/*
 *                    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/
 *
 */

package org.biojava.bio.program.gff3;

import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.NoSuchElementException;
import java.util.StringTokenizer;

import org.biojava.bio.Annotation;
import org.biojava.bio.BioError;
import org.biojava.bio.BioException;
import org.biojava.bio.program.gff.GFFErrorHandler;
import org.biojava.bio.program.gff.GFFTools;
import org.biojava.bio.program.gff.IgnoreRecordException;
import org.biojava.bio.seq.StrandedFeature;
import org.biojava.ontology.AlreadyExistsException;
import org.biojava.ontology.OntoTools;
import org.biojava.ontology.Ontology;
import org.biojava.ontology.OntologyException;
import org.biojava.ontology.Term;
import org.biojava.utils.ChangeVetoException;
import org.biojava.utils.ParserException;

/**
 * Parse a stream of GFF text into a stream of records and comments.
 *
 * <p>
 * Developed from {@link org.biojava.bio.program.gff.GFFParser GFFParser}.
 * </p>
 *
 * @author Matthew Pocock
 */
public class GFF3Parser {
  private GFFErrorHandler errors = GFFErrorHandler.ABORT_PARSING;

  /**
  * Set the error handler used by this parser.
  */

  public void setErrorHandler(GFFErrorHandler errors) {
    this.errors = errors;
  }

  /**
  * Find the error handler used by this parser.
  */

  public GFFErrorHandler getErrorHandler() {
    return errors;
  }

  /**
  * Informs <span class="arg">handler</span> of each line of
  * gff read from <span class="arg">bReader</span>.  This form
  * of the method should only be used if no locator string is
  * available for the resource being parsed.
  *
  * @param bReader the <span class="type">BufferedReader</span> to parse
  * @param handler the <span class="type">GFF3DocumentHandler</span> that will
  *                listen for 'stuff'
  * @param ontology  an Ontology that all terms should come from
  *
  * @throws <span class="type">IOException</span> if for any reason
  *         <span class="arg">bReader</span> throws one
  * @throws <span class="type">BioException</span> if
  *         <span class="arg">handler</span> can not correct a parse error
  */

  public void parse(
    BufferedReader bReader,
    GFF3DocumentHandler handler,
    Ontology ontology
  )
  throws IOException, BioException, ParserException
  {
    parse(bReader, handler, ontology, "unknown:");
  }

  /**
  * Informs <span class="arg">handler</span> of each line of
  * GFF read from <span class="arg">bReader</span>
  *
  * @param bReader the <span class="type">BufferedReader</span> to parse
  * @param handler the <span class="type">GFF3DocumentHandler</span> that will
  *                listen for 'stuff'
  * @param ontology  an Ontology that all terms should come from
  *
  * @throws <span class="type">IOException</span> if for any reason
  *         <span class="arg">bReader</span> throws one
  * @throws <span class="type">BioException</span> if
  *         <span class="arg">handler</span> can not correct a parse error
  */

  public void parse(
    BufferedReader bReader,
    GFF3DocumentHandler handler,
    Ontology ontology,
    String locator
  )
  throws IOException, BioException, ParserException
  {
    Ontology fallBack;
    try {
        fallBack = OntoTools.getDefaultFactory().createOntology(
            "Unknown in " + locator,
            ""
        );
    } catch (OntologyException ex) {
        throw new ParserException("Couldn't create fallback ontology", ex);
    }

    handler.startDocument(locator);
    ArrayList aList = new ArrayList();
    int lineNum = 0;
    for(String line = bReader.readLine(); line != null; line = bReader.readLine()) {
      ++lineNum;

      try {
        aList.clear();
        if(line.startsWith("#")) {
          handler.commentLine(line.substring(1));
        } else if (line.length() == 0) {
        } else {
          StringTokenizer st = new StringTokenizer(line, "\t", false);
          while(st.hasMoreTokens() && aList.size() < 8) {
            String token = st.nextToken();
            aList.add(token);
          }
          String rest = null;
          String comment = null;
          if(st.hasMoreTokens()) {
            try {
              rest = st.nextToken(((char) 0) + "");
            } catch (NoSuchElementException nsee) {
            }
          }
          if(rest != null) {
            int ci = rest.indexOf("#");
            if (ci != -1) {
              comment = rest.substring(ci);
              rest = rest.substring(0, ci);
            }
          }
          GFF3Record record = createRecord(handler, aList, rest, comment, ontology, fallBack);
          handler.recordLine(record);
        }
      } catch (ParserException ex) {
        throw new ParserException(ex, "",
        locator,
        lineNum,
        line);
      } catch (IgnoreRecordException ex) {
        // Silently skip any more work on this record
      }
    }
    handler.endDocument();
  }

  /**
  * Actually turns a list of tokens, some value string and a comment into a
  * <span class="type">GFF3Record</span> and informs
  * <span class="arg">handler</span>.
  *
  * @param handler a <span class="type">GFF3DocumentHandler</span> to inform of
  *                any parse errors, and the completed <span class="type">GFF3Record</span>
  * @param aList   a <span class="type">List</span> containing the 8 mandatory GFF columns
  * @param rest    a <span class="type">String</span> representing the unparsed
  *                attribute-value text, or <span class="kw">null</span> if there is none
  * @param comment a <span class="type">String</span> containing the comment (without the
  *                leading '<code>#</code>' character.
  * @param ontology  the Ontology to resolve Terms in
  * @throws <span class="type">BioException</span> if <span class="arg">handler</span>
  *         could not correct a parse error
  */
  protected GFF3Record createRecord(
    GFF3DocumentHandler handler,
    List aList,
    String rest,
    String comment,
    Ontology ontology,
    Ontology fallBack
  )
  throws BioException, ParserException, IgnoreRecordException
  {
    GFF3Record.Impl record = new GFF3Record.Impl();

    record.setSequenceID((String) aList.get(0));

