package jalview.datamodel;

import jalview.analysis.*;
import jalview.util.*;
import java.util.*;

/** Data structure to hold and manipulate a multiple sequence alignment
 */
public class Alignment implements AlignmentI
{

  protected Vector      sequences;
  protected Vector      groups = new Vector();
  protected Vector   superGroup = new Vector();
  protected char        gapCharacter = '-';
  public AlignmentAnnotation [] annotations;

  public boolean featuresAdded = false;

  /** Make an alignment from an array of Sequences.
  *
  * @param sequences
  */
  public Alignment(SequenceI[] seqs) {
    sequences = new Vector();

    for (int i=0; i < seqs.length; i++)
      sequences.addElement(seqs[i]);

    getWidth();
  }

  public Vector      getSequences() {
    return sequences;
  }

  public SequenceI getSequenceAt(int i) {
    if (i < sequences.size()) {
      return (SequenceI)sequences.elementAt(i);
    }

    return null;
  }

  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
   *
   * @param snew
   */
  public void addSequence(SequenceI snew) {
    sequences.addElement(snew);
  }

  public void addSequence(SequenceI[] seq) {
    for (int i=0; i < seq.length; i++) {
      addSequence(seq[i]);
    }
  }

  /** Adds a sequence to the alignment.  Recalculates maxLength and size.
    *
   * @param snew
   */
  public void setSequenceAt(int i,SequenceI snew) {
    SequenceI oldseq = getSequenceAt(i);
    deleteSequence(oldseq);

    sequences.setElementAt(snew,i);
  }

  public Vector getGroups() {
    return groups;
  }

  /** Sorts the sequences by sequence group size - largest to smallest.
   * Uses QuickSort.
   */
  public void sortGroups() {
    float[]  arr = new float [groups.size()];
    Object[] s   = new Object[groups.size()];

    for (int i=0; i < groups.size(); i++) {
      arr[i] = ((SequenceGroup)groups.elementAt(i)).sequences.size();
      s[i]   = groups.elementAt(i);
    }

    QuickSort.sort(arr,s);

    Vector newg = new Vector(groups.size());

    for (int i=groups.size()-1; i >= 0; i--) {
      newg.addElement(s[i]);
    }

    groups = newg;
  }

  /** Takes out columns consisting entirely of gaps (-,.," ")
   */
  public void removeGaps()
  {

    SequenceI current;
    int iSize = getWidth();
    for (int i=0; i < iSize; i++)
    {
      boolean delete = true;
      for (int j=0; j < getHeight(); j++)
      {
        current = getSequenceAt(j);
        if (current.getLength() > i)
        {
	    /* MC Should move this to a method somewhere */
          if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))
            delete = false;

        }
      }

      if ( delete )
      {
        deleteColumns(i,i);
        iSize--;
        i--;
      }
    }


  }

  /** Returns an array of Sequences containing columns
   * start to end (inclusive) only.
   *
   * @param start start column to fetch
   * @param end end column to fetch
   * @return Array of Sequences, ready to put into a new Alignment
   */
  public SequenceI[] getColumns(int start, int end) {
    return getColumns(0,getHeight()-1,start,end);
  }

  /** Removes a range of columns (start to end inclusive).
   *
   * @param start Start column in the alignment
   * @param end End column in the alignment
   */
  public void deleteColumns(int start, int end) {
    deleteColumns(0,getHeight()-1,start,end);
  }

  public void deleteColumns(int seq1, int seq2, int start, int end) {

    for (int i=0; i <= (end-start); i++) {
      for (int j=seq1; j <= seq2; j++) {
        getSequenceAt(j).deleteCharAt(start);
      }
    }
  }

  public void insertColumns(SequenceI[] seqs, int pos) {
    if (seqs.length == getHeight()) {
      for (int i=0; i < getHeight();i++) {
        String tmp = new String(getSequenceAt(i).getSequence());
        getSequenceAt(i).setSequence(tmp.substring(0,pos) + seqs[i].getSequence() + tmp.substring(pos));
      }

    }
  }

  public SequenceI[] getColumns(int seq1, int seq2, int start, int end) {
    SequenceI[] seqs = new Sequence[(seq2-seq1)+1];
    for (int i=seq1; i<= seq2; i++ ) {
      seqs[i] = new Sequence(getSequenceAt(i).getName(),
                             getSequenceAt(i).getSequence().substring(start,end),
                             getSequenceAt(i).findPosition(start),
                             getSequenceAt(i).findPosition(end));
    }
    return seqs;
  }

  public void trimLeft(int i) {
    for (int j = 0;j< getHeight();j++) {

      SequenceI s        = getSequenceAt(j);
      int       newstart = s.findPosition(i);

      s.setStart(newstart);
      s.setSequence(s.getSequence().substring(i));

