/*
 * 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.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.RNASequence;
import org.biojava.nbio.core.sequence.template.AbstractCompound;
import org.biojava.nbio.core.sequence.template.AbstractSequence;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * Stores all the content of a Stockholm file. <i><b>N.B.: This structure will undergo several enhancements later on.
 * Don't depend on it in a final code, otherwise it will be hard to maintain.</b></i>
 *
 * In general, Stockholm File contains the alignment mark-up lines.<br>
 * <br>
 *
 * <Table border="1" align="center">
 * <tr>
 * <td><b>Header Section</b></td>
 * </tr>
 * <tr>
 * <td><b>Reference Section</b></td>
 * </tr>
 * <tr>
 * <td><b>Comment Section</b></td>
 * </tr>
 * <tr>
 * <td><B>Alignment Section</B></td>
 * </tr>
 * </table>
 *
 * Sequence letters may include any characters except whitespace. Gaps may be indicated by "." or "-".<br>
 * Mark-up lines may include any characters except whitespace. Use underscore ("_") instead of space.<br>
 *
 * <Table border="1">
 * <th>section field</th>
 * <th>preferred location</th>
 * <tr>
 * <td>#=GF &lt;feature&gt; &lt;Generic per-File annotation, free text&gt;</td>
 * <td>Above the alignment</td>
 * <tr>
 * <td>#=GC &lt;feature&gt; &lt;Generic per-Column annotation, exactly 1 char per column&gt;</td>
 * <td>Below the alignment</td>
 * <tr>
 * <td>#=GS &lt;seqname&gt; &lt;feature&gt; &lt;Generic per-Sequence annotation, free text&gt;</td>
 * <td>Above the alignment or just below the corresponding sequence</td>
 * <tr>
 * <td>#=GR &lt;seqname&gt; &lt;feature&gt; &lt;Generic per-Residue annotation, exactly 1 char per residue&gt;</td>
 * <td>Just below the corresponding sequence</td>
 * </tr>
 * </table>
 *
 * @since 3.0.5
 * @author Amr AL-Hossary
 * @author Marko Vaz
 *
 */
public class StockholmStructure {

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

        public static final String PFAM = "PFAM";
        public static final String RFAM = "RFAM";
        private final StockholmFileAnnotation fileAnnotation;
        private final StockholmConsensusAnnotation consAnnotation;
        private final Map<String, StringBuffer> sequences;
        private final Map<String, StockholmSequenceAnnotation> seqsAnnotation;
        private final Map<String, StockholmResidueAnnotation> resAnnotation;

        public StockholmStructure() {
                fileAnnotation = new StockholmFileAnnotation();
                consAnnotation = new StockholmConsensusAnnotation();
                sequences = new HashMap<String, StringBuffer>();
                seqsAnnotation = new HashMap<String, StockholmSequenceAnnotation>();
                resAnnotation = new HashMap<String, StockholmResidueAnnotation>();
        }

        public StockholmFileAnnotation getFileAnnotation() {
                return fileAnnotation;
        }

        public StockholmConsensusAnnotation getConsAnnotation() {
                return consAnnotation;
        }

        /**
         * Actually this function should be called appendToSequence
         *
         * @param seqName
         * @param seqText
         * @deprecated Use {@link #appendToSequence(String,String)} instead
         */
        @Deprecated
        public void addSequence(String seqName, String seqText) {
                appendToSequence(seqName, seqText);
        }

        /**
         * @param seqName
         * @param seqText
         */
        public void appendToSequence(String seqName, String seqText) {
                StringBuffer seq = sequences.get(seqName);
                if (seq != null) {
                        // add sequence without space
                        seq.append(seqText);
                } else {
                        seq = new StringBuffer(seqText);
                        sequences.put(seqName, seq);
                }
        }

        public Map<String, StringBuffer> getSequences() {
                return sequences;
        }

        private StockholmSequenceAnnotation getSequenceAnnotation(String seqName) {
                if (!seqsAnnotation.containsKey(seqName)) {
                        seqsAnnotation.put(seqName, new StockholmSequenceAnnotation());
                }
                return seqsAnnotation.get(seqName);
        }

