/*
 *                    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;

import org.biojava.nbio.structure.io.mmcif.model.DatabasePdbrevRecord;
import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.text.DateFormat;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.text.SimpleDateFormat;
import java.util.*;


/**
 * A class that contains PDB Header information.
 *
 * @author Andreas Prlic
 * @since 1.6
 *
 */
public class PDBHeader implements PDBRecord {

        private static final long serialVersionUID = -5834326174085429508L;

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

        private String title;
        private String description;
        private String idCode;
        private String classification;

        private Date depDate;
        private Date relDate;
        private Date modDate;

        private Set<ExperimentalTechnique> techniques;
        private PDBCrystallographicInfo crystallographicInfo;

        private float resolution;
        private float rFree;
        private float rWork;

        private JournalArticle journalArticle;
        private String authors;

        public static final float DEFAULT_RESOLUTION = 99;
        public static final float DEFAULT_RFREE = 1; // worst possible rfree is the default


        private Long id;
        public static final String newline = System.getProperty("line.separator");

        private DateFormat dateFormat;

        private Map<Integer,BioAssemblyInfo> bioAssemblies ;

        List<DatabasePdbrevRecord> revisionRecords;

        public PDBHeader(){

                depDate = new Date(0);
                modDate = new Date(0);
                relDate = new Date(0);
                dateFormat = new SimpleDateFormat("dd-MMM-yy",Locale.US);

                resolution = DEFAULT_RESOLUTION;
                rFree = DEFAULT_RFREE;
                rWork = DEFAULT_RFREE;

                bioAssemblies = new LinkedHashMap<Integer, BioAssemblyInfo>();
                crystallographicInfo = new PDBCrystallographicInfo();

        }

        /** String representation
         *
         */
        @Override
        public String toString(){
                StringBuilder buf = new StringBuilder();

                try {


                        Class<?> c = Class.forName(PDBHeader.class.getName());
                        Method[] methods  = c.getMethods();

                        for (Method m : methods) {
                                String name = m.getName();

                                if (name.substring(0, 3).equals("get")) {
                                        if (name.equals("getClass")) {
                                                continue;
                                        }
                                        Object o = m.invoke(this);
                                        if (o != null) {
                                                buf.append(name.substring(3, name.length()));
                                                buf.append(": ").append(o).append(" ");
                                        }
                                }
                        }
                } catch (ClassNotFoundException e) {
                        logger.error("Exception caught while creating toString  ",e);
                } catch (InvocationTargetException e) {
                        logger.error("Exception caught while creating toString ",e);
                } catch (IllegalAccessException e) {
                        logger.error("Exception caught while creating toString ",e);
                }

                return buf.toString();
        }

        /** Return a PDB representation of the PDB Header
         *
         * @return a PDB file style display
         */
        @Override
        public String toPDB(){
                StringBuffer buf = new StringBuffer();
                toPDB(buf);
                return buf.toString();
        }

        /** Appends a PDB representation of the PDB header to the provided StringBuffer
         *
         * @param buf
         */
        @Override
        public void toPDB(StringBuffer buf){
                //          1         2         3         4         5         6         7
                //01234567890123456789012345678901234567890123456789012345678901234567890123456789
                //HEADER    COMPLEX (SERINE PROTEASE/INHIBITORS)    06-FEB-98   1A4W
                //TITLE     CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING
                //TITLE    2 INHIBITORS: PROBES OF THE S1' BINDING SITE

                printHeader(buf);
                printTitle(buf);
                printExpdata(buf);
                printAuthors(buf);
                printResolution(buf);

        }

        private void printResolution(StringBuffer buf){

                if (getResolution() == DEFAULT_RESOLUTION){
                        return;
                }

