/*
 *                    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/
 *
 * Created on 2012-11-20
 *
 */

package org.biojava.nbio.structure;

import java.util.*;
import java.util.Map.Entry;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
 * A chainName, a start residue, and an end residue. The chainName is matched
 * to {@link Chain#getName()}, so for mmCIF files it indicates the authorId
 * rather than the asymId.
 *
 * Chain may be null when referencing a single-chainName structure; for multi-chainName
 * structures omitting the chainName is an error. Start and/or end may also be null,
 * which is interpreted as the first and last residues in the chainName, respectively.
 *
 * @author dmyerstu
 * @see ResidueNumber
 * @see org.biojava.nbio.structure.ResidueRangeAndLength
 */
public class ResidueRange {

        private final String chainName;
        private final ResidueNumber end;
        private final ResidueNumber start;

        public static final Pattern RANGE_REGEX = Pattern.compile(
                        "^\\s*([a-zA-Z0-9]+|_)" + //chainName ID. Be flexible here, rather than restricting to 4-char IDs
                        "(?:" + //begin range, this is a "non-capturing group"
                                "(?::|_|:$|_$|$)" + //colon or underscore, could be at the end of a line, another non-capt. group.
                                "(?:"+ // another non capturing group for the residue range
                                        "([-+]?[0-9]+[A-Za-z]?|\\^)?" + // first residue
                                        "(?:" +
                                                "\\s*(-)\\s*" + // hyphen indicates a range was intended
                                                "([-+]?[0-9]+[A-Za-z]?|\\$)?" + // second residue
                                        ")?+"+
                                ")?+"+
                        ")?" + //end range
                        "\\s*");

        public static final Pattern CHAIN_REGEX = Pattern.compile("^\\s*([a-zA-Z0-9]+|_)$");

        /**
         * Parse the residue range from a string. Several formats are accepted:
         * <ul>
         *   <li> chainName.start-end
         *   <li> chainName.residue
         *   <li> chain_start-end (for better filename compatibility)
         * </ul>
         *
         * <p>Residues can be positive or negative and may include insertion codes.
         * See {@link ResidueNumber#fromString(String)}.
         *
         * <p>Examples:
         * <ul>
         * <li><code>A:5-100</code>
         * <li><code>A_5-100</code>
         * <li><code>A_-5</code>
         * <li><code>A:-12I-+12I</code>
         * <li><code>A:^-$</code>
         * </ul>
         *
         * @param s   residue string to parse
         * @return The unique ResidueRange corresponding to {@code s}
         */
        public static ResidueRange parse(String s) {
                Matcher matcher = RANGE_REGEX.matcher(s);
                if (matcher.matches()) {
                        ResidueNumber start = null, end = null;
                        String chain = null;
                        try {
                                chain = matcher.group(1);
                                if (matcher.group(2) != null) {
                                        // ^ indicates first res (start==null)
                                        if(!"^".equals(matcher.group(2)) ) {
                                                start = ResidueNumber.fromString(matcher.group(2));
                                                start.setChainName(chain);
                                        }
                                }
                                if(matcher.group(3) == null) {
                                        // single-residue range
                                        end = start;
                                } else
                                        // $ indicates last res (end==null)
                                        if( matcher.group(4) != null && !"$".equals(matcher.group(4)) ){
                                                end = ResidueNumber.fromString(matcher.group(4));
                                                end.setChainName(chain);
                                        }

                                return new ResidueRange(chain, start, end);
                        } catch (IllegalStateException e) {
                                throw new IllegalArgumentException("Range " + s + " was not valid", e);
                        }
                } else if (CHAIN_REGEX.matcher(s).matches()) {
                        return new ResidueRange(s, (ResidueNumber)null, null);
                }
                throw new IllegalArgumentException("Illegal ResidueRange format:" + s);
        }

