package jalview.analysis;

import java.util.*;

import jalview.datamodel.*;

public class Finder
{
  /**
   * Implements the search algorithms for the Find dialog box.
   */
  SearchResults searchResults;
  AlignmentI alignment;
  jalview.datamodel.SequenceGroup selection = null;
  Vector idMatch = null;
  boolean caseSensitive = false;
  boolean findAll = false;
  com.stevesoft.pat.Regex regex = null;
  /**
   * hold's last-searched position between calles to find(false)
   */
  int seqIndex = 0, resIndex = 0;
  public Finder(AlignmentI alignment, SequenceGroup selection)
  {
    this.alignment = alignment;
    this.selection = selection;
  }

  public Finder(AlignmentI alignment, SequenceGroup selectionGroup,
                int seqIndex, int resIndex)
  {
    this(alignment, selectionGroup);
    this.seqIndex = seqIndex;
    this.resIndex = resIndex;
  }

  public boolean find(String searchString)
  {
    boolean hasResults = false;
    if (!caseSensitive)
    {
      searchString = searchString.toUpperCase();
    }
    regex = new com.stevesoft.pat.Regex(searchString);
    searchResults = new SearchResults();
    idMatch = new Vector();
    Sequence seq;
    String item = null;
    boolean found = false;

    ////// is the searchString a residue number?
    try
    {
      int res = Integer.parseInt(searchString);
      found = true;
      if (selection == null || selection.getSize() < 1)
      {
        seq = (Sequence) alignment.getSequenceAt(0);
      }
      else
      {
        seq = (Sequence) (selection.getSequenceAt(0));
      }

      searchResults.addResult(seq, res, res);
      hasResults = true;
    }
    catch (NumberFormatException ex)
    {
    }

    ///////////////////////////////////////////////

    int end = alignment.getHeight();

    if (selection != null)
    {
      if ( (selection.getSize() < 1) ||
          ( (selection.getEndRes() - selection.getStartRes()) < 2))
      {
        selection = null;
      }
    }

    while (!found && (seqIndex < end))
    {
      seq = (Sequence) alignment.getSequenceAt(seqIndex);

      if ( (selection != null) && !selection.getSequences(null).contains(seq))
      {
        seqIndex++;
        resIndex = 0;

        continue;
      }

      item = seq.getSequenceAsString();
      // JBPNote - check if this toUpper which is present in the application implementation makes a difference
      //if(!caseSensitive)
      //  item = item.toUpperCase();

      if ( (selection != null) &&
          (selection.getEndRes() < alignment.getWidth() - 1))
      {
        item = item.substring(0, selection.getEndRes() + 1);
      }

      ///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
      StringBuffer noGapsSB = new StringBuffer();
      int insertCount = 0;
      Vector spaces = new Vector();

      for (int j = 0; j < item.length(); j++)
      {
        if (!jalview.util.Comparison.isGap(item.charAt(j)))
        {
          noGapsSB.append(item.charAt(j));
          spaces.addElement(new Integer(insertCount));
        }
        else
        {
          insertCount++;
        }
      }

      String noGaps = noGapsSB.toString();

      for (int r = resIndex; r < noGaps.length(); r++)
      {

        if (regex.searchFrom(noGaps, r))
        {
          resIndex = regex.matchedFrom();

          if ( (selection != null) &&
              ( (resIndex +
                 Integer.parseInt(spaces.elementAt(resIndex).toString())) <
               selection.getStartRes()))
          {
            continue;
          }

          int sres = seq.findPosition(resIndex +
                                      Integer.parseInt(spaces.elementAt(
              resIndex)
              .toString()));
          int eres = seq.findPosition(regex.matchedTo() - 1 +
                                      Integer.parseInt(spaces.elementAt(regex.
              matchedTo() -
              1).toString()));

          searchResults.addResult(seq, sres, eres);
          hasResults = true;
          if (!findAll)
          {
            // thats enough, break and display the result
            found = true;
            resIndex++;

            break;
          }

          r = resIndex;
        }
        else
        {
          break;
        }
      }

      if (!found)
      {
        seqIndex++;
        resIndex = 0;
      }
    }

    for (int id = 0; id < alignment.getHeight(); id++)
    {
      if (regex.search(alignment.getSequenceAt(id).getName()))
      {
        idMatch.addElement(alignment.getSequenceAt(id));
        hasResults = true;
      }
    }
    return hasResults;
  }

  /**
   * @return the alignment
   */
  public AlignmentI getAlignment()
  {
    return alignment;
  }

  /**
   * @param alignment the alignment to set
   */
  public void setAlignment(AlignmentI alignment)
  {
    this.alignment = alignment;
  }

  /**
   * @return the caseSensitive
   */
  public boolean isCaseSensitive()
  {
    return caseSensitive;
  }

  /**
   * @param caseSensitive the caseSensitive to set
   */
  public void setCaseSensitive(boolean caseSensitive)
  {
    this.caseSensitive = caseSensitive;
  }

  /**
   * @return the findAll
   */
  public boolean isFindAll()
  {
    return findAll;
  }

  /**
   * @param findAll the findAll to set
   */
  public void setFindAll(boolean findAll)
  {
    this.findAll = findAll;
  }

  /**
   * @return the selection
   */
  public jalview.datamodel.SequenceGroup getSelection()
  {
    return selection;
  }

  /**
   * @param selection the selection to set
   */
  public void setSelection(jalview.datamodel.SequenceGroup selection)
  {
    this.selection = selection;
  }

  /**
   * @return the idMatch
   */
  public Vector getIdMatch()
  {
    return idMatch;
  }

  /**
   * @return the regex
   */
  public com.stevesoft.pat.Regex getRegex()
  {
    return regex;
  }

  /**
   * @return the searchResults
   */
  public SearchResults getSearchResults()
  {
    return searchResults;
  }

  /**
   * @return the resIndex
   */
  public int getResIndex()
  {
    return resIndex;
  }

  /**
   * @param resIndex the resIndex to set
   */
  public void setResIndex(int resIndex)
  {
    this.resIndex = resIndex;
  }

  /**
   * @return the seqIndex
   */
  public int getSeqIndex()
  {
    return seqIndex;
  }

  /**
   * @param seqIndex the seqIndex to set
   */
  public void setSeqIndex(int seqIndex)
  {
    this.seqIndex = seqIndex;
  }
}