    }
  }

  public void  trimRight(int i) {
    for (int j = 0;j< getHeight();j++) {
      SequenceI s      = getSequenceAt(j);
      int       newend = s.findPosition(i);

      s.setEnd(newend);
      s.setSequence(s.getSequence().substring(0,i+1));
    }
  }

  public void deleteSequence(SequenceI s)
  {
    for (int i=0; i < getHeight(); i++)
      if (getSequenceAt(i) == s)
        deleteSequence(i);
  }

  public void  deleteSequence(int i)
  {
    sequences.removeElementAt(i);
  }


  public Vector removeRedundancy(float threshold, Vector sel) {
    Vector del = new Vector();

    for (int i = 1; i < sel.size(); i++)
    {
      for (int j = 0; j < i; j++)
      {
        // Only do the comparison if either have not been deleted
        if (!del.contains( (SequenceI) sel.elementAt(i)) ||
            !del.contains( (SequenceI) sel.elementAt(j)))
        {

          float pid = Comparison.compare( (SequenceI) sel.elementAt(j),
                                         (SequenceI) sel.elementAt(i));

          if (pid >= threshold)
          {
            // Delete the shortest one
            if ( ( (SequenceI) sel.elementAt(j)).getSequence().length() >
                ( (SequenceI) sel.elementAt(i)).getSequence().length())
              del.addElement(sel.elementAt(i));
            else
              del.addElement(sel.elementAt(i));
          }
        }
      }
    }

    // Now delete the sequences
    for (int i=0; i < del.size(); i++)
      deleteSequence((SequenceI)del.elementAt(i));

    return del;
  }

  public void sortByPID(SequenceI s) {

    float     scores[] = new float[getHeight()];
    SequenceI seqs[]   = new SequenceI[getHeight()];

    for (int i = 0; i < getHeight(); i++) {
      scores[i] = Comparison.compare(getSequenceAt(i),s);
      seqs[i]   = getSequenceAt(i);
    }

    QuickSort.sort(scores,0,scores.length-1,seqs);

    int len = 0;

    if (getHeight()%2 == 0) {
      len = getHeight()/2;
    } else {
      len = (getHeight()+1)/2;
    }

    for (int i = 0; i < len; i++) {
      SequenceI tmp = seqs[i];
      sequences.setElementAt(seqs[getHeight()-i-1],i);
      sequences.setElementAt(tmp,getHeight()-i-1);
    }
  }

  public void sortByID() {
    String    ids[]   = new String[getHeight()];
    SequenceI seqs[]  = new SequenceI[getHeight()];

    for (int i = 0; i < getHeight(); i++) {
      ids[i]  = getSequenceAt(i).getName();
      seqs[i] = getSequenceAt(i);
    }

    QuickSort.sort(ids,seqs);

    int len = 0;

    if (getHeight()%2 == 0) {
      len = getHeight()/2;
    } else {
      len = (getHeight()+1)/2;
      System.out.println("Sort len is odd = " + len);
    }
    for (int i = 0; i < len; i++) {
      System.out.println("Swapping " + seqs[i].getName() + " and " + seqs[getHeight()-i-1].getName());
      SequenceI tmp = seqs[i];
      sequences.setElementAt(seqs[getHeight()-i-1],i);
      sequences.setElementAt(tmp,getHeight()-i-1);
    }
  }

  /**    */
  public SequenceGroup findGroup(int i) {
    return findGroup(getSequenceAt(i));
  }

  /**    */
  public SequenceGroup findGroup(SequenceI s) {
    for (int i = 0; i < this.groups.size();i++)
    {
      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
      if (sg.sequences.contains(s))
        return sg;

    }
    return null;
  }

  public SequenceGroup [] findAllGroups(SequenceI s)
  {

    Vector temp = new Vector();

    for (int i = 0; i < this.groups.size();i++)
    {
      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);

      if (sg.sequences.contains(s))
       temp.addElement(sg);
    }

    SequenceGroup [] ret = new SequenceGroup[temp.size()];
    for(int i=0; i<temp.size(); i++)
      ret[i] = (SequenceGroup)temp.elementAt(i);

    return ret;

