50;  // test methods should request this
        assert initialized;
        try {
            if (pos >= 14) {
                throw new NoSuchElementException("No more sequences");
            }
            SequenceFragment result = new SequenceFragment(null, "Seq " + pos, 0, sections.get(pos), 50,
                    spectrumScanner);
            result.checkAvailable();
            //         Kcount result = theScanner.scanSequence(sections.get(pos), 50);
            //         result.getMetadata().setSequenceName("Seq " + pos);
            charactersRead += result.getLength();
            pos++;
            result.doneLabelling();
            return result;
        } catch (NotEnoughSequenceException e) {
            logger.error("Error", e);
            assert false;
        }
        //   assert false;
        throw new NoSuchElementException();
    }

    // -------------------------- OTHER METHODS --------------------------

    public void close() {
        // Do Nothing
    }

    public int estimatedTotalSamples() {
        throw new NotImplementedException();
    }

    public long getTotalSequence() {
        return "ATGGTGCGAGCTAGACCAGATTTAGACAAGAACTTGGCCTCGTAAGCTAT".length() * 14;
    }

    /*@Override
    public void releaseCachedResources()
       {
       }
    */

    public void reset() {
        pos = 0;
        for (ByteArraySequenceReader r : sections) {
            r.reset();
        }
        /*try
           {
           init();
           }
        catch (BMsensrExceptione)
           {
           logger.error("Error", e);
           assert false;
           }*/
    }
}