/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.aaproperties;

import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;

/**
 * This is an adaptor class which enable the ease of generating protein properties.
 * At least one adaptor method is written for each available properties provided in IPeptideProperties.
 *
 * @author kohchuanhock
 * @version 2011.08.22
 * @since 3.0.2
 * @see IPeptideProperties
 * @see PeptidePropertiesImpl
 */
public class PeptideProperties {

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

        /**
         * Enumeration of 20 standard amino acid code
         */
        public enum SingleLetterAACode { W, C, M, H, Y, F, Q, N, I, R, D, P, T, K, E, V, S, G, A, L}

        /**
         * Contains the 20 standard AA code in a set
         */
        public static Set<Character> standardAASet;

        /**
         * To initialize the standardAASet
         */
        static{
                standardAASet = Arrays.stream(SingleLetterAACode.values())
                                      .map(singleLetterAACode -> singleLetterAACode.toString().charAt(0))
                                      .collect(Collectors.toCollection(HashSet::new));
        }

        /**
         * An adaptor method to return the molecular weight of sequence.
         * The sequence argument must be a protein sequence consisting of only non-ambiguous characters.
         * This method will sum the molecular weight of each amino acid in the
         * sequence. Molecular weights are based on <a href="http://web.expasy.org/findmod/findmod_masses.html">here</a>.
         *
         * @param sequence
         *      a protein sequence consisting of non-ambiguous characters only
         * @return the total molecular weight of sequence + weight of water molecule
         */
        public static final double getMolecularWeight(String sequence){
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getMolecularWeight(pSequence);
        }

        /**
         * An adaptor method to return the molecular weight of sequence.
         * The sequence argument must be a protein sequence consisting of only non-ambiguous characters.
         * This method will sum the molecular weight of each amino acid in the
         * sequence. Molecular weights are based on the input xml file.
         *
         * @param sequence
         *      a protein sequence consisting of non-ambiguous characters only
         * @param elementMassFile
         *      xml file that details the mass of each elements and isotopes
         * @param aminoAcidCompositionFile
         *      xml file that details the composition of amino acids
         * @return the total molecular weight of sequence + weight of water molecule
         * @throws FileNotFoundException
         *      thrown if either elementMassFile or aminoAcidCompositionFile are not found
         * @throws JAXBException
         *      thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
         */
        public static final double getMolecularWeight(String sequence, File elementMassFile, File aminoAcidCompositionFile)
        throws FileNotFoundException, JAXBException{
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getMolecularWeight(pSequence, elementMassFile, aminoAcidCompositionFile);
        }

        /**
         * An adaptor method to return the molecular weight of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters.
         * This method will sum the molecular weight of each amino acid in the
         * sequence. Molecular weights are based on the input files. These input files must be XML using the defined schema.
         * Note that it assumes that ElementMass.xml file can be found in default location.
         *
         * @param sequence
         *      a protein sequence consisting of non-ambiguous characters only
         *      xml file that details the mass of each elements and isotopes
         * @param aminoAcidCompositionFile
         *      xml file that details the composition of amino acids
         * @return the total molecular weight of sequence + weight of water molecule
         * @throws JAXBException
         *      thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
         * @throws FileNotFoundException
         *      thrown if either elementMassFile or aminoAcidCompositionFile are not found
         */
        public static final double getMolecularWeight(String sequence, File aminoAcidCompositionFile) throws FileNotFoundException, JAXBException{
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getMolecularWeight(pSequence, aminoAcidCompositionFile);
        }

        /**
         * An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to
         * IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
         * Note that ElementMass.xml is assumed to be able to be seen in default location.
         *
         * @param aminoAcidCompositionFile
         *      xml file that details the composition of amino acids
         * @return the initialized amino acid composition table
         * @throws JAXBException
         *      thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
         * @throws FileNotFoundException
         *      thrown if either elementMassFile or aminoAcidCompositionFile are not found
         */
        public static final AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
        throws JAXBException, FileNotFoundException{
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.obtainAminoAcidCompositionTable(aminoAcidCompositionFile);
        }

        /**
         * An adaptor method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to
         * IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable).
         *
         * @param elementMassFile
         *      xml file that details the mass of each elements and isotopes
         * @param aminoAcidCompositionFile
         *      xml file that details the composition of amino acids
         * @return the initialized amino acid composition table
         * @throws JAXBException
         *      thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
         * @throws FileNotFoundException
         *      thrown if either elementMassFile or aminoAcidCompositionFile are not found
         */
        public static final AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile)
        throws JAXBException, FileNotFoundException{
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.obtainAminoAcidCompositionTable(elementMassFile, aminoAcidCompositionFile);
        }

