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/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
*    list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
*    this list of conditions and the following disclaimer in the documentation
*    and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
*    names of its contributors may be used to endorse or promote products
*    derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/

package com.actelion.research.chem.io;

import com.actelion.research.chem.Canonizer;
import com.actelion.research.chem.StereoMolecule;

import java.io.BufferedWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Properties;
import java.util.TreeMap;

public class DWARFileCreator {
	private BufferedWriter mWriter;
	private String[] mRow;
	private ArrayList mColumnTitleList;
	private TreeMap mColumnPropertiesMap;

	/**
	 * Use a DWARFileCreator for writing native DataWarrior files without a CompoundTableModel.
	 * (if you have a populated CompoundTableModel, use the CompoundTableSaver instead).
	 * To use the DWARFileCreator you need to follow these steps:

	 * - instantiate a new DWARFileCreator for every file

	 * - define individual columns with addStructureColumn(), addDescriptorColumn(), and addAlphanumericalColumn()

	 * - add custom column properties, if you need to with addColumnProperty()
	 * - call writeHeader() once to create the file and write file & table headers

	 * - for every row call setRowStructure() and setRowValue() for cell values and then writeCurrentRow()
	 * - call writeEnd() to close the file
	 */
	public DWARFileCreator(BufferedWriter writer) {
		mWriter = writer;
		mColumnTitleList = new ArrayList();
	}

	/**
	 * This adds a column to host canonical structure representations (idcodes).
	 * This call allocates the column and defines proper column properties.
	 * If you want DataWarrior to show structure in this column with the original
	 * atom coordinates, you need to also add a column for the encoded atom coordinates.
	 * Otherwise DataWarrior would generate 2D-coordinates for the structures atoms
	 * on the fly.
	 * @param name
	 * @param idColumnName null or column title of other column that hold a compound identifier
	 * @return new structure column index
	 */
	public int addStructureColumn(String name, String idColumnName) {
		int structureColumn = mColumnTitleList.size();
		String title = makeUnique(name);
		mColumnTitleList.add(title);
		addColumnProperty(structureColumn, "specialType", "idcode");
		if (idColumnName != null)
			addColumnProperty(structureColumn, "idColumn", idColumnName);
		return structureColumn;
	}

	/**
	 * Creates a new column to hold encoded 2-dimensional atom coordinates for the structures
	 * stored in the associated structure column. A structure column may not have more than one
	 * associated 2-dimensional atom coordinate column.
	 * This call allocates the column and defines proper column properties.
	 * @param structureColumn
	 * @return new coordinate column index
	 */
	public int add2DCoordinatesColumn(int structureColumn) {
		return addStructureChildColumn("idcoordinates2D", "idcoordinates2D", structureColumn);
	}

	/**
	 * Creates a new column to hold encoded 3-dimensional atom coordinates for the structures
	 * stored in the associated structure column. A structure column may have multiple
	 * associated 3-dimensional atom coordinate columns.
	 * This call allocates the column and defines proper column properties.
	 * @param name 3D-coordinate column names are used to distinguish multiple 3D-coordinate sets
	 * @param structureColumn
	 * @return new coordinate column index
	 */
	public int add3DCoordinatesColumn(String name, int structureColumn) {
		return addStructureChildColumn("idcoordinates3D", name, structureColumn);
	}

	/**
	 * Creates a new column to hold a chemical descriptor for the structures
	 * stored in the associated structure column. A structure column may have multiple
	 * associated descriptor columns, provided that these have distinct types.
	 * This call allocates the column and defines proper column properties.
	 * @param descriptorShortName name used to identify the descriptor type, e.g. 'FragFp'
	 * @param structureColumn
	 * @return new descriptor column index
	 */
	public int addDescriptorColumn(String descriptorShortName, String descriptorVersion, int structureColumn) {
		int column = addStructureChildColumn(descriptorShortName, descriptorShortName, structureColumn);
		addColumnProperty(column, "version", descriptorVersion);
		return column;
	}

	private int addStructureChildColumn(String specialType, String name, int structureColumn) {
		int column = mColumnTitleList.size();
		mColumnTitleList.add(makeUnique(name));
		addColumnProperty(column, "parent", mColumnTitleList.get(structureColumn));
		addColumnProperty(column, "specialType", specialType);
		return column;
	}

	/**
	 * Creates a new standard column to hold any alphanumerical content.
	 * @param name
	 * @return
	 */
	public int addAlphanumericalColumn(String name) {
		mColumnTitleList.add(makeUnique(name));
		return mColumnTitleList.size()-1;
	}

	/**
	 * This method may be used to define column properties, e.g. to associate the column
	 * with an URL for identifier lookups, to define a data range, or other special DataWarrior
	 * related features.
	 * @param column
	 * @param key
	 * @param value
	 */
	public void addColumnProperty(int column, String key, String value) {
		if (mColumnPropertiesMap == null)
			mColumnPropertiesMap = new TreeMap();
		Properties cp = mColumnPropertiesMap.get(column);
		if (cp == null) {
			cp = new Properties();
			mColumnPropertiesMap.put(column, cp);
		}
		cp.setProperty(key, value);
	}

	/**
	 * Call this after defining columns and specifying column properties
	 * @param rowCount -1 if row count is not known
	 * @throws IOException
	 */
	public void writeHeader(int rowCount) throws IOException {
		mWriter.write("");
		mWriter.newLine();
		mWriter.write("");
		mWriter.newLine();
		if (rowCount > 0) {
			mWriter.write("");
			mWriter.newLine();
		}
		mWriter.write("");
		mWriter.newLine();

		if (mColumnPropertiesMap != null) {
			mWriter.write("");
			mWriter.newLine();
			for (int column:mColumnPropertiesMap.keySet()) {
				mWriter.write("");
				mWriter.newLine();
				Properties cp = mColumnPropertiesMap.get(column);
				for (String key:cp.stringPropertyNames()) {
					String value = cp.getProperty(key);
					mWriter.write("");
					mWriter.newLine();
				}
			}
			mWriter.write("");
			mWriter.newLine();
		}

		boolean isFirst = true;
		for (int i=0; i