        /**
         * @param seqName
         * @param text
         */
        public void addGSAccessionNumber(String seqName, String text) {
                getSequenceAnnotation(seqName).setAccessionNumber(text);
        }

        public void addGSDescription(String seqName, String text) {
                getSequenceAnnotation(seqName).addToDescription(text);
        }

        /**
         * @param seqName
         * @param text
         */
        public void addGSdbReference(String seqName, String text) {
                getSequenceAnnotation(seqName).addDBReference(text);
        }

        public void addGSOrganismSpecies(String seqName, String text) {
                getSequenceAnnotation(seqName).setOrganism(text);
        }

        public void addGSOrganismClassification(String seqName, String text) {
                getSequenceAnnotation(seqName).setOrganismClassification(text);
        }

        public void addGSLook(String seqName, String text) {
                getSequenceAnnotation(seqName).setLook(text);
        }

        private StockholmResidueAnnotation getResidueAnnotation(String seqName) {
                if (!resAnnotation.containsKey(seqName)) {
                        resAnnotation.put(seqName, new StockholmResidueAnnotation());
                }
                return resAnnotation.get(seqName);
        }

        public void addSurfaceAccessibility(String seqName, String text) {
                getResidueAnnotation(seqName).setSurfaceAccessibility(text);
        }

        public void addTransMembrane(String seqName, String text) {
                getResidueAnnotation(seqName).setTransMembrane(text);
        }

        public void addPosteriorProbability(String seqName, String text) {
                getResidueAnnotation(seqName).setPosteriorProbability(text);
        }

        public void addLigandBinding(String seqName, String text) {
                getResidueAnnotation(seqName).setLigandBinding(text);
        }

        public void addActiveSite(String seqName, String text) {
                getResidueAnnotation(seqName).setActiveSite(text);
        }

        public void addASPFamPredicted(String seqName, String text) {
                getResidueAnnotation(seqName).setAsPFamPredicted(text);
        }

        public void addASSwissProt(String seqName, String text) {
                getResidueAnnotation(seqName).setAsSwissProt(text);
        }

        public void addIntron(String seqName, String text) {
                getResidueAnnotation(seqName).setIntron(text);
        }

        public void addSecondaryStructure(String seqName, String text) {
                getResidueAnnotation(seqName).setSecondaryStructure(text);
        }

        /**
         * used to retrieve sequences from the structure
         *
         * @return Biosequences (case sensitive)
         * @see #getBioSequences(boolean)
         * @see #getBioSequences(boolean, String)
         */
        public List<AbstractSequence<? extends AbstractCompound>> getBioSequences() {
                return getBioSequences(false);
        }

        /**
         * This function tolerates mixed case letters, and allows for forcing the output biosequence type (PFAM/RFAM).
         *
         * @param ignoreCase
         *            if <code>true</code>, the function will deal with small letters as if they are capital ones
         * @param forcedSequenceType
         *            either <code>null</code>, {@link #PFAM}, or {@link #RFAM}.
         * @return Biosequences according to the criteria specified
         * @see #getBioSequences()
         * @see #getBioSequences(boolean)
         */
        public List<AbstractSequence<? extends AbstractCompound>> getBioSequences(boolean ignoreCase,
                        String forcedSequenceType) {
                if (forcedSequenceType != null && !(forcedSequenceType.equals(PFAM) | forcedSequenceType.equals(RFAM))) {
                        throw new IllegalArgumentException("Illegal Argument " + forcedSequenceType);
                }
                List<AbstractSequence<? extends AbstractCompound>> seqs = new ArrayList<AbstractSequence<? extends AbstractCompound>>();
                for (String sequencename : sequences.keySet()) {
                        AbstractSequence<? extends AbstractCompound> seq = null;
                        String sequence = sequences.get(sequencename).toString();
                        if (ignoreCase) {
                                sequence = sequence.toUpperCase();
                        }

