/*
 * Arguments.java
 *
 * Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut
 *
 * This file is part of BEAST.
 * See the NOTICE file distributed with this work for additional
 * information regarding copyright ownership and licensing.
 *
 * BEAST is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as
 * published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 *  BEAST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with BEAST; if not, write to the
 * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
 * Boston, MA  02110-1301  USA
 */

package dr.app.util;

import java.util.StringTokenizer;

public class Arguments {

	public static final String ARGUMENT_CHARACTER = "-";

	public static class ArgumentException extends Exception {
		/**
		 *
		 */
		private static final long serialVersionUID = -3229759954341228233L;

        public ArgumentException() {
            super();
	}

        public ArgumentException(String message) {
            super(message);
        }
    }

	public static class Option {

		public Option(String label, String description) {
			this.label = label;
			this.description = description;
		}

		String label;
		String description;
		boolean isAvailable = false;
	}

	public static class StringOption extends Option {
        /**
         * @param label       Option name:
         * @param tag         Descriptive name of option argument.
         *                    Example - tag "file-name" will show '-save <file-name>' in the usage.
         * @param description
         */
		public StringOption(String label, String tag, String description) {
			super(label, description);
			this.tag = tag;
		}

		public StringOption(String label, String[] options, boolean caseSensitive, String description) {
			super(label, description);
			this.options = options;
			this.caseSensitive = caseSensitive;
		}

		String[] options = null;
		String tag = null;
		boolean caseSensitive = false;

		String value = null;
	}

	public static class IntegerOption extends Option {

		public IntegerOption(String label, String description) {
			super(label, description);
		}

		public IntegerOption(String label, int minValue, int maxValue, String description) {
			super(label, description);
			this.minValue = minValue;
			this.maxValue = maxValue;
		}

		int minValue = Integer.MIN_VALUE;
		int maxValue = Integer.MAX_VALUE;

		int value = 0;
	}

	public static class IntegerArrayOption extends IntegerOption {

        public IntegerArrayOption(String label, String description) {
            this(label, 0, Integer.MIN_VALUE, Integer.MAX_VALUE, description);
        }

		public IntegerArrayOption(String label, int count, String description) {
            this(label, count, Integer.MIN_VALUE, Integer.MAX_VALUE, description);
		}

        public IntegerArrayOption(String label, int minValue, int maxValue, String description) {
            this(label, 0, minValue, maxValue, description);
        }

		public IntegerArrayOption(String label, int count, int minValue, int maxValue, String description) {
			super(label, minValue, maxValue, description);
            this.count = count;
        }

		int count;

		int[] values = null;
	}

    public static class LongOption extends Option {

        public LongOption(String label, String description) {
            super(label, description);
        }

        public LongOption(String label, long minValue, long maxValue, String description) {
            super(label, description);
            this.minValue = minValue;
            this.maxValue = maxValue;
        }

        long minValue = Long.MIN_VALUE;
        long maxValue = Long.MAX_VALUE;

        long value = 0;
    }

	public static class RealOption extends Option {

		public RealOption(String label, String description) {
			super(label, description);
		}

		public RealOption(String label, double minValue, double maxValue, String description) {
			super(label, description);
			this.minValue = minValue;
			this.maxValue = maxValue;
		}

		double minValue = Double.NEGATIVE_INFINITY;
		double maxValue = Double.POSITIVE_INFINITY;

		double value = 0;
	}

	public static class RealArrayOption extends RealOption {

//        public RealArrayOption(String label, String description) {
//            this(label, 0, Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY, description);
//        }
        // A count of -1 means any length
		public RealArrayOption(String label, int count, String description) {
            this(label, count, Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY, description);
		}

//        public RealArrayOption(String label, double minValue, double maxValue, String description) {
//            this(label, 0, minValue, maxValue, description);
//        }

		public RealArrayOption(String label, int count, double minValue, double maxValue, String description) {
			super(label, minValue, maxValue, description);
			this.count = count;
        }

		private int count;

		double[] values = null;
	}

	/**
	 * Parse a list of arguments ready for accessing
	 */
	public Arguments(Option[] options) {
		this.options = options;
	}

	public Arguments(Option[] options, boolean caseSensitive) {
		this.options = options;
		this.caseSensitive = caseSensitive;
	}

