package jalview.gui;

import java.awt.*;
import java.awt.event.*;
import jalview.datamodel.*;
import javax.swing.*;
import jalview.schemes.*;
import jalview.analysis.*;


public class SeqPanel extends JPanel
{

  public    SeqCanvas         seqCanvas;
  public    AlignmentPanel    parent;

  protected int startres;
  protected int lastres;
  protected int endres;

  protected int startseq;
  protected int padseq;

  public    boolean editFlag;
  protected AlignViewport av;

  public SeqPanel(AlignViewport av, AlignmentPanel p) {
    this.av         = av;

    seqCanvas  = new SeqCanvas(av);
    setLayout(new BorderLayout());
    add(seqCanvas, BorderLayout.CENTER);

    parent = p;

    addMouseMotionListener( new MouseMotionAdapter()
    {
      public void mouseMoved(MouseEvent evt)
      {  doMouseMoved(evt);   }
      public void mouseDragged(MouseEvent evt)
      {      doMouseDragged(evt);  }
    });

    addMouseListener( new MouseAdapter()
    {
      public void mouseReleased(MouseEvent evt)
      {  doMouseReleased(evt);  }
      public void mousePressed(MouseEvent evt)
      {  doMousePressed(evt);   }

    });
    repaint();
  }


  public void doMouseReleased(MouseEvent evt) {

    int x = evt.getX();
      int res = (int)(x/av.getCharWidth()) + av.getStartRes();

      endres = res;

      // This is to detect edits - we're at the end of an edit if mouse is up
      editFlag = false;
      startseq = -1;
      startres = -1;
      lastres  = -1;

    parent.RefreshPanels();
    repaint();

  }

  public void doMousePressed(MouseEvent evt) {
  parent.alignFrame.addHistoryItem("sequence edit");
    int seq;
    int res;

    int x = evt.getX();
    int y = evt.getY();

    res = (int)(x/av.getCharWidth()) + av.getStartRes();
    seq = (y)/av.getCharHeight() + av.getStartSeq();

    if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength())
    {
      //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
      // Find the residue's position in the sequence (res is the position
      // in the alignment

      startseq = seq;

      if (startseq == (av.getAlignment().getHeight()-1)) {
        padseq = 1;
      } else {
        padseq = 1;
      }

      startres = res;
      lastres = res;

      } else {
      startseq = -1;
      startres = -1;
      lastres = -1;
    }

    return;
  }

  public void doMouseMoved(MouseEvent evt)
  {
    int res=0, seq=0;
    int x = evt.getX();
    int y = evt.getY();
    if(av.wrapAlignment)
    {
      y -= 2*av.charHeight;
      int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;


      res =   (int)((y/chunkHeight)*(getWidth()/av.charWidth)) +  (int)(x/av.getCharWidth()) + av.getStartRes();

      System.out.println( ((y/chunkHeight)*(getWidth()/av.charWidth)) +" "+((x / av.getCharWidth()) + av.getStartRes()) );
      y %= chunkHeight;
      seq =     y / av.getCharHeight() + av.getStartSeq();

      //   chunkHeight =  (da.getHeight() + 2)*charHeight;
      //  startx += chunkWidth;
    }
    else
    {
      res = (int) (x / av.getCharWidth()) + av.getStartRes();
      seq = y / av.getCharHeight() + av.getStartSeq();
    }


    if(seq>=av.getAlignment().getHeight())
      return;

    Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ;
    String aa = "";
    if(obj!=null)
         aa = obj.toString();

    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName());
    if(aa!="")
      text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");

    parent.alignFrame.statusBar.setText(text.toString());

  }

  public void doMouseDragged(MouseEvent evt) {
    // If we're dragging we're editing
    editFlag = true;
    int x = evt.getX();

    int res = (int)(x/av.getCharWidth()) + av.getStartRes();
    if (res < 0) {res = 0;}

    if (res  != lastres) {
      if (startseq != -1) {

	// Group editing
	if (av.getGroupEdit()) {
	  SequenceGroup sg = av.getAlignment().findGroup(startseq);

          if(sg!=null)
	  if (res < av.getAlignment().getWidth() && res < lastres)
          {
	    boolean flag = false;
	    for (int i= 0 ; i < sg.getSize(); i++)
            {
	      SequenceI s = (SequenceI)sg.getSequenceAt(i);
	      for (int j=lastres-1; j >= res; j--)
              {
		if (!flag)
                {
		  if (!s.getSequence().substring(j,j+1).equals(av.getAlignment().getGapCharacter()) &&
		      !s.getSequence().substring(j,j+1).equals(" "))
                  {
		    res = j+1;
		    flag = true;
		  }
		}
	      }
	    }
	  }

          if(sg!=null)
	  for (int i= 0 ; i < sg.getSize(); i++)
          {
	    SequenceI s = (SequenceI)sg.getSequenceAt(i);
	    boolean found = false;
	    int sno = -1;
	    for (int k = 0; k < av.getAlignment().getHeight(); k++)
            {
	      if (av.getAlignment().getSequenceAt(k) == s)
              {
		found = true;
		sno = k;
		break;
	      }
	    }
	    if (found && sno != -1) {
	      if (res < av.getAlignment().getWidth() && res > lastres)
              {
		for (int j = lastres; j < res; j++)
		  insertChar(j,sno);

		int index = av.getAlignment().findIndex(s);
		if (index != -1)
		  drawChars(index,index+1,lastres);


