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package signature.chemistry;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;

import signature.chemistry.Molecule.BondOrder;

public class MoleculeReader {

    public static Molecule readMolfile(String filename) {
        Molecule molecule = null;
        try {
            File file = new File(filename);
            BufferedReader reader = new BufferedReader(new FileReader(file));
            String line;
            List block = new ArrayList();
            while ((line = reader.readLine()) != null) {
                block.add(line);
            }
            molecule = makeMolecule(block);
            reader.close();
        } catch (IOException ioe) {
            System.err.println(ioe.toString());
        } catch (Exception e) {
            System.err.println(e.toString());
        }
        return molecule;
    }
    
    
	/**
	 * Read a list of Molecule from SDFile
	 * @param filename path to SDFile
	 * @return List of Molecules
	 */
    public static List readSDFFile(String filename) {

        File file = new File(filename);
        try {
            return readSDFfromStream(new FileInputStream(file));
        } catch (FileNotFoundException e) {
            System.err.println(e.toString());
        }
        return null;
    }
    
	/**
	 * Read a list of Molecule from an InputStream, providing SDFile contents
	 * @param stream InputStream to read from
	 * @return List of Molecules
	 */
    public static List readSDFfromStream(InputStream stream) {
        List molecules = new ArrayList();
        try {
            InputStreamReader ir = new InputStreamReader(stream);
            
            BufferedReader reader = new BufferedReader(ir);
            String line;
            int i = 0;
            List block = new ArrayList();
            while ((line = reader.readLine()) != null) {
                if (line.startsWith("$$$$")) {
                    Molecule molecule;
                    try {
                        molecule = MoleculeReader.makeMolecule(block); 
                        molecules.add(molecule);
                    } catch (Exception e) {
                        System.err.println("failed for block " + i + " " + e);
                        e.printStackTrace();
                    }
                    block.clear();
                    i++;
                } else {
                    block.add(line);
                }
            }
        } catch (IOException ioe) {
            System.err.println(ioe.toString());
        } 
        return molecules;
    }
    
    private static Molecule makeMolecule(List block) throws Exception {
        Molecule molecule = new Molecule();
        // counts are on the fourth line
        String countLine = block.get(3);
        int atomCount = Integer.parseInt(countLine.substring(0, 3).trim());
        int bondCount = Integer.parseInt(countLine.substring(3, 6).trim());
        
        // atom block starts on the fifth line (4th index)
        int atomLineStart = 4;
        int atomLineEnd   = atomCount + atomLineStart; 
        for (int i = atomLineStart; i < atomLineEnd; i++) {
            String symbol = block.get(i).substring(30, 33).trim();
            int atomIndex = i - atomLineStart;
            molecule.addAtom(atomIndex, symbol);
        }
        
        if (atomCount > 1) {
            // bond block starts right after the atom block
            int bondLineStart = atomLineEnd;
            int bondLineEnd = bondLineStart + bondCount;
            for (int i = bondLineStart; i < bondLineEnd; i++) {
                String bondLine = block.get(i);
                int atomNumberA = 
                    Integer.parseInt(bondLine.substring(0, 3).trim());
                int atomNumberB = 
                    Integer.parseInt(bondLine.substring(3, 6).trim());
                int order = Integer.parseInt(bondLine.substring(7, 10).trim());
                BondOrder o = convertIntToBondOrder(order);
                molecule.addBond(atomNumberA - 1, atomNumberB - 1, o);
        	}
        }
        return molecule;
    }
    
    private static BondOrder convertIntToBondOrder(int o) {
        switch (o) {
            case 1: return BondOrder.SINGLE;
            case 2: return BondOrder.DOUBLE;
            case 3: return BondOrder.TRIPLE;
            case 4: return BondOrder.AROMATIC;
            default : return BondOrder.SINGLE; 
        }
    }

}