/*
 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 * 
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 */
package jalview.gui;

import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.awt.*;

import javax.swing.*;
import javax.swing.event.*;

import java.awt.event.*;
import java.io.*;

import jalview.api.SequenceStructureBinding;
import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.structure.*;
import jalview.io.*;
import jalview.schemes.*;
import jalview.util.ShiftList;
import fr.orsay.lri.varna.VARNAPanel;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength;
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import fr.orsay.lri.varna.interfaces.InterfaceVARNAListener;
import fr.orsay.lri.varna.interfaces.InterfaceVARNASelectionListener;
import fr.orsay.lri.varna.models.BaseList;
import fr.orsay.lri.varna.models.VARNAConfig;
import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
import fr.orsay.lri.varna.models.rna.ModeleBase;
import fr.orsay.lri.varna.models.rna.ModeleBaseNucleotide;
import fr.orsay.lri.varna.models.rna.RNA;


public class AppVarna extends JInternalFrame implements InterfaceVARNAListener,SelectionListener, SecondaryStructureListener// implements Runnable,SequenceStructureBinding, ViewSetProvider
, InterfaceVARNASelectionListener, VamsasSource

{
  AppVarnaBinding vab;

  VARNAPanel varnaPanel;
  
  public String name;
  
  public StructureSelectionManager ssm;
  
  /*public AppVarna(){
	  vab = new AppVarnaBinding(); 
	  initVarna();
  }*/
  
 
  public AppVarna(SequenceI seq,String strucseq, String struc,String name,AlignmentPanel ap){
    ArrayList<RNA> rnaList = new ArrayList<RNA>();
    RNA rna1 = new RNA(name);
    try {
      rna1.setRNA(strucseq,replaceOddGaps(struc));
    } catch (ExceptionUnmatchedClosingParentheses e2) {
      e2.printStackTrace();
    } catch (ExceptionFileFormatOrSyntax e3) {
      e3.printStackTrace();
    }
    RNA trim=trimRNA(rna1);
    rnaList.add(trim);	  
    rnaList.add(rna1);
    rna1.setName("consensus_"+rna1.getName());
    
    {
      this.seqs.put(trim, seq);
      this.seqs.put(rna1, seq);
    }
    vab = new AppVarnaBinding(rnaList);
    //vab = new AppVarnaBinding(seq,struc);
    //System.out.println("Hallo: "+name);
    this.name=name;
    initVarna();
    ssm = ap.getStructureSelectionManager();
    ssm.addStructureViewerListener(this);
    ssm.addSelectionListener(this);
  }     
  
  public void initVarna(){
	  //vab.setFinishedInit(false);
	  varnaPanel=vab.get_varnaPanel();
	  setBackground(Color.white);
	  JSplitPane split = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,true,vab.getListPanel(),varnaPanel);
	  getContentPane().setLayout(new BorderLayout());
	  getContentPane().add(split, BorderLayout.CENTER);
	  //getContentPane().add(vab.getTools(), BorderLayout.NORTH);	
	  varnaPanel.addVARNAListener(this);
	  varnaPanel.addSelectionListener(this);
	  jalview.gui.Desktop.addInternalFrame(this,"VARNA -"+name,getBounds().width, getBounds().height);
	  this.pack();
	  showPanel(true);
  }
  
  public String replaceOddGaps(String oldStr){
	  String patternStr = "[^([{<>}])]";
      String replacementStr = ".";
      Pattern pattern = Pattern.compile(patternStr);
      Matcher matcher = pattern.matcher(oldStr);
      String newStr=matcher.replaceAll(replacementStr);
	  return newStr;
  }
  
  public RNA trimRNA(RNA rna){
    ShiftList offset=new ShiftList();
	  RNA rnaTrim = new RNA("trim_"+rna.getName());
	  try {
		  rnaTrim.setRNA(rna.getSeq(),replaceOddGaps(rna.getStructDBN()));
	  } catch (ExceptionUnmatchedClosingParentheses e2) {
		e2.printStackTrace();
	  } catch (ExceptionFileFormatOrSyntax e3) {
		e3.printStackTrace();
	  }

	  StringBuffer seq=new StringBuffer(rnaTrim.getSeq());
	  StringBuffer struc=new StringBuffer(rnaTrim.getStructDBN());
	  int ofstart=-1,sleng=rnaTrim.getSeq().length();
	  for(int i=0;i<sleng;i++){
		  //TODO: Jalview utility for gap detection java.utils.isGap()
		  //TODO: Switch to jalview rna datamodel
		  if(jalview.util.Comparison.isGap(seq.charAt(i))){
		    if (ofstart==-1)
		    {
		      ofstart=i;
		    }
			  if(!rnaTrim.findPair(i).isEmpty()){
				  int m=rnaTrim.findPair(i).get(1);
				  int l=rnaTrim.findPair(i).get(0);
				  
