/*
 *                    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 August 13, 2010
 * Author: Mark Chapman
 */

package org.biojava.nbio.alignment.io;

import org.biojava.nbio.alignment.io.StockholmStructure.DatabaseReference;

import java.util.*;

/**
 * Stores all the content parsed from the #=GF lines
 *
 *
 * @since 3.0.5
 * @author Amr ALHOSSARY
 * @author Marko Vaz
 *
 */
public class StockholmFileAnnotation {
        public static class StockholmFileAnnotationReference {
                private String refMedline;//TODO 8 digits
                private CharSequence refTitle;//on several lines
                private CharSequence refAuthor;//TODO comma-separated, semicolon terminated list;
                /**<b>TODO to be formatted later on.</b><br>
                 * RL  Journal abbreviation year;volume:page-page.<br>
                 * RL   Virus Genes 1997;14:163-165.<br>
                 * RL   J Mol Biol 1994;242:309-320.
                 */
                private String refLocation;


                public String getRefMedline() {
                        return refMedline;
                }
                public void setRefMedline(String refMedline) {
                        this.refMedline = refMedline;
                }
                public String getRefTitle() {
                        return refTitle.toString();
                }
                public void setRefTitle(String refTitle) {
                        this.refTitle = refTitle;
                }
                public void addToRefTitle(String refTitle) {
                        if (this.refTitle== null) {
                                this.refTitle = new StringBuffer(refTitle);
                        } else if (this.refTitle instanceof StringBuffer){
                                ((StringBuffer) this.refTitle).append(' ').append(refTitle);
                        }else {
                                this.refTitle = new StringBuffer(this.refTitle).append(' ').append(refTitle);
                        }
                }

                public String getRefAuthor() {
                        return refAuthor.toString();
                }
                public void setRefAuthor(StringBuffer refAuthor) {
                        this.refAuthor = refAuthor;
                }
                public void addToRefAuthor(String refAuthor) {
                        if (this.refAuthor== null) {
                                this.refAuthor = new StringBuffer(refAuthor);
                        } else if (this.refAuthor instanceof StringBuffer){
                                ((StringBuffer) this.refAuthor).append(' ').append(refAuthor);
                        }else {
                                this.refAuthor = new StringBuffer(this.refAuthor).append(' ').append(refAuthor);
                        }
                }

                public String getRefLocation() {
                        return refLocation;
                }
                public void setRefLocation(String refLocation) {
                        this.refLocation = refLocation;
                }



        }

        //TODO revise these 4 fields usage
        private final static String TREE_DEFAULT_ID = "DEFAULT_ID";
        private static final String PB_PFAM_STRING = "PB";
        private static final String PF_PFAM_STRING = "PF";
        private static final String RF_RFAM_STRING = "RF";

        private StringBuffer format;
        private StringBuffer version;
        private String accessionNumber;
        private StringBuffer identification;
        private StringBuffer definition;
        private String[] authors;
        private String alignmentMethod;
        private CharSequence buildMethod;
        private StringBuffer searchMethod;
        private StringBuffer sourceSeed;
        private StringBuffer sourceStructure;
        private float[] gatheringThreshs;
        private float[] noiseCutoffs;
        private float[] trustedCutoffs;
        private String typeField;
        private String[] previousIDs;
        private int numSequences;
        private StringBuffer dbComment;
        private Set<DatabaseReference> dbReferences;
        private StringBuffer refComment;
        /**TODO When implementing toString(), the function should loop on the vector */
        private Vector<StockholmFileAnnotationReference> references = new Vector<StockholmFileAnnotation.StockholmFileAnnotationReference>();
        private StringBuffer keywords;
        private CharSequence comment;
        private StringBuffer pfamAccession;
        private StringBuffer location;
        private StringBuffer wikipediaLink;
        private StringBuffer clan;
        private StringBuffer membership;
        private final Map<String, List<String>> embTrees;
        private float falseDiscoveryRate;

        public StockholmFileAnnotation() {
                embTrees = new HashMap<String, List<String>>();
        }

        public StringBuffer getDbComment() {
                return dbComment;
        }

        public void setDbComment(String dbComment) {
                if (this.dbComment != null) {
                        this.dbComment.append(dbComment);
                } else {
                        this.dbComment = new StringBuffer(dbComment);
                }
        }

        public Set<DatabaseReference> getDbReferences() {
                return dbReferences;
        }