                        try {
                        if (forcedSequenceType == null)
                                seq = fileAnnotation.isPFam() ? new ProteinSequence(sequence) : new RNASequence(sequence);
                        else if (forcedSequenceType.equals(PFAM))
                                seq = new ProteinSequence(sequence);
                        else
                                seq = new RNASequence(sequence);
                        } catch (CompoundNotFoundException e) {
                                logger.warn("Could not create sequence because of unknown compounds ({}). Sequence {} will be ignored.",e.getMessage(),sequencename);
                                continue;
                        }
                        String[] seqDetails = splitSeqName(sequencename);
                        seq.setDescription(seqDetails[0]);
                        seq.setBioBegin((seqDetails[1] == null || seqDetails[1].trim().equals("") ? null : new Integer(
                                        seqDetails[1])));
                        seq.setBioEnd((seqDetails[2] == null || seqDetails[2].trim().equals("") ? null : new Integer(seqDetails[2])));

                        seqs.add(seq);
                }
                return seqs;
        }

        /**
         * Because some database files have incorrectly small letters (e.g. Pfam23 structure PF00389.22 sequence
         * TKRA_BACSU/6-322), this function is used to ignore the small letters case.
         *
         * @param ignoreCase
         * @return
         * @see #getBioSequences()
         * @see #getBioSequences(boolean, String)
         */
        public List<AbstractSequence<? extends AbstractCompound>> getBioSequences(boolean ignoreCase) {
                return getBioSequences(ignoreCase, null);
        }

        /**
         * Returns an array with the following sequence related content: name, start, end.
         *
         * @param sequenceName
         *            the sequence from where to extract the content. It is supposed that it follows the following
         *            convention name/start-end (e.g.: COATB_BPIKE/30-81)
         * @return array with the following sequence related content: name, start, end.
         */
        private String[] splitSeqName(String sequenceName) {
                String[] result = new String[3];

                String[] barSplit = sequenceName.toString().split("/");
                if (barSplit.length == 2) {
                        result[0] = barSplit[0];
                        String[] positions = barSplit[1].split("-");
                        if (positions.length == 2) {
                                result[1] = positions[0];
                                result[2] = positions[1];
                        }
                } else {
                        result[0] = sequenceName;
                        result[1] = null;
                        result[2] = null;
                }

                return result;
        }

        @Override
        public String toString() {
                StringBuffer result = new StringBuffer();
                List<AbstractSequence<? extends AbstractCompound>> bioSeqs = getBioSequences(false);
                int sequenceLength = -1;
                for (AbstractSequence<? extends AbstractCompound> sequence : bioSeqs) {
                        String sequenceAsString = sequence.getSequenceAsString();
                        sequenceLength = sequenceAsString.length();
                        if (sequenceLength > 50) {
                                result.append(sequenceAsString.substring(0, 40));
                                result.append("...");
                                result.append(sequenceAsString.substring(sequenceLength - 3, sequenceLength));
                        } else {
                                result.append(sequenceAsString);
                        }
                        result.append(" " + sequence.getDescription() + "\n");
                }
                result.append("Alignment with " + bioSeqs.size() + " rows and " + sequenceLength + " columns");

                return result.toString();
        }

        public static class DatabaseReference {
                public static final String EXPERT = "EXPERT";
                public static final String MIM = "MIM";
                public static final String PFAMB = "PFAMB";
                public static final String PRINTS = "PRINTS";
                public static final String PROSITE = "PROSITE";
                public static final String PROSITE_PROFILE = "PROSITE_PROFILE";
                public static final String SCOP = "SCOP";
                public static final String PDB = "PDB";
                public static final String SMART = "SMART";
                public static final String URL = "URL";
                public static final String LOAD = "LOAD";
                public static final String HOMSTRAD = "HOMSTRAD";
                public static final String INTERPRO = "INTERPRO";

                private final String database;
                /** TODO this field should be subdivided into smaller fields if the database is SCOP or PDB. */
                private final String reference;

                public DatabaseReference(String database, String reference) {
                        this.database = database;
                        this.reference = reference;
                }

                public DatabaseReference(String representativeAnnotationString) {
                        int semiColonIndex = representativeAnnotationString.indexOf(';');
                        this.database = representativeAnnotationString.substring(0, semiColonIndex);
                        this.reference = representativeAnnotationString.substring(semiColonIndex + 1,
                                        representativeAnnotationString.lastIndexOf(';')).trim();
                }

                @Override
                public String toString() {
                        return new StringBuilder(this.database).append(';').append(' ').append(this.reference).append(';')
                                        .toString();
                }

                public String getDatabase() {
                        return database;
                }

                public String getReference() {
                        return reference;
                }
        }
}