import ij.io.OpenDialog;
import ij.io.SaveDialog;
import java.util.ArrayList;
import java.io.IOException;
import java.io.File;
import com.jmatio.types.*; //jmatio.types.*;
import com.jmatio.io.*; //jmatio.io.*;
import ij.gui.GenericDialog;
import ij.IJ;
import ij.Prefs;

public class ShiftsIO {
    
    public ShiftsIO () {}

    public double[][] load(String filename, String varname) {
        if (filename==null){
                String analysis_dir =  Prefs.get("peem.analysis_dir", "");
                OpenDialog od = new OpenDialog("Open_shifts .mat file:", analysis_dir, "shifts.mat");
                String dir = od.getDirectory();
                if (null == dir) return null; // dialog was canceled
                if (!dir.endsWith(File.separator)) dir += File.separator;
                filename = dir + od.getFileName();
                Prefs.set("peem.analysis_dir", dir);
            }
            return low_load(filename, varname);
    }

       private double[][] low_load(String filename, String varname) {
        MatFileReader mfr = null;
        try {
            mfr = new MatFileReader(filename);
        } catch (IOException e) {
                System.err.println("Caught IOException: "
                    + e.getMessage());
        }

        if (mfr != null) {
            MLDouble array = (MLDouble)mfr.getMLArray(varname);
            if (array != null){
                return array.getArray();
            } else {
                return null;
            }
        } else {
            return null;
        }
    }

    public void save(String filename, double[][] shifts, String varname) {
        boolean update = false;
        if (filename==null){
        String analysis_dir =  Prefs.get("peem.analysis_dir", "");
        SaveDialog sd = new SaveDialog("Save_shifts .mat file:", analysis_dir, "shifts.mat", ".mat");
            String dir = sd.getDirectory();
            String fname = sd.getFileName();
            if (null == fname) return; // user canceled dialog
            if (!dir.endsWith(File.separator)) dir += File.separator;
            Prefs.set("peem.analysis_dir", dir);       
        
            if ((new File(dir + fname)).exists()) { // if file exist, overwrite or update shifts ?
                GenericDialog gd = new GenericDialog("Update");
                String[] options = {"overwrite","update"};
            gd.addChoice("Mode of operation with existing file. You want to: ", options, options[0]);
            gd.showDialog();
            if (gd.wasCanceled()) return;
            if (gd.getNextChoiceIndex() == 1) update = true;
            }
            filename = dir + fname;
        } 
        double[][] final_shifts;
            if (update) {
                double[][] prev_shifts = low_load(filename, "directshifts");
                if (prev_shifts == null) {
                    IJ.error("Can't read the direct shifts in this file");
                    return;
                }

            if (prev_shifts.length == shifts.length) {
                    for (int j = 0; j < prev_shifts.length; j++) {
                        prev_shifts[j][3] += shifts[j][3];
                        prev_shifts[j][4] += shifts[j][4];
                    }
            } else if (shifts.length == 2) {// 2 shifts, like between two slices of different
                            // sequences
                 for (int j = 0; j < prev_shifts.length; j++) {
                        prev_shifts[j][3] += shifts[1][3];
                        prev_shifts[j][4] += shifts[1][4];
                    }
            } else {
                IJ.error("Old and new shifts have incompatible length !");
                return;
            }
            final_shifts = prev_shifts;
            } else {
            final_shifts = shifts;
            }
            
            MLDouble mlDouble = new MLDouble(varname, final_shifts);
            ArrayList<MLArray> list = new ArrayList<MLArray>();
        list.add(mlDouble);
        try {
            new MatFileWriter(filename, list);
        } catch (IOException e) {
                System.err.println("Caught IOException: "
                            + e.getMessage());
        }       
    }
}