        public void setDbReferences(Set<DatabaseReference> dbReferences) {
                this.dbReferences = dbReferences;
        }
        /**
         * @param dbReference the string without the initial annotation identifier ( #=GS DR )
         */
        public void addDBReference(String dbReferenceRepresentingString) {
                if (this.dbReferences == null) {
                        this.dbReferences = new HashSet<DatabaseReference>();
                }
                dbReferences.add(new DatabaseReference(dbReferenceRepresentingString));
        }

        public float getFalseDiscoveryRate() {
                return falseDiscoveryRate;
        }

        public void setFalseDiscoveryRate(float falseDiscoveryRate) {
                this.falseDiscoveryRate = falseDiscoveryRate;
        }

        public StringBuffer getRefComment() {
                return refComment;
        }

        public StringBuffer getKeywords() {
                return keywords;
        }

        public String getComment() {
                return comment.toString();
        }

        public StringBuffer getPfamAccession() {
                return pfamAccession;
        }

        public StringBuffer getLocation() {
                return location;
        }

        public StringBuffer getWikipediaLink() {
                return wikipediaLink;
        }

        public StringBuffer getClan() {
                return clan;
        }

        public StringBuffer getMembership() {
                return membership;
        }

        public Map<String, List<String>> getEmbTrees() {
                return embTrees;
        }

        public void setNumSequences(int numSequences) {
                this.numSequences = numSequences;
        }

        public StringBuffer getIdentification() {
                return identification;
        }

        public void setGFIdentification(String identification) {
                if (this.identification != null) {
                        this.identification.append(identification);
                } else {
                        this.identification = new StringBuffer(identification);
                }
        }

        public StringBuffer getDefinition() {
                return definition;
        }

        public void setGFDefinition(String definition) {
                if (this.definition != null) {
                        this.definition.append(definition);
                } else {
                        this.definition = new StringBuffer(definition);
                }
        }

        public String[] getAuthors() {
                return authors;
        }

        public void setGFAuthors(String authors) {
                this.authors = authors.split(",");
        }

        public String getBuildMethod() {
                return buildMethod.toString();
        }

        public void addGFBuildMethod(String buildMethod) {
                if (this.buildMethod == null) {
                        this.buildMethod = new StringBuffer(buildMethod);
                } else if (this.buildMethod instanceof StringBuffer){
                        ((StringBuffer) this.buildMethod).append(System.getProperty("line.seperator")).append(buildMethod);
                }else {
                        this.buildMethod = new StringBuffer(this.buildMethod).append(System.getProperty("line.seperator")).append(buildMethod);
                }
        }

        public StringBuffer getSearchMethod() {
                return searchMethod;
        }

        public void setGFSearchMethod(String searchMethod) {
                if (this.searchMethod != null) {
                        this.searchMethod.append(searchMethod);
                } else {
                        this.searchMethod = new StringBuffer(searchMethod);
                }
        }

        public StringBuffer getSourceSeed() {
                return sourceSeed;
        }

        public void setGFSourceSeed(String sourceSeed) {
                if (this.sourceSeed != null) {
                        this.sourceSeed.append(sourceSeed);
                } else {
                        this.sourceSeed = new StringBuffer(sourceSeed);
                }
        }

        public StringBuffer getSourceStructure() {
                return sourceStructure;
        }

        public void setGFSourceStructure(String sourceStructure) {
                if (this.sourceStructure != null) {
                        this.sourceStructure.append(sourceStructure);
                } else {
                        this.sourceStructure = new StringBuffer(sourceStructure);
                }
        }

        /**Not always 2.<br>
         * It may undergo further change.
         * @return
         */
        public float[] getGatheringThreshs() {
                return gatheringThreshs;
        }

        public void setGFGatheringThreshs(String gatheringThresh) {
                this.gatheringThreshs = stringToFloats(gatheringThresh);
        }

        /**Not always 2.<br>
         * It may undergo further change.
         * @return
         */
        public float[] getNoiseCutoffs() {
                return noiseCutoffs;
        }

        public void setGFNoiseCutoffs(String noiseCutoff) {
                this.noiseCutoffs=stringToFloats(noiseCutoff);
        }