	      } else if (res < av.getAlignment().getWidth() && res < lastres)
              {
		for (int j = res; j < lastres; j++)
                {
		  deleteChar(j,res,sno);
		  startres = res;
		}
		int index = av.getAlignment().findIndex(s);
		if (index != -1)
		  drawChars(index,index+1,res);

	      }
	    }

	  }
	  lastres = res;
	} else {


	  if (res < av.getAlignment().getWidth() && res > lastres) {
            // dragging to the right
	    for (int j = lastres; j < res; j++)
	      insertChar(j,startseq);

	    drawChars(startseq,startseq+1,lastres);

	  } else if (res < av.getAlignment().getWidth() && res < lastres)
          {

            // dragging to the left
	    for (int j = res; j < lastres; j++) {
	      deleteChar(j,res,startseq);
	      startres = res;
	    }
	    drawChars(startseq,startseq+1,res);
	  }
	}
      }
      lastres = res;
    }

    repaint();
    return;
  }

  public void drawChars(int seqstart, int seqend, int start) {
    seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);
    repaint();
  }

  public void insertChar(int j, int seq)
  {
    av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter().charAt(0));
    updateConservation(seq);
  }

  public void deleteChar(int j, int res, int sno)
  {

    if (av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(".") ||
        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals("-") ||
        av.getAlignment().getSequenceAt(sno).getSequence().substring(j,j+1).equals(" ") )
    {
        av.getAlignment().getSequenceAt(sno).deleteCharAt(j);
    }
    updateConservation(sno);
    av.getAlignment().getWidth();
    repaint();
  }


  void updateConservation(int i)
  {

    Alignment al = (Alignment) av.getAlignment();
    SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
    if(sg==null || !(sg.cs instanceof ConservationColourScheme))
      return;

    Conservation c = sg.getConservation();

    c = new Conservation("All", al.cons,
                         ResidueProperties.propHash, 3, sg.sequences, 0,
                         al.getWidth());
    c.calculate();
    c.verdict(false, 100);
    sg.setConservation(c);
    ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
    ccs.conserve = c;
 //   sg.cs = new ConservationColourScheme(sg);
  }

  public void setColourScheme(ColourSchemeI cs, boolean showConservation)
  {
    if (av.getSelection().size() == 0)
    {
      seqCanvas.cs = cs;
      for (int i = 0; i < av.alignment.getGroups().size();i++)
      {
        SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);
        sg.cs = cs;
        if(!showConservation
            && !(sg.cs instanceof Blosum62ColourScheme)
            && sg.cs instanceof ConservationColourScheme)
         {
           // remove ConservationColouring from existing Conservation group
           ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
           sg.cs = ccs.cs;
         }
         else if(showConservation && !(sg.cs instanceof ConservationColourScheme))
         {
           // add ConservationColouring to new group
           Conservation c = sg.getConservation();
           Alignment al = (Alignment) av.getAlignment();
           c = new Conservation("All", al.cons,
                                ResidueProperties.propHash, 3, sg.sequences, 0,
                                al.getWidth() );
           c.calculate();
           c.verdict(false, 100);
           sg.setConservation(c);
           sg.cs = new ConservationColourScheme(sg);
         }


      }
    }
    else
    {
      SequenceGroup sg = av.alignment.addGroup();
      sg.cs = cs;

      for (int i=0; i < av.getSelection().size(); i++)
      {
        av.alignment.removeFromGroup(av.alignment.findGroup((Sequence)av.sel.sequenceAt(i)),
                                     (Sequence)av.sel.sequenceAt(i));
        av.alignment.addToGroup(sg,(Sequence)av.sel.sequenceAt(i));
      }

      // Selection is made, we only want to change the conservationColour for selected group
      if(  showConservation
           && !(sg.cs instanceof ConservationColourScheme)
           && !(sg.cs instanceof Blosum62ColourScheme))
      {
        Conservation c = sg.getConservation();
        Alignment al = (Alignment) av.getAlignment();

        c = new Conservation("All", al.cons,
                             ResidueProperties.propHash, 3, sg.sequences, 0,
                             al.getWidth() );
        c.calculate();
        c.verdict(false, 100);
        sg.setConservation(c);
        sg.cs = new ConservationColourScheme(sg);
    }
    else  if( !showConservation && sg.cs instanceof ConservationColourScheme)
    {
      ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
      sg.cs = ccs.cs;
    }



   }
   seqCanvas.paintFlag = true;
   repaint();
  }


  public ColourSchemeI getColourScheme()
  {
    if(av.getSelection().size()>0)
       return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
    else
      return seqCanvas.cs;
  }
}