	/**
	 * Parse a list of arguments ready for accessing
	 */
    public int parseArguments(String[] arguments) throws ArgumentException {

		int[] optionIndex = new int[arguments.length];
		for (int i = 0; i < optionIndex.length; i++) {
			optionIndex[i] = -1;
		}

		for (int i = 0; i < options.length; i++) {
			Option option = options[i];

			int index = findArgument(arguments, option.label);
			if (index != -1) {

				if (optionIndex[index] != -1) {
					throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument");
				}

				// the first value may be appended to the option label (e.g., '-t1.0'):
				String arg = arguments[index].substring(option.label.length() + 1);
				optionIndex[index] = i;
				option.isAvailable = true;

				if (option instanceof IntegerArrayOption) {

                    IntegerArrayOption o = (IntegerArrayOption) option;
					o.values = new int[o.count];
					int k = index;
					int j = 0;

					while (j < o.count) {
						if (arg.length() > 0) {
							StringTokenizer tokenizer = new StringTokenizer(arg, ",\t ");
							while (tokenizer.hasMoreTokens()) {
								String token = tokenizer.nextToken();
								if (token.length() > 0) {
									try {
										o.values[j] = Integer.parseInt(token);
									} catch (NumberFormatException nfe) {
										throw new ArgumentException("Argument, " + arguments[index] +
											" has a bad integer value: " + token);
									}
									if (o.values[j] > o.maxValue || o.values[j] < o.minValue) {
										throw new ArgumentException("Argument, " + arguments[index] +
											" has a bad integer value: " + token);
									}
									j++;
								}
							}
						}

						k++;

						if (j < o.count) {
							if (k >= arguments.length) {
								throw new ArgumentException("Argument, " + arguments[index] +
									" is missing one or more values: expecting " + o.count + " integers");
							}

							if (optionIndex[k] != -1) {
								throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument");
							}

							arg = arguments[k];
							optionIndex[k] = i;
						}
					}
				} else if (option instanceof IntegerOption) {

                    IntegerOption o = (IntegerOption) option;
					if (arg.length() == 0) {
						int k = index + 1;
						if (k >= arguments.length) {
							throw new ArgumentException("Argument, " + arguments[index] +
								" is missing its value: expecting an integer");
						}

						if (optionIndex[k] != -1) {
							throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument");
						}
						arg = arguments[k];
						optionIndex[k] = i;
					}

					try {
						o.value = Integer.parseInt(arg);
					} catch (NumberFormatException nfe) {
						throw new ArgumentException("Argument, " + arguments[index] +
							" has a bad integer value: " + arg);
					}
					if (o.value > o.maxValue || o.value < o.minValue) {
						throw new ArgumentException("Argument, " + arguments[index] +
							" has a bad integer value: " + arg);
					}
                } else if (option instanceof LongOption) {

                    LongOption o = (LongOption) option;
                    if (arg.length() == 0) {
                        int k = index + 1;
                        if (k >= arguments.length) {
                            throw new ArgumentException("Argument, " + arguments[index] +
                                " is missing its value: expecting a long integer");
                        }

                        if (optionIndex[k] != -1) {
                            throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument");
                        }
                        arg = arguments[k];
                        optionIndex[k] = i;
                    }

                    try {
                        o.value = Long.parseLong(arg);
                    } catch (NumberFormatException nfe) {
                        throw new ArgumentException("Argument, " + arguments[index] +
                            " has a bad integer value: " + arg);
                    }
                    if (o.value > o.maxValue || o.value < o.minValue) {
                        throw new ArgumentException("Argument, " + arguments[index] +
                            " has a bad long integer value: " + arg);
                    }
				} else if (option instanceof RealArrayOption) {
                    // I fixed only the real case to handle a variable sized array
                    // I don't have the time to figure out the right way, so I duplicated some code so
                    // that I do not break code by mistake
                    RealArrayOption o = (RealArrayOption) option;
                    if (o.count >= 0) {
                        final int count = o.count;
                        o.values = new double[count];
                        int k = index;
                        int j = 0;

