IMetaPrint2DManager.java

/* *****************************************************************************
 * Copyright (c) 2008 The Bioclipse Project and others.
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 * 
 * Contributors:
 *     Ola Spjuth
 *     
 ******************************************************************************/
package net.bioclipse.metaprint2d.ui.business;

 import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
import java.util.List;
import java.util.Map;

import org.eclipse.core.resources.IFile;
import org.eclipse.core.runtime.CoreException;
import org.eclipse.ui.IEditorPart;
import org.openscience.cdk.exception.CDKException;

import net.sf.metaprint2d.MetaPrintResult;
import net.sf.metaprint2d.mol2.Molecule;
import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.core.PublishedClass;
import net.bioclipse.core.PublishedMethod;
import net.bioclipse.core.Recorded;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.domain.IMolecule;
import net.bioclipse.managers.business.IBioclipseManager;
import net.bioclipse.metaprint2d.ui.model.MetaPrint2DCalculation;

@PublishedClass( "Contains methods for calling MetaPrint2D")
/**
 * 
 * @author ola
 *
 */
public interface IMetaPrint2DManager extends IBioclipseManager{

    /**
     * Run MetaPrint2D on a molecule
     * @param molecule The IMolecule to run Metaprint2D on.
     * @throws BioclipseException 
     * @throws InvocationTargetException 
     */
    @PublishedMethod( methodSummary = "Run MetaPrint2D on a molecule.",
                      params = "IMolecule molecule" )
                      @Recorded
                      public List<MetaPrintResult> calculate(IMolecule molecule) throws BioclipseException, InvocationTargetException;

    /**
     * Run MetaPrint2D on a molecule
     * @param molecule The IMolecule to run Metaprint2D on.
     * @throws BioclipseException 
     * @throws InvocationTargetException 
     */
    @PublishedMethod( methodSummary = "Run MetaPrint2D on a molecule.",
                      params = "IMolecule molecule, " +
    "storeResults: true if results should be stored as properties in AC." )
    @Recorded
    public List<MetaPrintResult> calculate(IMolecule molecule, boolean storeResults) throws BioclipseException, InvocationTargetException;

    /**
     * Run MetaPrint2D on a molecular file
     * @param file a file comprising one or more molecules
     * @throws CoreException 
     * @throws BioclipseException 
     * @throws IOException 
     * @throws InvocationTargetException 
     * @throws CDKException 
     */
    public Map<IMolecule, List<MetaPrintResult>> calculate(IFile file, boolean storeResults) throws IOException, BioclipseException, CoreException, InvocationTargetException, CDKException;

    /**
     * Run MetaPrint2D on a molecular file
     * @param file a file comprising one or more molecules
     * @throws CoreException 
     * @throws BioclipseException 
     * @throws IOException 
     * @throws InvocationTargetException 
     */
    public Map<IMolecule, List<MetaPrintResult>> calculate(IFile file) throws IOException, BioclipseException, CoreException, InvocationTargetException;


    /**
     * Run MetaPrint2D on a molecular file.
     * @param path String that points to a file comprising one or more molecules
     * @throws InvocationTargetException 
     * @throws CoreException 
     * @throws BioclipseException 
     * @throws IOException 
     * @throws CDKException 
     */
    @PublishedMethod( methodSummary = "Run MetaPrint2D on a molecular file.",
                      params = "String path: points to a file comprising " +
    "one or more molecules." )
    @Recorded
    public Map<IMolecule, List<MetaPrintResult>> calculate(String path) throws IOException, BioclipseException, CoreException, InvocationTargetException, CDKException;

    /**
     * Run MetaPrint2D on a molecular file.
     * @param path String that points to a file comprising one or more molecules
     * @throws InvocationTargetException 
     * @throws CoreException 
     * @throws BioclipseException 
     * @throws IOException 
     * @throws CDKException 
     */
    @PublishedMethod( methodSummary = "Run MetaPrint2D on a molecular file.",
                      params = "String path: points to a file comprising " +
                      "one or more molecules, " +
    "storeResults: true if results should be stored as properties in AC." )    
    @Recorded
    public Map<IMolecule, List<MetaPrintResult>> calculate(String path, boolean storeResults)
    throws IOException, BioclipseException, CoreException, InvocationTargetException, CDKException;

    /**
     * 
     * @param mols
     * @return
     * @throws BioclipseException
     * @throws InvocationTargetException
     */
    @PublishedMethod( methodSummary = "Run MetaPrint2D on a list of IMolecules. " +
                      "Does not store results as properties.",
                      params = "List<IMolecule> molecules: List of molecules" )
                      @Recorded
                      public Map<IMolecule, List<MetaPrintResult>> calculate(List<? extends IMolecule> molecules)
                      throws BioclipseException, InvocationTargetException;

    /**
     * 
     * @param mols
     * @return
     * @throws BioclipseException
     * @throws InvocationTargetException
     */
    @PublishedMethod( methodSummary = "Run MetaPrint2D on a list of IMolecules.",
                      params = "List<IMolecule> molecules: List of molecules, " +
    "storeResults: true if results should be stored as properties in AC." )
    @Recorded
    Map<IMolecule, List<MetaPrintResult>> calculate(List<? extends IMolecule> mols,
                                                    boolean storeResults) throws BioclipseException,
                                                    InvocationTargetException;

    Map<IEditorPart, MetaPrint2DCalculation> getCalculationMap();

    Molecule doSybylAtomTyping(ICDKMolecule cdkmol)
    throws InvocationTargetException;

    /**
     * 
     * @param string Database to set, one of 'All', 'Human', 'Dog', and 'Rat'.
     */
    @PublishedMethod( methodSummary = "Set the active MetaPrint2D Database.",
                      params = "database: String to set; one of 'All', 'Human'," +
                      		" 'Dog', or 'Rat'" )
    @Recorded
    public void setDataBase( String database );

    /**
     * Gets the currently active MetaPrint2D database.
     */
    @PublishedMethod( methodSummary = "Gets the currently active MetaPrint2D database."
                      )
    @Recorded
    public String getActiveDatabase();

    /**
     * Remove the M2D property on the AC
     * @param mol
     */
    @PublishedMethod( methodSummary = "Clear MetaPrint2D results for the molecule"
    )
    @Recorded
    void clear( ICDKMolecule mol );
    
    /**
     * Remove the M2D property on the AC of all mols
     * @param mol
     */
    @PublishedMethod( methodSummary = "Clear MetaPrint2D results for the molecules"
    )
    @Recorded
    void clear( List<? extends ICDKMolecule> mols );

}