        /**
         * An adaptor method that returns the molecular weight of sequence. The sequence argument must be a protein sequence consisting of only non-ambiguous characters.
         * This method will sum the molecular weight of each amino acid in the
         * sequence. Molecular weights are based on the AminoAcidCompositionTable.
         * Those input files must be XML using the defined schema.
         *
         * @param sequence
         *      a protein sequence consisting of non-ambiguous characters only
         * @param aminoAcidCompositionTable
         *      a amino acid composition table obtained by calling IPeptideProperties.obtainAminoAcidCompositionTable
         * @return the total molecular weight of sequence + weight of water molecule
         *      thrown if the method IPeptideProperties.setMolecularWeightXML(File, File) is not successfully called before calling this method.
         */
        public static double getMolecularWeightBasedOnXML(String sequence, AminoAcidCompositionTable aminoAcidCompositionTable){
                sequence = Utils.checkSequence(sequence, aminoAcidCompositionTable.getSymbolSet());
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence, aminoAcidCompositionTable.getAminoAcidCompoundSet());
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getMolecularWeightBasedOnXML(pSequence, aminoAcidCompositionTable);
        }

        /**
         * An adaptor method to returns the absorbance (optical density) of sequence. The sequence argument
         * must be a protein sequence consisting of only non-ambiguous characters.
         * The computation of absorbance (optical density) follows the
         * documentation in <a href="http://web.expasy.org/protparam/protparam-doc.html">here</a>.
         *
         * @param sequence
         *      a protein sequence consisting of non-ambiguous characters only
         * @param assumeCysReduced
         *      true if Cys are assumed to be reduced and false if Cys are assumed to form cystines
         * @return the absorbance (optical density) of sequence
         */
        public static final double getAbsorbance(String sequence, boolean assumeCysReduced){
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getAbsorbance(pSequence, assumeCysReduced);
        }

        /**
         * An adaptor method to return the extinction coefficient of sequence. The sequence argument
         * must be a protein sequence consisting of only non-ambiguous characters.
         * The extinction coefficient indicates how much light a protein absorbs at
         * a certain wavelength. It is useful to have an estimation of this
         * coefficient for following a protein which a spectrophotometer when
         * purifying it. The computation of extinction coefficient follows the
         * documentation in <a href="http://web.expasy.org/protparam/protparam-doc.html">here</a>.
         *
         * @param sequence
         *            a protein sequence consisting of non-ambiguous characters only
         * @param assumeCysReduced
         *            true if Cys are assumed to be reduced and false if Cys are
         *            assumed to form cystines
         * @return the extinction coefficient of sequence
         */
        public static final double getExtinctionCoefficient(String sequence, boolean assumeCysReduced) {
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getExtinctionCoefficient(pSequence, assumeCysReduced);
        }

        /**
         * An adaptor method to return the instability index of sequence. The sequence argument must be
         * a protein sequence consisting of only non-ambiguous characters.
         * The instability index provides an estimate of the stability of your
         * protein in a test tube. The computation of instability index follows the
         * documentation in <a href="http://web.expasy.org/protparam/protparam-doc.html">here</a>.
         *
         * @param sequence
         *              a protein sequence consisting of non-ambiguous characters only
         * @return the instability index of sequence
         */
        public static final double getInstabilityIndex(String sequence) {
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getInstabilityIndex(pSequence);
        }

        /**
         * An adaptor method to return the apliphatic index of sequence. The sequence argument must be a
         * protein sequence consisting of only non-ambiguous characters.
         * The aliphatic index of a protein is defined as the relative volume
         * occupied by aliphatic side chains (alanine, valine, isoleucine, and
         * leucine). It may be regarded as a positive factor for the increase of
         * thermostability of globular proteins. The computation of aliphatic index
         * follows the documentation in <a href="http://web.expasy.org/protparam/protparam-doc.html">here</a>.
         * A protein whose instability index is smaller than 40 is predicted as stable, a value above 40 predicts that the protein may be unstable.
         *
         * @param sequence
         *              a protein sequence consisting of non-ambiguous characters only
         * @return the aliphatic index of sequence
         */
        public static final double getApliphaticIndex(String sequence) {
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }

                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getApliphaticIndex(pSequence);
        }

        /**
         * An adaptor method to return the average hydropathy value of sequence. The sequence argument
         * must be a protein sequence consisting of only non-ambiguous characters.
         * The average value for a sequence is calculated as the sum of hydropathy
         * values of all the amino acids, divided by the number of residues in the
         * sequence. Hydropathy values are based on (Kyte, J. and Doolittle, R.F.
         * (1982) A simple method for displaying the hydropathic character of a
         * protein. J. Mol. Biol. 157, 105-132).
         *
         * @param sequence
         *              a protein sequence consisting of non-ambiguous characters only
         * @return the average hydropathy value of sequence
         */
        public static final double getAvgHydropathy(String sequence) {
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getAvgHydropathy(pSequence);
        }