                        while (j < count) {
                            if (arg.length() > 0) {
                                StringTokenizer tokenizer = new StringTokenizer(arg, ",\t ");
                                while (tokenizer.hasMoreTokens()) {
                                    String token = tokenizer.nextToken();
                                    if (token.length() > 0) {
                                        try {
                                            o.values[j] = Double.parseDouble(token);
                                        } catch (NumberFormatException nfe) {
                                            throw new ArgumentException("Argument, " + arguments[index] +
                                                    " has a bad real value: " + token);
                                        }
                                        if (o.values[j] > o.maxValue || o.values[j] < o.minValue) {
                                            throw new ArgumentException("Argument, " + arguments[index] +
                                                    " has a bad real value: " + token);
                                        }
                                        j++;
                                    }
                                }
                            }

                            k++;

                            if (j < count) {
                                if (k >= arguments.length) {
                                    throw new ArgumentException("Argument, " + arguments[index] +
                                            " is missing one or more values: expecting " + count + " integers");
                                }

                                if (optionIndex[k] != -1) {
                                    throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument");
                                }

                                arg = arguments[k];
                                optionIndex[k] = i;
                            }
                        }
                    } else {

                        double[] values = new double[100];
                        index += 1;
                        arg = arguments[index];
                        optionIndex[index] = i;
                        
                        int j = 0;

                        if (arg.length() > 0) {
                            StringTokenizer tokenizer = new StringTokenizer(arg, ",\t ");
                            while (tokenizer.hasMoreTokens()) {
                                String token = tokenizer.nextToken();
                                if (token.length() > 0) {
                                    try {
                                        values[j] = Double.parseDouble(token);
                                    } catch (NumberFormatException nfe) {
                                        throw new ArgumentException("Argument, " + arguments[index] +
                                                " has a bad real value: " + token);
                                    }
                                    if (values[j] > o.maxValue || values[j] < o.minValue) {
                                        throw new ArgumentException("Argument, " + arguments[index] +
                                                " has a bad real value: " + token);
                                    }
                                    j++;
                                }
                            }
                        }
                        o.values = new double[j];
                        System.arraycopy(values, 0, o.values, 0, j);
                    }
				} else if (option instanceof RealOption) {

                    RealOption o = (RealOption) option;
					if (arg.length() == 0) {
						int k = index + 1;
						if (k >= arguments.length) {
							throw new ArgumentException("Argument, " + arguments[index] +
								" is missing its value: expecting a real number");
						}

						if (optionIndex[k] != -1) {
							throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument");
						}
						arg = arguments[k];
						optionIndex[k] = i;
					}

					try {
						o.value = Double.parseDouble(arg);
					} catch (NumberFormatException nfe) {
						throw new ArgumentException("Argument, " + arguments[index] +
							" has a bad real value: " + arg);
					}
					if (o.value > o.maxValue || o.value < o.minValue) {
						throw new ArgumentException("Argument, " + arguments[index] +
							" has a bad real value: " + arg);
					}
				} else if (option instanceof StringOption) {

                    StringOption o = (StringOption) option;
					if (arg.length() == 0) {
						int k = index + 1;
						if (k >= arguments.length) {
							throw new ArgumentException("Argument, " + arguments[index] +
								" is missing its value: expecting a string");
						}

						if (optionIndex[k] != -1) {
							throw new ArgumentException("Argument, " + arguments[index] + " overlaps with another argument");
						}
						arg = arguments[k];
						optionIndex[k] = i;
					}

					o.value = arg;

					if (o.options != null) {
						boolean found = false;
                        for (String option1 : o.options) {
                            if ((!caseSensitive && option1.equalsIgnoreCase(o.value)) || option1.equals(o.value)) {
                                found = true;
                                break;
                            }
                        }
                        if (!found) {
							throw new ArgumentException("Argument, " + arguments[index] +
								" has a bad string value: " + arg);
						}
					}
				} else { // is simply an Option - nothing to do...
				}
			}
		}

		int n = 0;
		int i = arguments.length - 1;
		while (i >= 0 && optionIndex[i] == -1 && !arguments[i].startsWith(ARGUMENT_CHARACTER)) {
			n++;
			i--;
		}
		leftoverArguments = new String[n];
		for (i = 0; i < n; i++) {
			leftoverArguments[i] = arguments[arguments.length - n + i];
		}

