package seqviewer;

import java.io.*;
import java.util.*;
import java.awt.*;
import java.awt.event.*;
import java.awt.geom.*;
import javax.swing.*;
import java.util.List;  // Tie-breaker

import org.biojava.utils.*;
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.seq.impl.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.gui.*;
import org.biojava.bio.gui.sequence.*;

public class EmblViewer2 {
  public static SequencePanel sp;
  static JFrame f;

  public static void main(String[] args) throws Exception {
    String seqFile = null;
    try {
	    seqFile = args[0];
    } catch (IndexOutOfBoundsException ex) {
	    throw new Exception("usage: java seqviewer.EmblViewer acc.embl");
    }

    final BasicFeatureRenderer fr;
    final FeatureRenderer split;
    
    SequenceFormat ef = new EmblLikeFormat();
    SequenceBuilderFactory sf = new EmblProcessor.Factory(SimpleSequenceBuilder.FACTORY);
    InputStream is = new FileInputStream(seqFile);
	    
    StreamReader sr = new StreamReader(is, ef, DNATools.getDNA().getTokenization("token"), sf);
    Sequence seq = sr.nextSequence();

    Feature source = (Feature) seq.filter(
      new FeatureFilter.ByType("source"), false
    ).features().next();
    seq.removeFeature(source);
    
    FeatureFilter repeatFilter = new FeatureFilter.ByType("repeat_region");
    FeatureFilter miscFilter = new FeatureFilter.ByType("misc_feature");
    
    f = new JFrame("EMBL View");
    sp = new SequencePanel();
    sp.setSequence(seq);
    sp.setRange(new RangeLocation(1, seq.length()));
    sp.setScale(0.2);
    sp.setDirection(SequencePanel.HORIZONTAL);
    
    fr = new BasicFeatureRenderer();
    split = new ZiggyFeatureRenderer();
    FeatureRenderer frChooser = new FeatureRenderer() {
      public void renderFeature(
        Graphics2D g, Feature f, SequenceRenderContext context
      ) {
        if(f.getLocation().isContiguous()) {
          fr.renderFeature(g, f, context);
        } else {
          split.renderFeature(g, f, context);
        }
      }
      
      public double getDepth(SequenceRenderContext context) {
        return Math.max(fr.getDepth(context), split.getDepth(context));
      }
      
      public FeatureHolder processMouseEvent(
        FeatureHolder hits,
        SequenceRenderContext src,
        MouseEvent me
      ) {
        return hits;
      }
    };
    FeatureBlockSequenceRenderer features = new FeatureBlockSequenceRenderer();
    FeatureBlockSequenceRenderer repeats = new FeatureBlockSequenceRenderer();
    FeatureBlockSequenceRenderer misc = new FeatureBlockSequenceRenderer();
    
//    features.setDepth(15);
//    repeats.setDepth(10);
//    misc.setDepth(10);
    
    features.setFeatureRenderer(frChooser);
    repeats.setFeatureRenderer(fr);
    misc.setFeatureRenderer(frChooser);
    
//    features.setLabel("features");
//    repeats.setLabel("repeats");
//    misc.setLabel("misc");
    
    FeatureFilter featuresFilter = new FeatureFilter.And(
      new FeatureFilter.Not(repeatFilter),
      new FeatureFilter.Not(miscFilter)
    );

    BumpedRenderer lsr = new BumpedRenderer();
    lsr.setRenderer(features);
    
    MultiLineRenderer mlRend = new MultiLineRenderer();
    mlRend.addRenderer(new FilteringRenderer(repeats, repeatFilter, false));
    mlRend.addRenderer(new FilteringRenderer(misc, miscFilter, false));
    mlRend.addRenderer(new FilteringRenderer(lsr, featuresFilter, false));
    mlRend.addRenderer(new SymbolSequenceRenderer());
    mlRend.addRenderer(new RulerRenderer());

    sp.setRenderer(mlRend);
    sp.addSequenceViewerListener(new SequenceViewerListener() {
      public void mouseClicked(SequenceViewerEvent sve) {
        System.out.println(sve.getMouseEvent().getPoint() + "\t" + sve.getSource());
        Object t = sve.getTarget();
        for(Iterator ri = sve.getPath().iterator(); ri.hasNext(); ) {
          SequenceRenderer sr = (SequenceRenderer) ri.next();
          System.out.println("\t" + sr);
        }
        if(t instanceof FeatureHolder) {
          FeatureHolder fh = (FeatureHolder) t;
          for(Iterator fi = fh.features(); fi.hasNext(); ) {
            Feature f = (Feature) fi.next();
            System.out.println("\t" + f.getType() + "\t: " + f.getLocation());
          }
        }
      }
      
      public void mousePressed(SequenceViewerEvent sve) {
        //System.out.println("pressed: " + sve);
      }
      
      public void mouseReleased(SequenceViewerEvent sve) {
        //System.out.println("released: " + sve);
      }
    });
    
    f.getContentPane().setLayout(new BorderLayout());
    f.getContentPane().add(new JScrollPane(sp), BorderLayout.CENTER);
    JPanel panel = new JPanel();
    panel.setLayout(new FlowLayout());
    f.getContentPane().add(panel, BorderLayout.NORTH);
    
    JButton vert = new JButton("Vertical");
    vert.addActionListener(new ActionListener() {
	    public void actionPerformed(ActionEvent ae) {
        sp.setDirection(SequencePanel.VERTICAL);
	    }
    } );
    JButton horiz = new JButton("Horizontal");
    horiz.addActionListener(new ActionListener() {
	    public void actionPerformed(ActionEvent ae) {
        sp.setDirection(SequencePanel.HORIZONTAL);
	    }
    } );
    JButton blue = new JButton("Blue");
    blue.addActionListener(new ActionListener() {
      public void actionPerformed(ActionEvent ae) {
        try {
          fr.setFill(Color.blue);
        } catch (ChangeVetoException cve) {
          throw new BioError(cve, "oops");
        }
      }
    } );
    JButton red = new JButton("Red");
    red.addActionListener(new ActionListener() {
      public void actionPerformed(ActionEvent ae) {
        try {
          fr.setFill(Color.red);
        } catch (ChangeVetoException cve) {
          throw new BioError(cve, "oops");
        }
      }
    } );
    JScrollBar scale = new JScrollBar(JScrollBar.HORIZONTAL);
    scale.addAdjustmentListener(
      new AdjustmentListener() {
        public void adjustmentValueChanged(AdjustmentEvent e) {
          int val = e.getValue();
          double s = Math.exp(-val / 7.0) * 20.0;
          System.out.println("Scale now at " + s);
          sp.setScale(s);
        }
      } 
    );
    
    panel.add(vert);
    panel.add(horiz);
    panel.add(blue);
    panel.add(red);
    panel.add(scale);

    f.setSize(500, 500);
    f.setVisible(true);
  }
}