        /**
         * An adaptor method to return the isoelectric point of sequence. The sequence argument must be
         * a protein sequence consisting of only non-ambiguous characters.
         * The isoelectric point is the pH at which the protein carries no net
         * electrical charge. The isoelectric point will be computed based on
         * approach stated in
         * <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#PI">here</a>
         *
         * pKa values used will be either
         * those used by Expasy which referenced "Electrophoresis 1994, 15, 529-539"
         * OR
         * A.Lehninger, Principles of Biochemistry, 4th Edition (2005), Chapter 3, page78, Table 3-1.
         *
         * @param sequence
         *              a protein sequence consisting of non-ambiguous characters only
         * @param useExpasyValues
         *              whether to use Expasy values (Default) or Innovagen values
         * @return the isoelectric point of sequence
         */
        public static final double getIsoelectricPoint(String sequence, boolean useExpasyValues) {
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getIsoelectricPoint(pSequence, useExpasyValues);
        }

        public static final double getIsoelectricPoint(String sequence){
                return getIsoelectricPoint(sequence, true);
        }

        /**
         * An adaptor method to return the net charge of sequence at pH 7. The sequence argument must be
         * a protein sequence consisting of only non-ambiguous characters.
         * The net charge will be computed using the approach stated in
         * <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#PI">here</a>
         *
         * pKa values used will be either
         * those used by Expasy which referenced "Electrophoresis 1994, 15, 529-539"
         * OR
         * A.Lehninger, Principles of Biochemistry, 4th Edition (2005), Chapter 3, page78, Table 3-1.
         *
         * @param sequence
         *              a protein sequence consisting of non-ambiguous characters only
         * @param useExpasyValues
         *              whether to use Expasy values (Default) or Innovagen values
         * @param pHPoint
         *              the pH value to use for computation of the net charge. Default at 7.
         * @return the net charge of sequence at given pHPoint
         */
        public static final double getNetCharge(String sequence, boolean useExpasyValues, double pHPoint){
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getNetCharge(pSequence, useExpasyValues, pHPoint);
        }

        public static final double getNetCharge(String sequence, boolean useExpasyValues) {
                return getNetCharge(sequence, useExpasyValues, 7.0);
        }

        public static final double getNetCharge(String sequence){
                return getNetCharge(sequence, true);
        }

        /**
         * An adaptor method to return the composition of specified amino acid in the sequence. The
         * sequence argument must be a protein sequence consisting of only
         * non-ambiguous characters. The aminoAcidCode must be a non-ambiguous
         * character.
         * The composition of an amino acid is the total number of its occurrence,
         * divided by the total length of the sequence.
         *
         * @param sequence
         *            a protein sequence consisting of non-ambiguous characters only
         * @param aminoAcidCode
         *            the code of the amino acid to compute
         * @return the composition of specified amino acid in the sequence
         * @see SingleLetterAACode
         */
        public static final double getEnrichment(String sequence, SingleLetterAACode aminoAcidCode) {
                return getEnrichment(sequence, aminoAcidCode.toString());
        }

        /**
         * An adaptor method to return the composition of specified amino acid in the sequence. The
         * sequence argument must be a protein sequence consisting of only
         * non-ambiguous characters. The aminoAcidCode must be a non-ambiguous
         * character.
         * The composition of an amino acid is the total number of its occurrence,
         * divided by the total length of the sequence.
         *
         * @param sequence
         *              a protein sequence consisting of non-ambiguous characters only
         * @param aminoAcidCode
         *              the code of the amino acid to compute
         * @return the composition of specified amino acid in the sequence
         */
        public static final double getEnrichment(String sequence, char aminoAcidCode){
                return getEnrichment(sequence, aminoAcidCode);
        }

        /**
         * An adaptor method to return the composition of specified amino acid in the sequence. The
         * sequence argument must be a protein sequence consisting of only
         * non-ambiguous characters. The aminoAcidCode must be a non-ambiguous
         * character.
         * The composition of an amino acid is the total number of its occurrence,
         * divided by the total length of the sequence.
         *
         * @param sequence
         *            a protein sequence consisting of non-ambiguous characters only
         * @param aminoAcidCode
         *            the code of the amino acid to compute
         * @return the composition of specified amino acid in the sequence
         */
        public static final double getEnrichment(String sequence, String aminoAcidCode){
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
                return pp.getEnrichment(pSequence, aaSet.getCompoundForString(aminoAcidCode));
        }

