package jalview.gui;

import jalview.jbgui.GAlignmentPanel;
import jalview.schemes.*;
import jalview.analysis.*;
import jalview.datamodel.*;
import java.awt.*;
import java.awt.event.*;
import java.awt.print.*;
import java.io.*;
import java.awt.image.*;
import org.jibble.epsgraphics.*;
import javax.imageio.*;



public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
{

  AlignViewport     av;
  OverviewPanel overviewPanel;
  SeqPanel   seqPanel;
  IdPanel    idPanel;
  IdwidthAdjuster idwidthAdjuster;
  public AlignFrame alignFrame;
  ScalePanel scalePanel;
  AnnotationPanel annotationPanel;
  AnnotationLabels alabels;

  public AlignmentPanel(AlignFrame af, final AlignViewport av)
  {
    alignFrame = af;
    this.av         = av;
    seqPanel        = new SeqPanel  (av, this);
    idPanel         = new IdPanel   (av, this);

    scalePanel = new ScalePanel(av, this);

    idPanelHolder.add(idPanel, BorderLayout.CENTER);
    idwidthAdjuster = new IdwidthAdjuster(this);
    idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);

    annotationPanel = new AnnotationPanel(this);
    alabels = new AnnotationLabels(this);

    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
    annotationScroller.setViewportView(annotationPanel);
    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);

    Dimension d = calculateIdWidth();
    d.setSize( d.width+4, d.height);
    idPanel.idCanvas.setPreferredSize( d );
    hscrollFillerPanel.setPreferredSize( d );

    scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
    seqPanelHolder.add(seqPanel, BorderLayout.CENTER);


    if(seqPanel.seqCanvas.getWidth()==0)
    javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
       public void run()
       {
         setScrollValues(0,0);
         Dimension d = calculateIdWidth();
         d.setSize( d.width+4, d.height);
         idPanel.idCanvas.setPreferredSize( d );
         RefreshPanels();
       }
    });


    hscroll.addAdjustmentListener(this);
    vscroll.addAdjustmentListener(this);

    addComponentListener(new ComponentAdapter()
   {
     public void componentResized(ComponentEvent evt)
     {
          RefreshPanels();
     }
   });

   setFocusable(true);
   addKeyListener(new KeyAdapter()
   {
     public void keyPressed(KeyEvent evt)
     {
       switch(evt.getKeyCode())
       {
         case  27: // escape key
           av.setSelectionGroup(null);
           RefreshPanels();
           break;
         case KeyEvent.VK_X:
           if(evt.isControlDown())
           alignFrame.cut_actionPerformed(null);
           break;
         case KeyEvent.VK_C:
         if(evt.isControlDown())
           alignFrame.copy_actionPerformed(null);
           break;
         case KeyEvent.VK_V:
          if(evt.isControlDown())
           alignFrame.paste(true);
           break;
         case KeyEvent.VK_A:
         if(evt.isControlDown())
           alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
           break;
        case KeyEvent.VK_DOWN:
          alignFrame.moveSelectedSequences(false);
          break;
        case KeyEvent.VK_UP:
          alignFrame.moveSelectedSequences(true);
          break;
        case KeyEvent.VK_F:
         if(evt.isControlDown())
          alignFrame.findMenuItem_actionPerformed(null);
          break;
       }
     }
   });
  }

  Dimension calculateIdWidth()
  {
    Graphics g = this.getGraphics();
    if(g==null)
    {
      javax.swing.JFrame f = new javax.swing.JFrame();
      f.addNotify();
      g = f.getGraphics();
    }

    FontMetrics fm = g.getFontMetrics(av.font);
    AlignmentI al = av.getAlignment();

       int i   = 0;
       int idWidth = 0;
       String id;
       while (i < al.getHeight() && al.getSequenceAt(i) != null)
       {
         SequenceI s   = al.getSequenceAt(i);
         if(av.getShowFullId())
           id   = s.getDisplayId();
         else
           id = s.getName();

         if (fm.stringWidth(id) > idWidth)
           idWidth = fm.stringWidth(id);
         i++;
       }

       return new Dimension(idWidth, 12);
  }


 public void highlightSearchResults(int [] results)
 {
   seqPanel.seqCanvas.highlightSearchResults( results );

   // do we need to scroll the panel?
   if(results!=null && (av.getStartSeq()>results[0]
                        || av.getEndSeq()<results[0]
                        || av.getStartRes()>results[1]
                        || av.getEndRes()<results[2]))
       setScrollValues(results[1], results[0]);


 }


 public OverviewPanel getOverviewPanel()
 {
   return overviewPanel;
 }

 public void setOverviewPanel(OverviewPanel op)
 {
   overviewPanel = op;
 }


  public void setAnnotationVisible(boolean b)
  {
    annotationSpaceFillerHolder.setVisible(b);
    annotationScroller.setVisible(b);
    javax.swing.SwingUtilities.invokeLater(new Runnable()
     {
       public void run()
       {
         RefreshPanels();
       }
    });

