/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview 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 General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.io;

import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;

import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.util.Hashtable;
import java.util.Map;

import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;

import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;

import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;

/**
 * Preliminary reader for Bioinformatics Sequence Markup Language
 * http://www.bsml.org
 * 
 * @author hansonr
 *
 */
public class BSMLFile extends AlignFile
{

  public BSMLFile()
  {
    super();

  }

  public BSMLFile(String inFile, DataSourceType type) throws IOException
  {
    super(inFile, type);

  }

  public BSMLFile(FileParse source) throws IOException
  {
    super(source);

  }

  public BufferedReader CreateReader() throws FileNotFoundException
  {
    FileReader fr = null;
    fr = new FileReader(inFile);

    BufferedReader r = new BufferedReader(fr);
    return r;
  }

  /*
   * (non-Javadoc)
   * 
   * @see jalview.io.AlignFile#parse()
   */
  @Override
  public void parse() throws IOException
  {
    try
    {
      _parse();
    } catch (ExceptionPermissionDenied pdx)
    {
      errormessage = MessageManager.formatMessage(
              "exception.BSML_couldnt_access_datasource", new String[]
              { pdx.getMessage() });
      throw new IOException(pdx);
    } catch (ExceptionLoadingFailed lf)
    {
      errormessage = MessageManager.formatMessage(
              "exception.BSML_couldnt_process_data", new String[]
              { lf.getMessage() });
      throw new IOException(lf);
    } catch (ExceptionFileFormatOrSyntax iff)
    {
      errormessage = MessageManager
              .formatMessage("exception.BSML_invalid_file", new String[]
              { iff.getMessage() });
      throw new IOException(iff);
    } catch (Exception x)
    {
      error = true;
      errormessage = MessageManager.formatMessage(
              "exception.BSML_problem_parsing_data", new String[]
              { x.getMessage() });
      throw new IOException(errormessage, x);
    }
  }

  @SuppressWarnings("unchecked")
  public void _parse()
          throws ExceptionPermissionDenied, ExceptionLoadingFailed,
          ExceptionFileFormatOrSyntax, ParserConfigurationException,
          SAXException, IOException
  {

    DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();

    dbf.setIgnoringElementContentWhitespace(true);
    dbf.setIgnoringComments(true);
    dbf.setValidating(true);
    dbf.setCoalescing(true);
    dbf.setNamespaceAware(true);
      dbf.setFeature("http://xml.org/sax/features/namespaces", false);
      dbf.setFeature("http://xml.org/sax/features/validation", false);
      dbf.setFeature(
              "http://apache.org/xml/features/nonvalidating/load-dtd-grammar",
              false);
      dbf.setFeature(
              "http://apache.org/xml/features/nonvalidating/load-external-dtd",
              false);

      DocumentBuilder db = dbf.newDocumentBuilder();

      Map<String, SequenceI> htSeq = new Hashtable<>();
      InputSource is = new InputSource(getReader());
      Document d = db.parse(is);
      NodeList sequences = d.getElementsByTagName("Sequence-data");
      int n = sequences.getLength();
      SequenceI[] sqs = new SequenceI[n];
      for (int i = 0; i < n; i++)
      {
        Element e = (Element) sequences.item(i);
        String s = e.getTextContent();
        String id = e.getAttribute("seq-name");
        SequenceI seq = sqs[i] = new Sequence(id, s, 1, s.length());
        htSeq.put(id, seq);
        // ?? sqs[i].setEnd(sqs[i].findPosition(sqs[i].getLength()));
      }

      sequences = d.getElementsByTagName("Sequence");
      n = sequences.getLength();
      for (int i = 0; i < n; i++)
      {
        Element e = (Element) sequences.item(i);
        String mol = e.getAttribute("molecule"); // dna or rna
        if (!"dna".equals(mol))
        {
          System.err.println("BSML molecule=rna not implemented");
          continue;
        }
        String title = e.getAttribute("title");
        SequenceI seq = htSeq.get(title);
        if (seq == null)
        {
          continue;
        }
      NodeList features = e.getElementsByTagName("Feature");
        int featureCount = features.getLength();
        for (int f = 0; f < featureCount; f++)
        {
          Element feature = (Element) features.item(f);
          // <Feature class="GENE" title="CPXV-GER_1980_EP4-211">
          // <Interval-loc complement="0" endpos="217104" startpos="216643"/>
          // <Resource id="GENE-ID:119705"/>
          // </Feature>
        Element iloc = (Element) feature
                .getElementsByTagName("Interval-loc").item(0);
          String complement = iloc.getAttribute("complement");
          if (!"0".equals(complement))
          {
            // Jalview cannot handle complement genes (running backward on the
            // complementary strand);
            continue;
          }
          String fclass = feature.getAttribute("class");
          if (!"GENE".equals(fclass))
          {
            // just processing GENE features for now;
            continue;
          }
          String ftitle = feature.getAttribute("title");
        int start = Integer.parseInt(iloc.getAttribute("startpos"));
        int end = Integer.parseInt(iloc.getAttribute("endpos"));
        SequenceFeature sf = new SequenceFeature("GENE", ftitle, start, end,
                null);
        seq.addSequenceFeature(sf);
        }
        setSeqs(sqs);
      }

  }

  @Override
  public String print(SequenceI[] s, boolean jvSuffix)
  {
    return "not yet implemented";
  }

}