    {
      Term st;
      String stn = (String) aList.get(1);
      if(ontology.containsTerm(stn)) {
        st = ontology.getTerm(stn);
      } else if(fallBack.containsTerm(stn)) {
        st = fallBack.getTerm(stn);
      } else {
        try {
          st = fallBack.createTerm(stn, "");
        } catch (AlreadyExistsException te) {
          throw new BioError("Assertion Failure: Term should not yet exist", te);
        } catch (ChangeVetoException cve) {
          throw new BioError("Assertion Failure: Unable to create term", cve);
        }
      }
      record.setSource(st);
    }

    {
      Term tt;
      String ttn = (String) aList.get(2);
      if(ontology.containsTerm(ttn)) {
        tt = ontology.getTerm(ttn);
      } else if(fallBack.containsTerm(ttn)) {
        tt = fallBack.getTerm(ttn);
      } else {
        try {
          tt = fallBack.createTerm(ttn, "");
        } catch (AlreadyExistsException te) {
          throw new BioError("Assertion Failure: Term should not yet exist", te);
        } catch (ChangeVetoException cve) {
          throw new BioError("Assertion Failure: Unable to create term", cve);
        }
      }
      record.setType(tt);
    }

    int start = -1;
    try {
      start = Integer.parseInt( (String) aList.get(3));
    } catch (NumberFormatException nfe) {
      start = errors.invalidStart((String) aList.get(3));
    }
    record.setStart(start);

    int end = -1;
    try {
      end = Integer.parseInt( (String) aList.get(4));
    } catch (NumberFormatException nfe) {
      end = errors.invalidEnd((String) aList.get(3));
    }
    record.setEnd(end);

    String score = (String) aList.get(5);
    if(
      score == null     ||
      score.equals("")  ||
    score.equals(".") ||
    score.equals("0")
    )
    {
      record.setScore(GFFTools.NO_SCORE);
    } else {
      double sc = 0.0;
      try {
        sc = Double.parseDouble(score);
      } catch (NumberFormatException nfe) {
        sc = errors.invalidScore(score);
      }
      record.setScore(sc);
    }

    String strand = (String) aList.get(6);
    if(strand == null || strand.equals("") || strand.equals(".")) {
      record.setStrand(StrandedFeature.UNKNOWN);
    } else {
      if(strand.equals("+")) {
        record.setStrand(StrandedFeature.POSITIVE);
      } else if(strand.equals("-")) {
        record.setStrand(StrandedFeature.NEGATIVE);
      } else {
        record.setStrand(errors.invalidStrand(strand));
      }
    }

    String frame = (String) aList.get(7);
    if(frame.equals(".")) {
      record.setPhase(GFFTools.NO_FRAME);
    } else {
      int fr = 0;
      try {
        fr = Integer.parseInt(frame);
      } catch (NumberFormatException nfe) {
        fr = errors.invalidFrame(frame);
      }
      record.setPhase(fr);
    }

    if (rest != null) {
      try {
        parseAttribute(rest, record.getAnnotation(), ontology, fallBack);
      } catch (ChangeVetoException cve) {
        throw new BioException("Unable to populate annotations", cve);
      }
    }

    return record;
  }

  /**
  * Parse <span class="arg">attValList</span> into a
  * <span class="type">Map</span> of attributes and value lists.
  * <p>
  * Populates an Annotation instance with Ontology Term keys and string/list
  * values.
  * </p>
  *
  * @param attValList  the <span class="type">String</span> to parse
  */

  protected void parseAttribute(String attValList, Annotation anno, Ontology onto, Ontology fallBack)
  throws ChangeVetoException {
    StringTokenizer sTok = new StringTokenizer(attValList, ";", false);
    while(sTok.hasMoreTokens()) {
      String attVal = sTok.nextToken().trim();
      String attName;
      List valList = new ArrayList();
      int spaceIndx = attVal.indexOf("=");
      if(spaceIndx == -1) {
        attName = attVal;
      } else {
        attName = attVal.substring(0, spaceIndx);
        attValList = attVal.substring(spaceIndx+1).trim();
        while(attValList.length() > 0) {
          if(attValList.startsWith("\"")) {
            // System.out.println("Quoted");
            int quoteIndx = 0;
            do {
              quoteIndx++;
              quoteIndx = attValList.indexOf("\"", quoteIndx);
            } while(quoteIndx != -1 && attValList.charAt(quoteIndx-1) == '\\');
            if(quoteIndx > 0){
              valList.add(attValList.substring(1, quoteIndx));
              attValList = attValList.substring(quoteIndx+1).trim();
            }else{
              valList.add(attValList);
              attValList = "";
            }
          } else {
            int commaIndx = attValList.indexOf(",");
            if(commaIndx == -1) {
              valList.add(attValList);
              attValList = "";
            } else {
              valList.add(attValList.substring(0, commaIndx));
              attValList = attValList.substring(commaIndx+1).trim();
            }
          }
        }
      }

      Term key;
      if(onto.containsTerm(attName)) {
        key = onto.getTerm(attName);
      } else if(fallBack.containsTerm(attName)) {
        key = fallBack.getTerm(attName);
      } else {
        try {
          key = fallBack.createTerm(attName, "");
        } catch (AlreadyExistsException te) {
          throw new BioError("Assertion Failure: Term should not be there yet",te);
        } catch (ChangeVetoException cve) {
          throw new BioError("Assertion Failure: Unable to create term", cve);
        }
      }
      anno.setProperty(key, valList);
    }
  }
}