  }


  public void setWrapAlignment(boolean wrap)
  {
    scalePanelHolder.setVisible(!wrap);
    hscroll.setVisible(!wrap);
    idwidthAdjuster.setVisible(!wrap);
    annotationScroller.setVisible(!wrap);
    annotationSpaceFillerHolder.setVisible(!wrap);
    idSpaceFillerPanel1.setVisible(!wrap);

    RefreshPanels();

  }


  public void setColourScheme()
  {
    ColourSchemeI cs = av.getGlobalColourScheme();

    if(av.getConservationSelected())
    {

       Alignment al = (Alignment)av.getAlignment();
       Conservation c = new Conservation("All",
                            ResidueProperties.propHash, 3, al.getSequences(), 0,
                            al.getWidth() );

       c.calculate();
       c.verdict(false, 100);
       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);

       av.setGlobalColourScheme( ccs );

    }

    RefreshPanels();
  }


  public void RefreshPanels()
  {
    requestFocus();
    invalidate();

    Dimension d = idPanel.idCanvas.getPreferredSize();
    idPanelHolder.setPreferredSize(d);
    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));

    if (av.getWrapAlignment())
    {
      int max = av.alignment.getWidth() /
          (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;
      vscroll.setValues(0, 1, 0, max);
    }
    else
    {
      if (overviewPanel != null)
        overviewPanel.updateOverviewImage();
      setScrollValues(av.getStartRes(), av.getStartSeq());
    }

    validate();
    repaint();
  }

  int hextent = 0;
  int vextent = 0;

  // return value is true if the scroll is valid
  public boolean scrollUp(boolean up)
  {
    if(up)
    {
      if(vscroll.getValue()<1)
        return false;
      vscroll.setValue(vscroll.getValue() - 1);
    }
    else
    {
     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
       return false;
      vscroll.setValue(vscroll.getValue() + 1);
    }
    return true;
  }

  public boolean scrollRight(boolean right)
  {
    if(right)
   {
     if(hscroll.getValue()<1)
       return false;
     hscroll.setValue(hscroll.getValue() - 1);
   }
   else
   {
    if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())
      return false;
     hscroll.setValue(hscroll.getValue() + 1);
   }

   return true;
 }


  public void setScrollValues(int x, int y)
  {
    hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
    vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;

    if(hextent > av.alignment.getWidth())
      hextent = av.alignment.getWidth();
    if(vextent > av.alignment.getHeight())
      vextent = av.alignment.getHeight();

    if(hextent+x  >  av.getAlignment().getWidth())
      x =  av.getAlignment().getWidth()- hextent;

    if(vextent+y > av.getAlignment().getHeight())
      y = av.getAlignment().getHeight() - vextent;

    if(y<0)
      y = 0;

    if(x<0)
      x=0;

    hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
    vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );

  }


  public void adjustmentValueChanged(AdjustmentEvent evt)
  {
    int oldX = av.getStartRes();
    int oldY = av.getStartSeq();

    if (evt.getSource() == hscroll)
    {
      int x = hscroll.getValue();
      av.setStartRes(x);
      av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
    }

    if (evt.getSource() == vscroll)
    {
      int offy = vscroll.getValue();
      if (av.getWrapAlignment())
      {
        av.setStartRes( vscroll.getValue() * av.getChunkWidth());
      }
      else
      {
        av.setStartSeq(offy);
        av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
      }
    }


    if(overviewPanel!=null)
      overviewPanel.setBoxPosition();

    seqPanel.seqCanvas.fastPaint(av.getStartRes()-oldX, av.getStartSeq()-oldY);
    idPanel.idCanvas.fastPaint( av.getStartSeq()-oldY );
    scalePanel.repaint();
    annotationPanel.fastPaint(av.getStartRes()-oldX);

  }

  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
  {
    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());

    int pwidth = (int) pf.getImageableWidth();
    int pheight = (int) pf.getImageableHeight();

    if (av.getWrapAlignment())
      return printWrappedAlignment(pg, pwidth,pheight, pi);
    else
      return printUnwrapped(pg,pwidth, pheight,pi);
  }

  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
  {

    int idWidth = calculateIdWidth().width + 4;


    pg.setColor(Color.white);
    pg.fillRect(0,0,pwidth, pheight);
    pg.setFont( av.getFont() );

    ////////////////////////////////////
    /// How many sequences and residues can we fit on a printable page?
    int totalRes = (pwidth - idWidth)/av.getCharWidth();
    int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
    int pagesWide = av.getAlignment().getWidth() / totalRes +1;
    int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;

    if (pi >= pagesWide*pagesHigh)
     return Printable.NO_SUCH_PAGE;

