/*
 *                    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.core.alignment.matrices;

import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;



public class AAIndexFileParser {
        int scale = -1;

        Map<String,SubstitutionMatrix<AminoAcidCompound>> matrices;

        ScaledSubstitutionMatrix currentMatrix;
        String currentRows;
        String currentCols;
        int currentRowPos;
        private short[][] matrix;
        short max;
        short min;
        private List<AminoAcidCompound> rows, cols;
        boolean inMatrix;
        boolean symmetricMatrix ;


        public AAIndexFileParser(){
                matrices  = new HashMap<String, SubstitutionMatrix<AminoAcidCompound>>();
        }

        /** parse an inputStream that points to an AAINDEX database file
         *
         * @param inputStream
         * @throws IOException
         */
        public void parse(InputStream inputStream) throws IOException {

                currentMatrix = null;
                currentRows = "";
                currentCols = "";
                max = Short.MIN_VALUE;
                min = Short.MAX_VALUE;
                inMatrix = false;

                BufferedReader buf = new BufferedReader (new InputStreamReader (inputStream));
                String line = null;
                line = buf.readLine();

                while (  line != null ) {

                        if ( line.startsWith("//")) {
                                finalizeMatrix();
                                inMatrix = false;

                        } else if ( line.startsWith("H ")){
                                // a new matric!
                                newMatrix(line);
                        } else if ( line.startsWith("D ")) {
                                currentMatrix.setDescription(line.substring(2));
                        } else if ( line.startsWith("M ")) {
                                initMatrix(line);
                                inMatrix = true;
                        } else if ( line.startsWith("  ")){
                                if ( inMatrix)
                                        processScores(line);
                        }

                        line = buf.readLine();
                }

        }


        //  process a line such as >    -0.3     1.6     0.7     0.8    -2.6     3.0<
        private void processScores(String line) {

                String[] values = line.trim().split(" +");

                // increment the current row we are talking about
                currentRowPos++;



                for ( int i =0 ; i < values.length ; i++){

                        if ( values[i].endsWith(".")) {
                                values[i] = values[i] + "0";
                        }

                        // special case: MEHP950101
                        if (values[i].equals("-")) {
                                values[i] = "0";
                        }

                        if ( scale == -1 ) {
                                scale = determineScale(values[0]);
                        }


                        Float score = Float.parseFloat(values[i]);
                        score = scale * score;

                        Short s = (short) Math.round(score);

                        matrix[currentRowPos][i] = s;

                        if ( values.length < cols.size() || ( symmetricMatrix)){
                                //System.out.println(values.length + " " + cols.size() + " " + currentRowPos + " " + i + " " +  line);

                                matrix[i][currentRowPos] = s;

                                symmetricMatrix = true;

                        }

                        if ( score > max)
                                max = s;
                        if ( score < min)
                                min = s;


                }
        }

        private int determineScale(String value) {

                String[] spl = value.split("\\.");

                if (spl.length <= 1)
                        return 1;

                String digits = spl[1];

                return (int)Math.round(Math.pow(10, digits.length()));

        }

        // process a line of type >M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV<
        private void initMatrix(String line) {
                String[] spl = line.split(" ");

                // trim off the final , character
                currentRows = spl[3].substring(0, spl[3].length()-1);
                currentCols = spl[6];
                currentRowPos = -1;

                int nrRows = currentRows.length();
                int nrCols = currentCols.length();

                matrix = new short[nrRows][nrCols];

                rows = new ArrayList<AminoAcidCompound>();
                cols = new ArrayList<AminoAcidCompound>();


                //System.out.println(">" + currentRows+"<");
                AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
                for ( int i = 0 ; i < currentRows.length() ; i ++){
                        char c = currentRows.charAt(i);
                        AminoAcidCompound aa = compoundSet.getCompoundForString(c+"");

                        rows.add(aa);
                }

                for ( int i = 0 ; i < currentCols.length() ; i ++){
                        char c = currentRows.charAt(i);
                        AminoAcidCompound aa = compoundSet.getCompoundForString(c+"");

                        cols.add(aa);
                }





                currentMatrix.setScale(scale);
        }


        private void newMatrix(String line) {
                symmetricMatrix = false;
                scale = -1;

                currentMatrix = new ScaledSubstitutionMatrix();
                currentMatrix.setName(line.substring(2));


                //System.out.println("new Matrix " + currentMatrix.getName());
        }

        //
        private SubstitutionMatrix<AminoAcidCompound> finalizeMatrix() {

                currentMatrix.setMatrix(matrix);
                currentMatrix.setMax(max);
                currentMatrix.setMin(min);
                currentMatrix.setCols(cols);
                currentMatrix.setRows(rows);
                currentMatrix.setScale(scale);
                matrices.put(currentMatrix.getName(), currentMatrix);

                return currentMatrix;

        }

        public Map<String, SubstitutionMatrix<AminoAcidCompound>> getMatrices() {
                return matrices;
        }
}