                DecimalFormat d2 = (DecimalFormat)NumberFormat.getInstance(java.util.Locale.UK);
                d2.setMaximumIntegerDigits(2);
                d2.setMinimumFractionDigits(2);
                d2.setMaximumFractionDigits(2);

                buf.append("REMARK   2 RESOLUTION. ");
                String x = d2.format(resolution);
                buf.append(x);
                buf.append(" ANGSTROMS.");
                fillLine(buf,34+x.length());

                buf.append(newline);
        }

        private void printExpdata(StringBuffer buf){
                Set<ExperimentalTechnique> exp = getExperimentalTechniques();
                if ( exp == null )
                        return;


                buf.append("EXPDTA    ");

                int length = 0;
                int i = 0;
                for (ExperimentalTechnique et:exp) {
                        if (i>0) {
                                buf.append("; ");
                                length+=2;
                        }
                        buf.append(et.getName());
                        length+=et.getName().length();
                        i++;
                }

                // fill up the white space to the right column
                int l =  length + 10;
                fillLine(buf,l);

                buf.append(newline);

        }

        private void printAuthors(StringBuffer buf){
                String authors = getAuthors();
                if ( authors == null)
                        return;
                if ( authors.equals("")){
                        return;
                }

                printMultiLine(buf, "AUTHOR   ", authors,',');

        }

        private void printMultiLine(StringBuffer buf, String lineStart, String data, char breakChar){
                if ( lineStart.length() !=  9)
                        logger.info("lineStart != 9, there will be problems :" + lineStart);

                if ( data.length() < 58) {
                        buf.append(lineStart);
                        buf.append(" ");
                        buf.append(data);
                        buf.append(newline);
                        return;
                }
                String thisLine = "";
                int count = 1;
                while (data.length() > 57) {
                        // find first whitespace from left
                        // there are 10 chars to the left, so the cutoff position is 56
                        boolean charFound = false;
                        for ( int i =57;i>-1;i--){
                                char c = data.charAt(i);
                                if (c == breakChar){
                                        // found the whitespace

                                        thisLine = data.substring(0,i+1);

                                        // prevent endless loop
                                        if (i == 0 )
                                                i++;
                                        data = data.substring(i);
                                        charFound = true;
                                        break;
                                }
                        }
                        // for emergencies...  prevents an endless loop
                        if ( ! charFound){
                                thisLine = data.substring(0,58);
                                data = data.substring(57);
                        }
                        if ( ( breakChar == ',' ) && ( data.charAt(0)== ',')) {
                                data =   data.substring(1);
                        }

                        //TODO: check structures that have more than 10  lines...
                        // start printing..

                        buf.append(lineStart);
                        if ( count > 1) {
                                buf.append(count);
                                if ( breakChar != ' ' )
                                        buf.append(" ");
                        }
                        else
                                buf.append(" ");
                        buf.append(thisLine);

                        // fill up the white space to the right column
                        int l =  thisLine.length()+ 10;
                        while (l < 67){
                                l++;
                                buf.append(" ");
                        }

                        buf.append(newline);
                        count++;

                }

                // last line...
                if (!data.trim().isEmpty()){
                        buf.append(lineStart);
                        buf.append(count);
                        int filledLeft = 10;
                        if ( breakChar != ' ' ) {
                                buf.append(" ");
                                filledLeft++;
                        }
                        buf.append(data);
                        // fill up the white space to the right column
                        int l =  data.length()+ filledLeft;
                        fillLine(buf,l);
                        buf.append(newline);
                }

        }

        private void fillLine(StringBuffer buf, int currentPos){
                int l = currentPos;
                while (l < 67){
                        l++;
                        buf.append(" ");
                }
        }

        private void printHeader(StringBuffer buf){

                String classification = getClassification();

                if (classification == null || classification.isEmpty()) return;

                // we can;t display this line since the classification is not there...

                buf.append("HEADER    ");
                buf.append(classification);
                buf.append(" ");

                // fill up the white space to the right column
                int l =  classification.length() + 10 ;
                while (l < 49){
                        l++;
                        buf.append(" ");
                }

                Date d = getDepDate();
                if ( d !=  null){
                        // provide correct display of Dep date...
                        buf.append(dateFormat.format(d));
                } else {
                        buf.append("         ");
                }
                buf.append("   ");

