ClothoFormat.java

/*
 Copyright (c) 2010 The Regents of the University of California.
 All rights reserved.
 Permission is hereby granted, without written agreement and without
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 of this software.

 IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY
 FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES
 ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
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 THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES,
 INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
 MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE
 PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE UNIVERSITY OF
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 */

package org.clothocore.api.plugin;

import java.util.ArrayList;
import org.clothocore.api.data.NucSeq;
import org.clothocore.api.data.Part;
import org.clothocore.api.data.Plasmid;
import org.clothocore.api.data.Vector;

/**
 * Interface for a ClothoFormat
 * @author J.Christopher Anderson
 * @author Douglas Densmore
 */
public interface ClothoFormat  extends ClothoPlugin {


    ///////////////////////////////////////////////////////////////////
    ////                         public methods                    ////

    /**
     * Test whether a part is a valid member of the ClothoFormat specs
     * @param p Part to test
     * @return true if adheres to the format; false otherwise
     */
    public boolean checkPart(Part p);

    /**
     * Test whether a vector is a valid member of the ClothoFormat specs
     * @param v Vector to test
     * @return true if adheres to the format; false otherwise
     */
    public boolean checkVector(Vector v);

    /**
     * Check to see if an arraylist of parts permits making a composite part
     * @param composition
     * @param additionalRequirements
     * @return
     */
    public boolean checkComposite(ArrayList<Part> composition, Object additionalRequirements);


    /**
     * Check to see if a plasmid can be made out of the vector and part
     * @param p
     * @param v
     * @param additionalRequirements
     * @return
     */
    public boolean checkPlasmid(Part p, Vector v, Object additionalRequirements);


     /**
     * Generates the sequence of a plasmid, call this from the plasmid which calls it from the format
     * @param composition
     * @param additionalRequirements
     * @return
     */
    public NucSeq generateCompositeSequence(ArrayList<Part> composition, Object additionalRequirements);
    
    /**
     * Generates the sequence of a plasmid, call this from the plasmid which calls it from the format
     * @param p
     * @return
     */
    public NucSeq generatePlasmidSequence(Plasmid p);


    /**
     * Generate the part with flanking sequence appropriate for sequencing analysis
     * @param p
     * @return
     */
    public NucSeq generateSequencingRegion(Plasmid p);
}