        /**
         * @param s
         *            A string of the form chain_start-end,chain_start-end, ... For example:
         *            <code>A.5-100,R_110-190,Z_200-250</code>.
         * @return The unique ResidueRange corresponding to {@code s}.
         * @see #parse(String)
         */
        public static List<ResidueRange> parseMultiple(String s) {
                s = s.trim();
                // trim parentheses, for backwards compatibility
                if ( s.startsWith("("))
                        s = s.substring(1);
                if ( s.endsWith(")")) {
                        s = s.substring(0,s.length()-1);
                }

                String[] parts = s.split(",");
                List<ResidueRange> list = new ArrayList<ResidueRange>(parts.length);
                for (String part : parts) {
                        list.add(parse(part));
                }
                return list;
        }

        public ResidueRange(String chainName, String start, String end) {
                this.chainName = chainName;
                this.start = ResidueNumber.fromString(start);
                this.start.setChainName(chainName);
                this.end = ResidueNumber.fromString(end);
                this.end.setChainName(chainName);
        }

        public ResidueRange(String chainName, ResidueNumber start, ResidueNumber end) {
                this.chainName = chainName;
                this.start = start;
                this.end = end;
        }

        @Override
        public boolean equals(Object obj) {
                if (this == obj) return true;
                if (obj == null) return false;
                if (getClass() != obj.getClass()) return false;
                ResidueRange other = (ResidueRange) obj;
                if (chainName == null) {
                        if (other.chainName != null) return false;
                } else if (!chainName.equals(other.chainName)) return false;
                if (end == null) {
                        if (other.end != null) return false;
                } else if (!end.equals(other.end)) return false;
                if (start == null) {
                        if (other.start != null) return false;
                } else if (!start.equals(other.start)) return false;
                return true;
        }

        public String getChainName() {
                return chainName;
        }

        public ResidueNumber getEnd() {
                return end;
        }

        public ResidueNumber getStart() {
                return start;
        }

        @Override
        public int hashCode() {
                final int prime = 31;
                int result = 1;
                result = prime * result + (chainName == null ? 0 : chainName.hashCode());
                result = prime * result + (end == null ? 0 : end.hashCode());
                result = prime * result + (start == null ? 0 : start.hashCode());
                return result;
        }

        @Override
        public String toString() {
                if( start == null && end == null) {
                        // Indicates the full chainName
                        return chainName;
                }
                return chainName + "_" + start + "-" + end;
        }

        /**
         * Returns the ResidueNumber that is at position {@code positionInRange} in
         * <em>this</em> ResidueRange.
         * @return The ResidueNumber, or false if it does not exist or is not within this ResidueRange
         */
        public ResidueNumber getResidue(int positionInRange, AtomPositionMap map) {
                if (map == null) throw new NullPointerException("The AtomPositionMap must be non-null");
                int i = 0;
                for (Map.Entry<ResidueNumber, Integer> entry : map.getNavMap().entrySet()) {
                        if (i == positionInRange) return entry.getKey();
                        if (contains(entry.getKey(), map)) {
                                i++;
                        }
                }
                return null;
        }

        /**
         * @return True if and only if {@code residueNumber} is within this ResidueRange
         */
        public boolean contains(ResidueNumber residueNumber, AtomPositionMap map) {

                if (residueNumber == null)
                        throw new NullPointerException("Can't find the ResidueNumber because it is null");

                if (map == null)
                        throw new NullPointerException("The AtomPositionMap must be non-null");

                Integer pos = map.getPosition(residueNumber);
                if (pos == null) throw new IllegalArgumentException("Couldn't find residue " + residueNumber.printFull());

                ResidueNumber startResidue = getStart()==null? map.getFirst(getChainName()) : getStart();
                Integer startPos = map.getPosition(startResidue);
                if (startPos == null) throw new IllegalArgumentException("Couldn't find the start position");

                ResidueNumber endResidue = getEnd()==null? map.getLast(getChainName()) : getEnd();
                Integer endPos = map.getPosition(endResidue);
                if (endPos == null) throw new IllegalArgumentException("Couldn't find the end position");
                return pos >= startPos && pos <= endPos;
        }