    /////////////////////////////
    /// Only print these sequences and residues on this page
    int startRes, endRes, startSeq, endSeq;
    startRes = (pi % pagesWide) * totalRes;
    endRes = startRes + totalRes-1;
    if(endRes>av.getAlignment().getWidth())
      endRes = av.getAlignment().getWidth();

     startSeq = (pi / pagesWide) * totalSeq;
     endSeq = startSeq + totalSeq;
     if(endSeq > av.getAlignment().getHeight())
       endSeq = av.getAlignment().getHeight();


    ////////////////
    //draw Scale
    pg.translate(idWidth,0);
    scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);

    pg.translate(-idWidth, 30);
    ////////////////
    // Draw the ids
    Color currentColor=null;
    Color currentTextColor=null;
    for(int i=startSeq; i<endSeq; i++)
    {
      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
      {
        currentColor = Color.gray;
        currentTextColor = Color.black;
      }
      else
      {
        currentColor = av.getAlignment().getSequenceAt(i).getColor();
        currentTextColor = Color.black;
      }

      pg.setColor(currentColor);
      pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
                              idWidth,
                              av.getCharHeight());

      pg.setColor(currentTextColor);

      String string = av.getAlignment().getSequenceAt(i).getName();
      if(av.getShowFullId())
        string = av.getAlignment().getSequenceAt(i).getDisplayId();

      pg.drawString(string, 0,  jalview.analysis.AlignmentUtil.getPixelHeight
                    (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
    }

    // draw main sequence panel
    pg.translate(idWidth,0);
    pg.setClip(0,0,pwidth-idWidth, pheight);
    seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);

    return Printable.PAGE_EXISTS;
  }


  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
  {

    int idWidth = calculateIdWidth().width+4;

    if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
      pwidth = seqPanel.seqCanvas.getWidth() + idWidth;


    pg.setColor(Color.white);
    pg.fillRect(0,0,pwidth, pheight);
    pg.setFont( av.getFont() );

    ////////////////////////////////////
    /// How many sequences and residues can we fit on a printable page?
    AlignmentI da = av.alignment;
    int endy   = da.getHeight();
    int chunkHeight =  (da.getHeight() + 2)*av.charHeight;
    int chunkWidth  =   (pwidth-idWidth)/av.charWidth;

    int noChunksOnPage = pheight / chunkHeight;
    int totalChunks = da.getWidth() / chunkWidth;

    if ( pi*noChunksOnPage > totalChunks )
     return Printable.NO_SUCH_PAGE;

    ////////////////
    // Draw the ids
    pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);

    int row = pi*noChunksOnPage;
    pg.setColor(Color.black);
    for(int ypos=2*av.charHeight;
        ypos <= pheight && row*chunkWidth<da.getWidth();
        ypos += chunkHeight, row++ )
    {
      for (int i = 0; i < endy; i++)
      {
        SequenceI s = da.getSequenceAt(i);
        String string = s.getName();
        if (av.getShowFullId())
          string = s.getDisplayId();

        pg.drawString(string, 0,
                      AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
                      av.charHeight - (av.charHeight / 5));
      }
    }

    // draw main sequence panel
    pg.translate(idWidth,0);
    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);


    return Printable.PAGE_EXISTS;

  }


  public void makeEPS()
  {
    int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
    int width = seqPanel.getWidth() + idPanel.getWidth();

    if (!av.getWrapAlignment())
    {
      height = (av.alignment.getHeight()+1) * av.charHeight + 30;
      width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
    }

    try
    {
      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
          "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
      chooser.setFileView(new jalview.io.JalviewFileView());
      chooser.setDialogTitle("Create EPS file from alignment");
      chooser.setToolTipText("Save");

      int value = chooser.showSaveDialog(this);
      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
        return;

      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
      EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);

        if (av.getWrapAlignment())
          printWrappedAlignment(pg, width, height, 0);
        else
          printUnwrapped(pg, width, height, 0);


        pg.flush();
        pg.close();
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }

  public void makePNG()
  {
      int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
      int width = seqPanel.getWidth() + idPanel.getWidth();

      if (!av.getWrapAlignment())
      {
        height = (av.alignment.getHeight()+1) * av.charHeight + 30;
        width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
      }



    try
    {
      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
          "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
      chooser.setFileView(new jalview.io.JalviewFileView());
      chooser.setDialogTitle("Create EPS file from alignment");
      chooser.setToolTipText("Save");

      int value = chooser.showSaveDialog(this);
      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
        return;

      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());

      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
      Graphics png = bi.getGraphics();


        if (av.getWrapAlignment())
          printWrappedAlignment(png, width, height, 0);
        else
          printUnwrapped(png, width, height, 0);

        ImageIO.write(bi, "png", out);
        out.close();
    }
    catch (Exception ex)
    {
      ex.printStackTrace();
    }
  }

}