/*
 *                    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.structure.quaternary.io;

import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.biojava.nbio.structure.io.FileParsingParameters;
import org.biojava.nbio.structure.io.MMCIFFileReader;
import org.biojava.nbio.structure.io.mmcif.SimpleMMcifConsumer;
import org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssembly;
import org.biojava.nbio.structure.io.mmcif.model.PdbxStructAssemblyGen;
import org.biojava.nbio.structure.io.mmcif.model.PdbxStructOperList;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;



/** A provider for information about biological units for PDB files that is based on reading local MMcif files.
 *
 * @author Andreas Prlic
 *
 */
public class MmCifPDBBiolAssemblyProvider implements RawBioUnitDataProvider{

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

        private String pdbId;
        private List<PdbxStructAssembly> pdbxStructAssemblies;
        private List<PdbxStructAssemblyGen> pdbxStructAssemblyGens;
        private List<PdbxStructOperList> pdbxStructOperList;
        private Structure asymUnit;

        private AtomCache cache ;

        public MmCifPDBBiolAssemblyProvider(){
                //reset();
        }

        @Override
        public void setPdbId(String pdbId) {
                if ( cache == null)
                        cache =new AtomCache();

                if (
                                this.pdbId != null &&
                                (this.pdbId.equals(pdbId))
                                ) {
                        // we already have all the data we need...
                        return;
                }

                this.pdbId= pdbId;

                reset();

                MMCIFFileReader reader = new MMCIFFileReader(cache.getPath());
                FileParsingParameters params = cache.getFileParsingParams();
                params.setAlignSeqRes(true);
                params.setParseBioAssembly(true);
                reader.setFileParsingParameters(params);
                reader.setFetchBehavior(cache.getFetchBehavior());
                reader.setObsoleteBehavior(cache.getObsoleteBehavior());

                try{
                        asymUnit = reader.getStructureById(pdbId);
                        if ( asymUnit.nrModels() > 1) {
                                // why do some NMR structures have bio units???
                                asymUnit = StructureTools.removeModels(asymUnit);
                        }

                        SimpleMMcifConsumer consumer = reader.getMMcifConsumer();


                        pdbxStructOperList              = consumer.getStructOpers();
                        pdbxStructAssemblies    = consumer.getStructAssemblies();
                        pdbxStructAssemblyGens  = consumer.getStructAssemblyGens();

                        //System.out.println(asymUnit.getPDBHeader());

                        //System.out.println("OPER:" + pdbxStructOperList);
                        //System.out.println("ASSEMBLIES:" + pdbxStructAssemblies);
                        //System.out.println("ASSEMBLYGENS:" + pdbxStructAssemblyGens);

                        // reset the consumer data to avoid memory leaks
                        consumer.documentStart();


                        // here we trim in the same way as we do in SimpleMmcifConsumer, removing PAU and XAU bioassemblies, see #230 in github
                        Iterator<PdbxStructAssembly> it = pdbxStructAssemblies.iterator();
                        while (it.hasNext()) {
                                PdbxStructAssembly psa = it.next();
                                try {
                                        Integer.parseInt(psa.getId());
                                } catch (NumberFormatException e) {
                                        logger.info("Ignoring bioassembly with id {} for PDB id {}", psa.getId(), pdbId);
                                        it.remove();
                                }
                        }

                } catch (IOException e){
                        // TODO this should be thrown but setPdbId doesn't have a throws in contract, we need a better solution - JD 2016-01-27
                        logger.error("IOException caught when reading mmcif file to get bioassembly for PDB " + pdbId, e);

                }
        }

        private void reset() {

                pdbxStructOperList      = new ArrayList<PdbxStructOperList>();
                pdbxStructAssemblies    = new ArrayList<PdbxStructAssembly>();
                pdbxStructAssemblyGens  = new ArrayList<PdbxStructAssemblyGen>();
                asymUnit = null;
        }

        public String getPdbId(){
                return pdbId;
        }

        @Override
        public List<PdbxStructAssembly> getPdbxStructAssemblies() {
                return pdbxStructAssemblies;
        }

        @Override
        public List<PdbxStructAssemblyGen> getPdbxStructAssemblyGens() {
                return pdbxStructAssemblyGens;
        }

        @Override
        public List<PdbxStructOperList> getPdbxStructOperList() {
                return pdbxStructOperList;
        }

        @Override
        public int getNrBiolAssemblies() {
                return pdbxStructAssemblies.size();
        }

        @Override
        public boolean hasBiolAssembly() {
                int nrAssemblies = getNrBiolAssemblies();
                if ( nrAssemblies > 0)
                        return true;

                return false;
        }

        @Override
        public PdbxStructAssembly getPdbxStructAssembly(int biolAssemblyNr) {
                if ( biolAssemblyNr < getNrBiolAssemblies())
                        return pdbxStructAssemblies.get(biolAssemblyNr);
                return null;
        }

        @Override
        public List<PdbxStructAssemblyGen> getPdbxStructAssemblyGen(int biolAssemblyNr) {
                if ( biolAssemblyNr > getNrBiolAssemblies())
                        return null;

                List<PdbxStructAssemblyGen> psags = new ArrayList<PdbxStructAssemblyGen>();
                for (PdbxStructAssemblyGen psag : pdbxStructAssemblyGens){
                        if ( psag.getAssembly_id().equals((biolAssemblyNr +1)+ ""))
                                psags.add(psag);
                }
                return psags;
        }

        /** get the asym unit for this PDB ID
         *
         * @return
         */
        public Structure getAsymUnit(){
                return asymUnit;
        }

        public void setAsymUnit(Structure s){
                this.asymUnit = s;
        }

        public AtomCache getAtomCache() {
                return cache;
        }

        public void setAtomCache(AtomCache cache) {
                this.cache = cache;
        }



}