        /**
         * Returns a new Iterator over every {@link ResidueNumber} in this ResidueRange.
         * Stores the contents of {@code map} until the iterator is finished, so calling code should set the iterator to {@code null} if it did not finish.
         */
        public Iterator<ResidueNumber> iterator(final AtomPositionMap map) {
                //Use Entries to guarentee not null
                final Iterator<Entry<ResidueNumber, Integer>> entryIt = map.getNavMap().entrySet().iterator();
                if(! entryIt.hasNext()) {
                        // empty iterator
                        return Arrays.asList(new ResidueNumber[0]).iterator();
                }
                // Peek at upcoming entry

                return new Iterator<ResidueNumber>() {
                        Entry<ResidueNumber,Integer> next = loadNext();

                        private Entry<ResidueNumber,Integer> loadNext() {

                                while( entryIt.hasNext() ) {
                                        next = entryIt.next();
                                        ResidueNumber nextPos = next.getKey();
                                        if( contains(nextPos, map)) {
                                                // loaded a valid next value
                                                return next;
                                        }
                                }
                                next = null;
                                return next;
                        }

                        @Override
                        public boolean hasNext() {
                                return next != null;
                        }

                        @Override
                        public ResidueNumber next() {
                if(!hasNext()){
                    throw new NoSuchElementException();
                }
                ResidueNumber pos = next.getKey();
                                loadNext();
                                return pos;
                        }

                        @Override
                        public void remove() {
                                throw new UnsupportedOperationException("Not modifiable");
                        }
                };
        }

        /**
         * Returns a new Iterator over every {@link ResidueNumber} in the list of ResidueRanges.
         * Stores the contents of {@code map} until the iterator is finished, so calling code should set the iterator to {@code null} if it did not finish.
         */
        public static Iterator<ResidueNumber> multiIterator(final AtomPositionMap map, final ResidueRange... rrs) {
                return new Iterator<ResidueNumber>() {
                        private int r = 0;
                        private Iterator<ResidueNumber> internal;
                        @Override
                        public boolean hasNext() {
                                if (r == rrs.length - 1) {
                                        init();
                                        return internal.hasNext();
                                }
                                return true;
                        }
                        private void init() {
                                if (internal == null) {
                                        internal = rrs[r].iterator(map);
                                }
                        }
                        @Override
                        public ResidueNumber next() {
                                if (rrs.length == 0) throw new NoSuchElementException();
                                init();
                                if (!hasNext()) throw new NoSuchElementException();
                                if (!internal.hasNext()) {
                                        r++;
                                        internal = rrs[r].iterator(map);
                                }
                                return internal.next();
                        }
                        @Override
                        public void remove() {
                                throw new UnsupportedOperationException("Not modifiable");
                        }
                };
        }

        /**
         * Returns a new Iterator over every {@link ResidueNumber} in the list of ResidueRanges.
         * Stores the contents of {@code map} until the iterator is finished, so calling code should set the iterator to {@code null} if it did not finish.
         */
        public static Iterator<ResidueNumber> multiIterator(AtomPositionMap map, List<? extends ResidueRange> rrs) {
                ResidueRange[] ranges = new ResidueRange[rrs.size()];
                for (int i = 0; i < rrs.size(); i++) {
                        ranges[i] = rrs.get(i);
                }
                return multiIterator(map, ranges);
        }

        public static List<ResidueRange> parseMultiple(List<String> ranges) {
                List<ResidueRange> rrs = new ArrayList<ResidueRange>(ranges.size());
                for (String range : ranges) {
                        ResidueRange rr = ResidueRange.parse(range);
                        if (rr != null) rrs.add(rr);
                }
                return rrs;
        }

        public static List<String> toStrings(List<? extends ResidueRange> ranges) {
                List<String> list = new ArrayList<String>(ranges.size());
                for (ResidueRange range : ranges) {
                        list.add(range.toString());
                }
                return list;
        }

        public static String toString(List<? extends ResidueRange> ranges) {
                StringBuilder sb = new StringBuilder();
                for (int i = 0; i < ranges.size(); i++) {
                        sb.append(ranges.get(i));
                        if (i < ranges.size() - 1) sb.append(",");
                }
                return sb.toString();
        }

}