package jalview.datamodel;

import jalview.schemes.*;
import jalview.analysis.*;
import jalview.datamodel.*;
import java.util.Vector;
import java.awt.*;

public class SequenceGroup
{
  String groupName;
  Conservation conserve;
  Vector aaFrequency;
  boolean displayBoxes;
  boolean displayText;
  boolean colourText;
  public Vector sequences = new Vector();
  int width = -1;
  public ColourSchemeI cs;
  int startRes = 0;
  int endRes = 0;
  Color outlineColour = Color.black;

  public SequenceGroup()
  {
    groupName = "Group";
    this.displayBoxes = true;
    this.displayText = true;
    this.colourText = false;
    cs = null;
  }

  public SequenceGroup(String groupName, ColourSchemeI scheme,
                       boolean displayBoxes, boolean displayText,
                       boolean colourText,
                       int start,
                       int end)
  {

    this.groupName = groupName;
    this.displayBoxes = displayBoxes;
    this.displayText = displayText;
    this.colourText = colourText;
    this.cs = scheme;
    startRes = start;
    endRes = end;
  }

  public boolean adjustForRemoveLeft(int col)
  {
    // return value is true if the group still exists
    if(startRes>=col)
      startRes = startRes - col;
    if(endRes>=col)
    {
      endRes = endRes - col;
      if(startRes>endRes)
        startRes = 0;
    }
    else
    {
        // must delete this group!!
        return false;
    }

    return true;
  }

  public boolean adjustForRemoveRight(int col)
  {

    if(startRes>col)
    {
      // delete this group
      return false;
    }

    if(endRes>=col)
      endRes = col;

    return true;
  }


  public String getName()
  {
    return groupName;
  }

  public void setName(String name)
  {
    groupName = name;
  }

  public Conservation getConservation()
  {
    return conserve;
  }

  public void setConservation(Conservation c)
  {
    conserve = c;
  }

  public void addSequence(SequenceI s)
  {
    if(!sequences.contains(s))
      sequences.addElement(s);


    if(cs!=null)
      cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );

    if(cs instanceof ConservationColourScheme)
      recalcConservation();
  }

  void recalcConservation()
  {
      Conservation c = new Conservation(groupName,
                                        ResidueProperties.propHash, 3,
                                        sequences, 0, getWidth());
      c.calculate();
      c.verdict(false, 25);
      ConservationColourScheme ccs = (ConservationColourScheme)cs;
      ccs.conserve = c;
  }

  public void addOrRemove(SequenceI s)
  {
    if(sequences.contains(s))
      deleteSequence(s);
    else
      addSequence(s);
  }

  public void deleteSequence(SequenceI s)
  {
    sequences.removeElement(s);

    if(cs!=null)
      cs.setConsensus( AAFrequency.calculate(sequences, 0, getWidth()) );

    if(cs instanceof ConservationColourScheme)
      recalcConservation();
  }


  public int getStartRes()
  {
    return startRes;
  }

  public int getEndRes()
  {
    return endRes;
  }

  public void setStartRes(int i)
  {
    startRes = i;
  }

  public void setEndRes(int i)
  {
    endRes = i;
  }

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

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

  public void setColourText(boolean state)
  {
    colourText = state;
  }

  public boolean getColourText()
  {
    return colourText;
  }

  public void setDisplayText(boolean state)
  {
    displayText = state;
  }

  public boolean getDisplayText()
  {
    return displayText;
  }

  public void setDisplayBoxes(boolean state)
  {
    displayBoxes = state;
  }

  public boolean getDisplayBoxes()
  {
    return displayBoxes;
  }

  public int getWidth()
  {
    // MC This needs to get reset when characters are inserted and deleted
    if (sequences.size()>0)
      width = ((SequenceI) sequences.elementAt(0)).getLength();
    for (int i = 1; i < sequences.size(); i++)
    {
      SequenceI seq = (SequenceI) sequences.elementAt(i);
      if (seq.getLength() > width)
        width = seq.getLength();
    }
    return width;
  }


  public void setOutlineColour(Color c)
  {
    outlineColour = c;
  }
  public Color getOutlineColour()
  {
    return outlineColour;
  }
  /**
   *
   * returns the sequences in the group ordered by the ordering given by al
   *
   * @param al Alignment
   * @return SequenceI[]
   */
  public SequenceI[] getSequencesInOrder(Alignment al) {
    int sz;
    java.util.Hashtable orderedSeqs = new java.util.Hashtable();
    SequenceI[] seqs=new SequenceI[sz=sequences.size()];
    for(int i=0; i<sz; i++)
    {
      SequenceI seq = (SequenceI) sequences.get(i);
      int index = al.findIndex(seq);
      orderedSeqs.put(index+"", seq);
    }

    int index=0;
    for(int i=0; i<sz; i++) {
      SequenceI seq = null;
      while (seq == null)
      {
        if (orderedSeqs.containsKey(index + ""))
        {
          seq = (SequenceI) orderedSeqs.get(index + "");
          index++;
          break;
        }
        else
          index++;
      }
      seqs[index] = seq;
    }
    return seqs;
  }
}