        /**Not always 2.<br>
         * It may undergo further change.
         * @return
         */
        public float[] getTrustedCutoffs() {
                return trustedCutoffs;
        }

        public void setGFTrustedCutoffs(String trustedCutoff) {
                this.trustedCutoffs = stringToFloats(trustedCutoff);
        }

        public float[] stringToFloats(String string) {
                String[] coublets= string.split(";");
                float[] floats = new float[coublets.length*2];
                int counter=0;
                for (int i = 0; i < coublets.length; i++) {
                        String[] subStrings = coublets[i].trim().split("\\s");
                        float f = Float.parseFloat(subStrings[i]);
                        floats[counter++]=f;
                }
                return floats;
        }

        public String getTypeField() {
                return typeField;
        }

        public void setGFTypeField(String typeField) {
                this.typeField = typeField;
        }

        public String[] getPreviousIDs() {
                return previousIDs;
        }

        public void setGFPreviousIDs(String previousIDs) {
                this.previousIDs = previousIDs.split(";");
        }

        public StringBuffer getFormat() {
                return format;
        }

        public void setFormat(String format) {
                if (this.format != null) {
                        this.format.append(format);
                } else {
                        this.format = new StringBuffer(format);
                }
        }

        public StringBuffer getVersion() {
                return version;
        }

        public void setVersion(String version) {
                if (this.version != null) {
                        this.version.append(version);
                } else {
                        this.version = new StringBuffer(version);
                }
        }

        public String getAccessionNumber() {
                return accessionNumber;
        }

        public void setGFAccessionNumber(String accessionNumber) {
                this.accessionNumber = accessionNumber;
        }

        public boolean isPFam() {
                return accessionNumber != null
                                && (accessionNumber.startsWith(PF_PFAM_STRING) || accessionNumber.startsWith(PB_PFAM_STRING));
        }

        public boolean isRFam() {
                return accessionNumber == null
                                || accessionNumber.startsWith(RF_RFAM_STRING);
        }

        public int getNumSequences() {
                return numSequences;
        }

        public void setGFNumSequences(String numSequences) {
                this.numSequences = Integer.parseInt(numSequences);
        }

        public void setGFDBComment(String dbComment) {
                if (this.dbComment != null) {
                        this.dbComment.append(dbComment);
                } else {
                        this.dbComment = new StringBuffer(dbComment);
                }
        }


        public void setGFRefComment(String refComment) {
                if (this.refComment != null) {
                        this.refComment.append(refComment);
                } else {
                        this.refComment = new StringBuffer(refComment);
                }
        }

        public void setGFKeywords(String keywords) {
                if (this.keywords != null) {
                        this.keywords.append(keywords);
                } else {
                        this.keywords = new StringBuffer(keywords);
                }
        }

        public void addToGFComment(String comment) {
                if (this.comment == null) {
                        this.comment = new StringBuffer(comment);
                } else if (this.comment instanceof StringBuffer){
                        ((StringBuffer) this.comment).append(' ').append(comment);
                }else {
                        this.comment = new StringBuffer(this.comment).append(' ').append(comment);
                }
        }

        public void setGFPfamAccession(String pfamAccession) {
                if (this.pfamAccession != null) {
                        this.pfamAccession.append(pfamAccession);
                } else {
                        this.pfamAccession = new StringBuffer(pfamAccession);
                }
        }

        public void setGFLocation(String location) {
                if (this.location != null) {
                        this.location.append(location);
                } else {
                        this.location = new StringBuffer(location);
                }
        }

        public void setGFWikipediaLink(String wikipediaLink) {
                if (this.wikipediaLink != null) {
                        this.wikipediaLink.append(wikipediaLink);
                } else {
                        this.wikipediaLink = new StringBuffer(wikipediaLink);
                }
        }

        public void setGFClan(String clan) {
                if (this.clan != null) {
                        this.clan.append(clan);
                } else {
                        this.clan = new StringBuffer(clan);
                }
        }

        public void setGFMembership(String membership) {
                if (this.membership != null) {
                        this.membership.append(membership);
                } else {
                        this.membership = new StringBuffer(membership);
                }
        }

        public void addGFNewHampshire(String newHampshire) {
                List<String> hampshireTree = embTrees.get(TREE_DEFAULT_ID);
                if (hampshireTree == null) {
                        hampshireTree = new ArrayList<String>();
                }
                hampshireTree.add(newHampshire);
                embTrees.put(TREE_DEFAULT_ID, hampshireTree);
        }

        public void addGFTreeID(String treeID) {
                List<String> hampshireTree = embTrees.remove(TREE_DEFAULT_ID);
                embTrees.put(treeID, hampshireTree);
        }

        public void addGFFalseDiscoveryRate(String falseDiscoveryRate) {
                this.falseDiscoveryRate = Float.parseFloat(falseDiscoveryRate);
        }

        public String getAlignmentMethod() {
                return alignmentMethod;
        }

        public void setAlignmentMethod(String alignmentMethod) {
                this.alignmentMethod = alignmentMethod;
        }

        public Vector<StockholmFileAnnotationReference> getReferences() {
                return references;
        }

        public void setReferences(Vector<StockholmFileAnnotationReference> references) {
                this.references = references;
        }

}