                String id = getIdCode();
                if ( id != null){
                        buf.append(getIdCode());
                        buf.append(" ");
                }
                else
                        buf.append("    ");
                buf.append(newline);


        }

        private void printTitle(StringBuffer buf) {
                //          1         2         3         4         5         6         7
                //01234567890123456789012345678901234567890123456789012345678901234567890123456789

                //HEADER    COMPLEX (SERINE PROTEASE/INHIBITORS)    06-FEB-98   1A4W
                //TITLE     CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING
                //TITLE    2 INHIBITORS: PROBES OF THE S1' BINDING SITE

                String title = getTitle();

                if ( (title == null) || (title.trim().isEmpty()) )
                        return;

                printMultiLine(buf, "TITLE    ", title,' ');

        }

        /** Get the ID used by Hibernate.
         *
         * @return the ID used by Hibernate
         * @see #setId(Long)
         */
        public Long getId() {
                return id;
        }

        /** Set the ID used by Hibernate.
         *
         * @param id the id assigned by Hibernate
         * @see #getId()
         *
         */

        @SuppressWarnings("unused")
        private void setId(Long id) {
                this.id = id;
        }

        /** Compare two PDBHeader objects
         *
         * @param other a PDBHeader object to compare this one to.
         * @return true if they are equal or false if they are not.
         */
        public boolean equals(PDBHeader other){
                try {

                        Class<?> c = Class.forName(PDBHeader.class.getName());
                        Method[] methods  = c.getMethods();

                        for (Method m : methods) {
                                String name = m.getName();

                                if (name.substring(0, 3).equals("get")) {
                                        if (name.equals("getClass")) {
                                                continue;
                                        }
                                        Object a = m.invoke(this);
                                        Object b = m.invoke(other);
                                        if (a == null) {
                                                if (b == null) {
                                                        continue;
                                                } else {
                                                        logger.warn(name + " a is null, where other is " + b);
                                                        return false;
                                                }
                                        }
                                        if (b == null) {
                                                logger.warn(name + " other is null, where a is " + a);
                                                return false;
                                        }
                                        if (!(a.equals(b))) {
                                                logger.warn("mismatch with " + name + " >" + a + "< >" + b + "<");
                                                return false;
                                        }
                                }
                        }
                } catch (ClassNotFoundException e) {
                        logger.error("Exception caught while comparing PDBHeader objects ",e);
                        return false;
                } catch (InvocationTargetException e) {
                        logger.error("Exception caught while comparing PDBHeader objects ",e);
                        return false;
                } catch (IllegalAccessException e) {
                        logger.error("Exception caught while comparing PDBHeader objects ",e);
                        return false;
                }
                return true;
        }


        /** The PDB code for this protein structure.
         *
         * @return the PDB identifier
         * @see #setIdCode(String)
         */
        public String getIdCode() {
                return idCode;
        }
        /** The PDB code for this protein structure.
         *
         * @param idCode the PDB identifier
         * @see #getIdCode()
         *
         */
        public void setIdCode(String idCode) {
                this.idCode = idCode;
        }


        public String getClassification() {
                return classification;
        }

        public void setClassification(String classification) {
                this.classification = classification;
        }

        /**
         * Return the deposition date of the structure in the PDB.
         *
         * @return the deposition date
         */
        public Date getDepDate() {
                return depDate;
        }

        /**
         * The deposition date of the structure in the PDB
         *
         * @param depDate the deposition date
         */
        public void setDepDate(Date depDate) {
                this.depDate = depDate;
        }

        /**
         * Return the Set of ExperimentalTechniques, usually the set is of size 1 except for hybrid
         * experimental techniques when the Set will contain 2 or more values
         * @return the Set of ExperimentalTechniques or null if not set
         */
        public Set<ExperimentalTechnique> getExperimentalTechniques() {
                return techniques;
        }

        /**
         * Adds the experimental technique to the set of experimental techniques of this header.
         * Note that if input is not a recognised technique string then no errors will be produced but
         * false will be returned
         * @param techniqueStr
         * @return true if the input corresponds to a recognised technique string (see {@link ExperimentalTechnique})
         * and it was not already present in the current set of ExperimentalTechniques
         */
        public boolean setExperimentalTechnique(String techniqueStr) {

