/*
 *                    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 at May 25, 2008
 */
package org.biojava.nbio.structure.gui.util;


import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.io.File;
import java.io.IOException;
import java.net.URL;
import java.util.Arrays;

import javax.swing.AbstractAction;
import javax.swing.Action;
import javax.swing.Box;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JPanel;
import javax.swing.JTextField;

import org.biojava.nbio.structure.ResidueRange;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.SubstructureIdentifier;
import org.biojava.nbio.structure.align.util.UserConfiguration;
import org.biojava.nbio.structure.io.CifFileReader;
import org.biojava.nbio.structure.io.PDBFileReader;
import org.biojava.nbio.structure.io.StructureIOFile;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/** A JPanel to upload 2 custom PDB files.
 *
 * @author Andreas Prlic
 * @since 1.7
 */
public class PDBUploadPanel
extends JPanel
implements StructurePairSelector {

        /**
         *
         */
        private static final long serialVersionUID = 1L;



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



        private JComboBox<String> fileType ;

        JTextField filePath1;
        JTextField filePath2;
        JTextField chain1;
        JTextField chain2;

        public static JComboBox<String> getFileFormatSelect(){
                JComboBox<String> fileType = new JComboBox<>();
                        fileType = new JComboBox<String>(new String[] {UserConfiguration.PDB_FORMAT,UserConfiguration.MMCIF_FORMAT});
                        fileType.setSelectedIndex(0);
                        fileType.setMaximumSize(new Dimension(10,50));

                return fileType;
        }
        public PDBUploadPanel(){
                this(true);
        }
        public PDBUploadPanel(boolean show2boxes){
                Box vBox = Box.createVerticalBox();

                filePath1 = new JTextField(20);
                filePath2 = new JTextField(20);
                chain1 = new JTextField(1);
                chain2 = new JTextField(1);

                JPanel p1 = getLocalFilePanel(1,filePath1,chain1);
                JPanel p2 = getLocalFilePanel(2,filePath2,chain2);

                vBox.add(p1);
                if ( show2boxes)
                        vBox.add(p2);

                JLabel ftype = new JLabel("File format:");
                Box hBox = Box.createHorizontalBox();
                hBox.add(Box.createGlue());
                hBox.add(ftype);
                fileType = getFileFormatSelect();
                hBox.add(fileType);
                hBox.add(Box.createGlue());

                vBox.add(hBox);

                this.add(vBox);
        }


        public String getFilePath1(){
                return filePath1.getText();
        }

        public String getChain1(){
                return chain1.getText();
        }

        @Override
        public Structure getStructure1() throws StructureException{

                return getStructure(filePath1,chain1);
        }

        @Override
        public Structure getStructure2() throws StructureException{

                return getStructure(filePath2,chain2);
        }

        private Structure getStructure(JTextField filePath,JTextField chainId) throws StructureException{
                //PDBFileReader reader = new PDBFileReader();

                StructureIOFile reader = null;
                String fileFormat = (String)fileType.getSelectedItem();
                if ( fileFormat.equals(UserConfiguration.PDB_FORMAT)){
                        reader = new PDBFileReader();
                } else if ( fileFormat.equals(UserConfiguration.MMCIF_FORMAT)){
                        reader = new CifFileReader();
                } else {
                        throw new StructureException("Unkown file format " + fileFormat);
                }

                String path = filePath.getText();
                File f = new File(path);
                Structure s = null;
                try {
                        s = reader.getStructure(f);
                } catch (IOException  e){
                        logger.warn(e.getMessage());
                        //e.printStackTrace();
                        throw new StructureException(e);
                }

//              Structure reduced = StructureTools.getReducedStructure(s, chainId.getText());
//              Structure reduced = new SubstructureIdentifier(s.getPdbId().getId()+"."+ chainId.getText()).reduce(s);  //TODO double check this
                Structure reduced = new SubstructureIdentifier(s.getPdbId(),
                                Arrays.asList(new ResidueRange(chainId.getText(), (String) null, null))).reduce(s);

                String fileURL = "";
                try {

                        URL u ;

                        if ( chainId.getText() == null || chainId.getText().equals("")){

                                u = f.toURI().toURL();
                        } else {
                                u = new URL(f.toURI().toURL().toString() + "?chainId=" + chainId.getText());
                        }
                        fileURL = u.toString() ;

                } catch (Exception e){
                        e.printStackTrace();
                }

                reduced.setPDBCode(fileURL);  //TODO FIXME This usage seems wrong and should be changed.
                reduced.setName(fileURL);
                return reduced;

        }



        private JPanel getLocalFilePanel(int pos ,JTextField filePath, JTextField  chainId){

                JPanel panel = new JPanel();
                //panel.setBorder(BorderFactory.createLineBorder(Color.black));

                JLabel l01 = new JLabel("File "+pos+":");
                panel.add(l01);

                panel.add(filePath);
                Action action3 = new ChooseAction(filePath);
                JButton chooser = new JButton(action3);
                panel.add(chooser);

                JLabel chainLabel = new JLabel("Chain "+pos+": (optional)");
                panel.add(chainLabel);
                panel.add(chainId);

                return panel;

        }
}

class ChooseAction extends AbstractAction{

        JTextField textField;
        public ChooseAction (JTextField textField){
                super("Choose");
                this.textField = textField;
        }
        public static final long serialVersionUID = 0l;
        // This method is called when the button is pressed
        @Override
        public void actionPerformed(ActionEvent evt) {
                // Perform action...
                final JFileChooser fc = new JFileChooser();

                //              In response to a button click:
                int returnVal = fc.showOpenDialog(null);
                if ( returnVal == JFileChooser.APPROVE_OPTION) {
                        File file = fc.getSelectedFile();
                        textField.setText(file.getAbsolutePath());
                        textField.repaint();


                }

        }
}