  }
  /**    */
  public void addToGroup(SequenceGroup g, SequenceI s) {
    if (!(g.sequences.contains(s))) {
      g.sequences.addElement(s);
    }
  }
  /**    */
  public void removeFromGroup(SequenceGroup g,SequenceI s) {
    if (g != null && g.sequences != null) {
      if (g.sequences.contains(s)) {
        g.sequences.removeElement(s);
        if (g.sequences.size() == 0) {
          groups.removeElement(g);
        }
      }
    }
  }

  public void addSuperGroup(SuperGroup sg)
  {
    superGroup.addElement(sg);
  }

  public void removeSuperGroup(SuperGroup sg)
  {
    superGroup.removeElement(sg);
  }

  public SuperGroup     getSuperGroup(SequenceGroup sg)
  {
    for (int i = 0; i < this.superGroup.size(); i++)
    {
      SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
      if (temp.sequenceGroups.contains(sg))
        return temp;
    }
    return null;
  }

  /**    */
  public void addGroup(SequenceGroup sg) {
    if(!groups.contains(sg))
      groups.addElement(sg);
  }

  public void deleteAllGroups()
  {
    groups.removeAllElements();
    superGroup.removeAllElements();
   int i=0;
    while (i < sequences.size()) {
     SequenceI s = getSequenceAt(i);
     s.setColor(java.awt.Color.white);
     i++;
   }


  }

  /**    */
  public void deleteGroup(SequenceGroup g) {
    if (groups.contains(g)) {
      groups.removeElement(g);
    }
  }

  /**    */
  public SequenceI findName(String name) {
    int i = 0;
    while (i < sequences.size()) {
      SequenceI s = getSequenceAt(i);
      if (s.getName().equals(name))
        return s;

      i++;
    }
    return null;
  }

  /**    */
  public SequenceI findbyDisplayId(String name) {
    int i = 0;
    while (i < sequences.size()) {
      SequenceI s = getSequenceAt(i);
      if (s.getDisplayId().equals(name))
        return s;

      i++;
    }
    return null;
  }

  /**    */
  public int findIndex(SequenceI s)
  {
    int i=0;
    while (i < sequences.size())
    {
      if (s == getSequenceAt(i))
        return i;

      i++;
    }
    return -1;
  }

  public int getHeight() {
    return sequences.size();
  }


  public int getWidth()
  {
    int maxLength = -1;
    for (int i = 0; i < sequences.size(); i++)
    {
      if (getSequenceAt(i).getLength() > maxLength)
        maxLength = getSequenceAt(i).getLength();
    }

    return maxLength;
  }


  public int getMaxIdLength() {
    int max = 0;
    int i   = 0;

    while (i < sequences.size()) {
      SequenceI seq = getSequenceAt(i);
      String    tmp = seq.getName() + "/" + seq.getStart() + "-" + seq.getEnd();

      if (tmp.length() > max) {
        max = tmp.length();
      }

      i++;
    }
    return max;
  }

  public void setGapCharacter(char gc)
  {
    gapCharacter = gc;
    for (int i=0; i < sequences.size(); i++)
     {
       Sequence seq = (Sequence)sequences.elementAt(i);
       seq.sequence = seq.sequence.replace('.', gc);
       seq.sequence = seq.sequence.replace('-', gc);
     }
  }

  public char getGapCharacter() {
    return gapCharacter;
  }

  public Vector getAAFrequency()
  {
    return AAFrequency.calculate(sequences, 0, getWidth());
  }

  public boolean isAligned()
  {
    int width = getWidth();
    for (int i = 0; i < sequences.size(); i++)
      if (getSequenceAt(i).getLength() != width)
        return false;

    return true;
  }

   public void deleteAnnotation(AlignmentAnnotation aa)
   {
     int aSize = 1;
     if(annotations!=null)
       aSize = annotations.length;

     AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize-1];

     int tIndex = 0;
     for (int i = 0; i < aSize; i++)
      {
        if(annotations[i]==aa)
          continue;


        temp[tIndex] = annotations[i];
        tIndex++;
      }

     annotations = temp;

   }

  public void addAnnotation(AlignmentAnnotation aa)
  {
    int aSize = 1;
    if(annotations!=null)
      aSize = annotations.length+1;

    AlignmentAnnotation [] temp = new AlignmentAnnotation [aSize];
    int i=0;
    if (aSize > 1)
      for (i = 0; i < aSize-1; i++)
        temp[i] = annotations[i];

    temp[i] = aa;

    annotations = temp;
  }
  public AlignmentAnnotation[] getAlignmentAnnotation()
  {
    return annotations;
  }

}