                ExperimentalTechnique et = ExperimentalTechnique.getByName(techniqueStr);

                if (et==null) return false;

                if (techniques==null) {
                        techniques = EnumSet.of(et);
                        return true;
                } else {
                        return techniques.add(et);
                }

        }

        public PDBCrystallographicInfo getCrystallographicInfo() {
                return crystallographicInfo;
        }

        public void setCrystallographicInfo(PDBCrystallographicInfo crystallographicInfo) {
                this.crystallographicInfo = crystallographicInfo;
        }

        public float getResolution() {
                return resolution;
        }

        public void setResolution(float resolution) {
                this.resolution = resolution;
        }

        public float getRfree() {
                return rFree;
        }

        public void setRfree(float rFree) {
                this.rFree = rFree;
        }

        /**
         * Return the latest modification date of the structure.
         *
         * @return the latest modification date
         */
        public Date getModDate() {
                return modDate;
        }

        /**
         * The latest modification date of the structure.
         *
         * @param modDate the latest modification date
         */
        public void setModDate(Date modDate) {
                this.modDate = modDate;
        }

        /**
         * Return the release date of the structure in the PDB.
         *
         * @return the release date
         */
        public Date getRelDate() {
                return relDate;
        }

        /**
         *
         * The release date of the structure in the PDB.
         *
         * @param relDate the release date
         */
        public void setRelDate(Date relDate) {
                this.relDate = relDate;
        }

        public String getTitle() {
                return title;
        }
        public void setTitle(String title) {
                this.title = title;
        }
        public String getDescription() {
                return description;
        }
        public void setDescription(String description) {
                this.description = description;
        }

        /**
         * Return the names of the authors as listed in the AUTHORS section of a PDB file.
         * Not necessarily the same authors as listed in the AUTH section of the primary citation!
         *
         * @return Authors as a string
         */
        public String getAuthors()
        {
                return authors;
        }

        public void setAuthors(String authors)
        {
                this.authors = authors;
        }

        /**
         * Return whether or not the entry has an associated journal article
         * or publication. The JRNL section is not mandatory and thus may not be
         * present.
         * @return flag if a JournalArticle could be found.
         */
        public boolean hasJournalArticle() {
                return this.journalArticle != null;
        }

        /**
         * Get the associated publication as defined by the JRNL records in a PDB
         * file.
         * @return a JournalArticle
         */
        public JournalArticle getJournalArticle() {
                return this.journalArticle;
        }

        /**
         * Set the associated publication as defined by the JRNL records in a PDB
         * file.
         * @param journalArticle the article
         */
        public void setJournalArticle(JournalArticle journalArticle) {
                this.journalArticle = journalArticle;
        }

        /**
         * Return the map of biological assemblies. The keys are the
         * biological assembly identifiers (starting at 1). Non-numerical identifiers
         * such as PAU or XAU are not supported.
         * @return
         */
        public Map<Integer,BioAssemblyInfo> getBioAssemblies() {
                return bioAssemblies ;
        }

        public void setBioAssemblies(Map<Integer,BioAssemblyInfo> bioAssemblies) {
                this.bioAssemblies = bioAssemblies;
        }

        /**
         * Get the number of biological assemblies available in the PDB header
         * @return
         */
        public int getNrBioAssemblies() {
                return this.bioAssemblies.size();
        }

        public List<DatabasePdbrevRecord> getRevisionRecords() {
                return revisionRecords;
        }

        public void setRevisionRecords(List<DatabasePdbrevRecord> revisionRecords) {
                this.revisionRecords = revisionRecords;
        }

        /**
         * @return the R-work for this structure.
         */
        public float getRwork() {
                return rWork;
        }

        /**
         * @param rWork  the R-work for this structure.
         */
        public void setRwork(float rWork) {
                this.rWork = rWork;
        }
}