				  struc.replace(m, m+1, "*");
				  struc.replace(l, l+1, "*");
			  }else{
				  struc.replace(i, i+1, "*");
			  }
		  } else {
		    if (ofstart>-1)
		    {
		      offset.addShift(ofstart, ofstart-i);
		      ofstart=-1;
		    }
		  }
	    }
	  // final gap
          if (ofstart>-1)
          {
            offset.addShift(ofstart, ofstart-sleng);
            ofstart=-1;
          }
  	  String newSeq=rnaTrim.getSeq().replace("-", "");
	  rnaTrim.getSeq().replace(".", "");
	  String newStruc=struc.toString().replace("*", "");

	  try {
		rnaTrim.setRNA(newSeq,newStruc);
		registerOffset(rnaTrim,offset);
	  } catch (ExceptionUnmatchedClosingParentheses e) {
		// TODO Auto-generated catch block
		e.printStackTrace();
	  } catch (ExceptionFileFormatOrSyntax e) {
		// TODO Auto-generated catch block
		e.printStackTrace();
	  }
	  return rnaTrim;
  }
  Map<RNA,SequenceI> seqs=new Hashtable<RNA,SequenceI>();
  Map<RNA,ShiftList> offsets=new Hashtable<RNA,ShiftList>();
  Map<RNA,ShiftList> offsetsInv=new Hashtable<RNA,ShiftList>();
  private void registerOffset(RNA rnaTrim, ShiftList offset)
  {
    offsets.put(rnaTrim, offset);
    offsetsInv.put(rnaTrim,offset.getInverse());
  }

  public void showPanel(boolean show){
	  this.setVisible(show);
  }
  
  private boolean _started = false;

  public void run(){
	  _started = true;
	  
	  try
      {
        initVarna();
      } catch (OutOfMemoryError oomerror)
      {
        new OOMWarning("When trying to open the Varna viewer!", oomerror);
      } catch (Exception ex)
      {
        Cache.log.error("Couldn't open Varna viewer!", ex);
      }
  }

@Override
public void onUINewStructure(VARNAConfig v, RNA r) {
  
}

@Override
public void onWarningEmitted(String s) {
	// TODO Auto-generated method stub
	
}
private class VarnaHighlighter {
  private  HighlightRegionAnnotation _lastHighlight;
  private RNA _lastRNAhighlighted=null;
  public void highlightRegion(RNA rna, int start,int end)
  {
  if (_lastRNAhighlighted!=null)
  {
    _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
  }
  HighlightRegionAnnotation highlight = new HighlightRegionAnnotation(rna.getBasesBetween(start,end));
  rna.addHighlightRegion(highlight);
  _lastHighlight=highlight;
  _lastRNAhighlighted=rna;

  }
  public HighlightRegionAnnotation getLastHighlight() {
    return _lastHighlight;
  }
  public RNA getLastRNA()
  {
    return _lastRNAhighlighted;
  }
}
VarnaHighlighter mouseOverHighlighter=new VarnaHighlighter(),
selectionHighlighter=new VarnaHighlighter();
/**
 * If a mouseOver event from the AlignmentPanel 
 * is noticed the currently selected RNA in the 
 * VARNA window is highlighted at the specific position. 
 * To be able to remove it before the next highlight
 * it is saved in _lastHighlight
 */
@Override
public void mouseOverSequence(SequenceI sequence, int index) {
        RNA rna=vab.getSelectedRNA();
	ShiftList shift=offsets.get(rna);
	if (shift!=null)
	{
	  index=shift.shift(index);
	}
	mouseOverHighlighter.highlightRegion(rna, index, index);
	vab.updateSelectedRNA(rna);
}

@Override
public void mouseOverStructure(int atomIndex, String strInfo) {
	// TODO Auto-generated method stub
	
}

@Override
public void onStructureRedrawn()
{
  // TODO Auto-generated method stub
  
}

@Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
        SelectionSource source)
{
  int start=seqsel.getStartRes(),end=seqsel.getEndRes();
  RNA rna=vab.getSelectedRNA();
  ShiftList shift=offsets.get(rna);
  if (shift!=null)
  {
    start=shift.shift(start);
    end=shift.shift(end);
  }
  selectionHighlighter.highlightRegion(rna, start, end);
  selectionHighlighter.getLastHighlight().setOutlineColor(seqsel.getOutlineColour());
  vab.updateSelectedRNA(rna);
}

@Override
public void onHoverChanged(ModeleBase arg0, ModeleBase arg1)
{
  RNA rna=vab.getSelectedRNA();
  ShiftList shift=offsetsInv.get(rna);
  SequenceI seq=seqs.get(rna);
  if (arg1!=null && seq!=null)
  {
    if (shift!=null)
    {
      ssm.mouseOverVamsasSequence(seq, seq.findIndex(arg1.getIndex()), this);
    } else {
      ssm.mouseOverVamsasSequence(seq, arg1.getIndex(),  this);
    }
  }
}

@Override
public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
{
  // TODO Auto-generated method stub
  
}


}