        /**
         * An adaptor method to return the composition of the 20 standard amino acid in the sequence.
         * The sequence argument must be a protein sequence consisting of only
         * non-ambiguous characters.
         * The composition of an amino acid is the total number of its occurrence,
         * divided by the total length of the sequence.
         *
         * @param sequence
         *            a protein sequence consisting of non-ambiguous characters only
         * @return the composition of the 20 standard amino acid in the sequence
         * @see AminoAcidCompound
         */
        public static final Map<AminoAcidCompound, Double> getAAComposition(String sequence) {
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getAAComposition(pSequence);
        }

        /**
         * An adaptor method to return the composition of the 20 standard amino acid in the sequence.
         * The sequence argument must be a protein sequence consisting of only
         * non-ambiguous characters.
         * The composition of an amino acid is the total number of its occurrence,
         * divided by the total length of the sequence.
         *
         * @param sequence
         *              a protein sequence consisting of non-ambiguous characters only
         * @return the composition of the 20 standard amino acid in the sequence
         */
        public static final Map<String, Double> getAACompositionString(String sequence){
                Map<AminoAcidCompound, Double> aa2Composition = getAAComposition(sequence);
                Map<String, Double> aaString2Composition = new HashMap<>();
                aaString2Composition = aa2Composition.keySet().stream() .collect(Collectors.toMap(aaCompound -> aaCompound.getShortName(),aaCompound ->aa2Composition.get(aaCompound)));
                return aaString2Composition;
        }

        /**
         * An adaptor method to return the composition of the 20 standard amino acid in the sequence.
         * The sequence argument must be a protein sequence consisting of only
         * non-ambiguous characters.
         * The composition of an amino acid is the total number of its occurrence,
         * divided by the total length of the sequence.
         *
         * @param sequence
         *              a protein sequence consisting of non-ambiguous characters only
         * @return the composition of the 20 standard amino acid in the sequence
         */
        public static final Map<Character, Double> getAACompositionChar(String sequence){
                Map<AminoAcidCompound, Double> aa2Composition = getAAComposition(sequence);
                Map<Character, Double> aaChar2Composition = new HashMap<>();
                for(AminoAcidCompound aaCompound:aa2Composition.keySet()){
                        aaChar2Composition.put(aaCompound.getShortName().charAt(0), aa2Composition.get(aaCompound));
                }
                return aaChar2Composition;
        }

        /**
         * Returns the array of charges of each amino acid in a protein. At pH=7, two are negative charged: aspartic acid (Asp, D) and glutamic acid (Glu, E) (acidic side chains),
         * and three are positive charged: lysine (Lys, K), arginine (Arg, R) and histidine (His, H) (basic side chains).
         *
         * @param sequence
         *              a protein sequence consisting of non-ambiguous characters only
         * @return the array of charges of amino acids in the protein (1 if amino acid is positively charged, -1 if negatively charged, 0 if not charged)
         */
        public static final int[] getChargesOfAminoAcids(String sequence) {
                int[] charges = new int[sequence.length()];
                for ( int i=0; i < sequence.length(); i++ ) {
                        char aa = sequence.toCharArray()[i];
                        charges[i] = AminoAcidProperties.getChargeOfAminoAcid(aa);
                }
                return charges;
        }

        /**
         * Returns the array of polarity values of each amino acid in a protein sequence.
         *
         * @param sequence
         *              a protein sequence consisting of non-ambiguous characters only
         * @return the array of polarity of amino acids in the protein (1 if amino acid is polar, 0 if not)
         */
        public static final int[] getPolarityOfAminoAcids(String sequence) {
                int[] polarity = new int[sequence.length()];
                for ( int i=0; i < sequence.length(); i++ ) {
                        char aa = sequence.toCharArray()[i];
                        polarity[i] = AminoAcidProperties.getPolarityOfAminoAcid(aa);
                }
                return polarity;
        }

        /**
         * An adaptor method to return the aromaticity value of sequence. The sequence argument
         * must be a protein sequence consisting of only non-ambiguous characters.
         * <p>
         * Calculates the aromaticity value of a protein according to Lobry, 1994.
         * It is simply the relative frequency of Phe+Trp+Tyr.
         * *
         *
         * @param sequence a protein sequence consisting of non-ambiguous characters only
         * @return the aromaticity value of sequence
         */
        public static final double getAromaticity(String sequence) {
                sequence = Utils.checkSequence(sequence);
                ProteinSequence pSequence = null;
                try {
                        pSequence = new ProteinSequence(sequence);
                } catch (CompoundNotFoundException e) {
                        // the sequence was checked with Utils.checkSequence, this shouldn't happen
                        logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
                }
                IPeptideProperties pp = new PeptidePropertiesImpl();
                return pp.getAromaticity(pSequence);
        }
}