		for (i = 0; i < arguments.length - n; i++) {
			if (optionIndex[i] == -1) {
				throw new ArgumentException("Unrecognized argument: " + arguments[i]);
			}
		}
        return n;
	}

	private int findArgument(String[] arguments, String label) {
		for (int i = 0; i < arguments.length; i++) {

			if (arguments[i].length() - 1 >= label.length()) {
				if (arguments[i].startsWith(ARGUMENT_CHARACTER)) {
//					String l = arguments[i].substring(1, label.length() + 1);
//                                                String l = arguments[i];
                                                  String l = arguments[i].substring(1, arguments[i].length());
					if ((!caseSensitive && label.equalsIgnoreCase(l)) || label.equals(l)) {
						return i;
					}

				}
			}
		}
		return -1;
	}

	/**
	 * Does an argument with label exist?
	 */
	public boolean hasOption(String label) {
		int n = findOption(label);
		if (n == -1) {
			return false;
		}

		return options[n].isAvailable;
	}

	/**
	 * Return the value of an integer option
	 */
	public int getIntegerOption(String label) {
		IntegerOption o = (IntegerOption)options[findOption(label)];
		return o.value;
	}

	/**
	 * Return the value of an integer array option
	 */
	public int[] getIntegerArrayOption(String label) {
		IntegerArrayOption o = (IntegerArrayOption)options[findOption(label)];
		return o.values;
	}

    /**
     * Return the value of an integer option
     */
    public long getLongOption(String label) {
        LongOption o = (LongOption)options[findOption(label)];
        return o.value;
    }

	/**
	 * Return the value of an real number option
	 */
	public double getRealOption(String label) {
		RealOption o = (RealOption)options[findOption(label)];
		return o.value;
	}

	/**
	 * Return the value of an real array option
	 */
	public double[] getRealArrayOption(String label) {
		RealArrayOption o = (RealArrayOption)options[findOption(label)];
		return o.values;
	}

	/**
	 * Return the value of an string option
	 */
	public String getStringOption(String label) {
		StringOption o = (StringOption)options[findOption(label)];
		return o.value;
	}

	/**
	 * Return any arguments leftover after the options
	 */
	public String[] getLeftoverArguments() {
		return leftoverArguments;
	}

	public void printUsage(String name, String commandLine) {

		System.out.print("  Usage: " + name);
        for (Option option : options) {
            System.out.print(" [-" + option.label);

            if (option instanceof IntegerArrayOption) {

                IntegerArrayOption o = (IntegerArrayOption) option;
                for (int j = 1; j <= o.count; j++) {
                    System.out.print(" <i" + j + ">");
                }
                System.out.print("]");
            } else if (option instanceof IntegerOption) {

                System.out.print(" <i>]");
            } else if (option instanceof RealArrayOption) {

                RealArrayOption o = (RealArrayOption) option;
                for (int j = 1; j <= o.count; j++) {
                    System.out.print(" <r" + j + ">");
                }
                System.out.print("]");
            } else if (option instanceof RealOption) {

                System.out.print(" <r>]");
            } else if (option instanceof StringOption) {

                StringOption o = (StringOption) option;
                if (o.options != null) {
                    System.out.print(" <" + o.options[0]);
                    for (int j = 1; j < o.options.length; j++) {
                        System.out.print("|" + o.options[j]);
                    }
                    System.out.print(">]");
                } else {
                    System.out.print(" <" + o.tag + ">]");
                }
            } else {
                System.out.print("]");
            }
        }
		System.out.println(" " + commandLine);

        for (Option option : options) {
            System.out.println("    -" + option.label + " " + option.description);
        }
	}

	private int findOption(String label) {
		for (int i = 0; i < options.length; i++) {
			String l = options[i].label;
			if ((!caseSensitive && label.equalsIgnoreCase(l)) || label.equals(l)) {
				return i;
			}
		}
		return -1;
	}

	private Option[] options = null;

	private String[] leftoverArguments = null;

	private boolean caseSensitive = false;
}

