package jalview.io;





import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.SecondaryStructureAnnotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.ws.jws1.Annotate3D;

import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.Reader;
import java.io.FileReader;
import java.lang.reflect.Array;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Hashtable;
import java.util.List;
import java.util.Vector;

import javax.xml.parsers.ParserConfigurationException;
import javax.xml.parsers.SAXParser;
import javax.xml.parsers.SAXParserFactory;

import org.xml.sax.InputSource;
import org.xml.sax.SAXException;

import com.stevesoft.pat.Regex;

import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import fr.orsay.lri.varna.factories.RNAFactory;
import fr.orsay.lri.varna.factories.RNAFactory.RNAFileType;
import fr.orsay.lri.varna.models.rna.RNA;
import fr.orsay.lri.varna.utils.RNAMLParser;




public class RnamlFile extends AlignFile
{
	 public String id;
	 protected ArrayList<RNA> result;
	 
	 public RnamlFile()
	  {
		 super();
		
	  }
	 
	 public RnamlFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
	  {
	    super(inFile, type);
	    
	  }

	  public RnamlFile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
	  {
	    super(source);
	    
	  }
	  
//	  public RnamlFile(BufferedReader r) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed
//	  {
//		  	super();	    
//		    parse(r);
//		    // sets the index of each sequence in the alignment
//		    for( int i=0,c=seqs.size(); i<c; i++ ) {  
//		    	seqs.get(i).setIndex(i);  
//		    }
//		  
//	    
//	  }
	  
	public BufferedReader CreateReader() throws FileNotFoundException
	{
		 FileReader fr = null;
		  fr = new FileReader(inFile); 
		  
		  BufferedReader r = new BufferedReader (fr);
		  return r;
	}
	
	
	@SuppressWarnings("unchecked")
	public void parse() throws FileNotFoundException, ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax
	{
		 FileReader fr = null;
		  fr = new FileReader(inFile); 
		  
		  BufferedReader r = new BufferedReader (fr);
	
		  //ArrayList<String> seq =new ArrayList();
		  //System.out.println(r);
		   
		  
		 result = RNAFactory.loadSecStrRNAML(r);
		  
		 System.out.println("this is the secondary scructure:" +result.size());
		  //System.out.println("this is the secondary scructure:" +result.toString());
		  //System.out.println("this is the secondary scructure:" +result.size());
		 SequenceI[] seqs = new SequenceI[result.size()];
		  System.out.println(type); //the type is "File"
		  System.out.println(inFile );//inFile is the path
		  
		 for(int i=0;i<result.size();i++)
			{
			 RNA current = result.get(i);
		  System.out.println(current.getSeq());
		  //System.out.println(result.get(i).getStructBPSEQ());
		  System.out.println(result.get(i).getStructDBN(true));
		  System.out.println(i);
		  String rna =current.getStructDBN(true);
		  //System.out.println(result.get(0).getAnnotations());
		  String seq = current.getSeq();
	
		  int begin=0;
		  int end = seq.length()-1;
		  
		  id = safeName(getDataName());
		  seqs[i] = new Sequence(id, seq, begin, end);
		  //System.out.println(seq);
		  System.out.println("Rna is still "+rna);
		  //SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
		  //seqs[i].addSequenceFeature(feat);
		  
		  String[] annot=new String[rna.length()] ;
		  Annotation[] ann = new Annotation[rna.length()];
		
		  for(int j=0;j<rna.length();j++)
			{
			  annot[j] =rna.substring(j,j+1);
		  
			}
		  
		  for(int k=0;k<rna.length();k++)
		{
			  ann[k] = new Annotation(annot[k], "", jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0), 0f);
			  			  
		}
		  AlignmentAnnotation align = new AlignmentAnnotation("Sec. str.",current.getID(),ann);
		  
		  seqs[i].addAlignmentAnnotation(align);
		  seqs[i].setRNA(result.get(i));
		  this.annotations.addElement(align);
		}
   	  this.setSeqs(seqs);
		 
		 
		

	}
	  
	
	  public void parse(BufferedReader r) throws ExceptionPermissionDenied, ExceptionLoadingFailed, ExceptionFileFormatOrSyntax 
	  {
		   System.out.println("parse with Buffer (RnamlFile");
		  Hashtable seqhash = new Hashtable();
		  Vector headers = new Vector();
		  //ArrayList<String> seq =new ArrayList();
		  //System.out.println(r);
		  
		  result = RNAFactory.loadSecStr(r,RNAFileType.FILE_TYPE_RNAML);
		  
		  System.out.println("this is the secondary scructure:" +result.toArray());
		  System.out.println("this is the secondary scructure:" +result.toString());
		  System.out.println("this is the secondary scructure:" +result.size());
			for(int i=0;i<result.size();i++)
			{
		  System.out.println(result.get(0).getSeq());
		  System.out.println(result.get(0).getStructBPSEQ());
		  System.out.println(result.get(0).getStructDBN(true));
		  String rna1 =result.get(0).getStructDBN(true);
		  System.out.println(result.get(0).getAnnotations());
		  String seq = result.get(0).getSeq();
		  System.out.println(type); //the type is "File"
		  System.out.println(inFile );//inFile is the path
		  int begin=0;
		  int end = seq.length()-1;
		  SequenceI[] seqs = new SequenceI[1];
		  id = safeName(getDataName());
		  seqs[0] = new Sequence(id, seq, begin, end);
		  SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
		  seqs[0].addSequenceFeature(feat);
		  this.setSeqs(seqs);
		  
		  String[] annot=new String[10000] ;
		  Annotation[] ann = new Annotation[1000];
		  for(int j=0;j<rna1.length();j++)
			{
		  annot[j] =rna1.substring(j,j+1);
		  //System.out.println(annot[j]);
			}
		  
		  for(int k=0;k<rna1.length();k++)
		{
			  ann[k] = new Annotation(annot[k], "", ' ', 0f);
			  
			  ann[k].secondaryStructure = jalview.schemes.ResidueProperties.getRNASecStrucState(annot[k]).charAt(0);
			  
		}
		  AlignmentAnnotation align = new AlignmentAnnotation("Secondary structure","",ann);
		  seqs[0].addAlignmentAnnotation(align);
		  this.annotations.addElement(align);
		}
		//Annotate3D tintin = new Annotate3D();
		  
		//System.out.println(tintin);  
		  
		  
		  
		  
		  
		  
		 
	
//					for(RNAMLParser.RNATmp rnaTmp : RNAMLData.getMolecules())
//					{
//						// Retrieving parsed data
//						seq = rnaTmp.getSequence(); //contient la séquence sous forme de liste
//						System.out.println(seq);
//						String seqAsStr = "";
//						for(String s:seq)
//						{
//							// Only consider last character, e.g. in case of modified nucleotide
//							seqAsStr += s.charAt(s.length()-1);
//						}
//						int begin=0;
//						int end = seqAsStr.length()-1;
//						SequenceI[] seqs = new SequenceI[1];
//						id = safeName(getDataName());
//						seqs[0] = new Sequence(id, seqAsStr, begin, end);
//						SequenceFeature feat = new SequenceFeature(type, "",5, 13, 0f, null);
//
//	                    seqs[0].addSequenceFeature(feat);
//						this.setSeqs(seqs);
						
						//String pos = annot.substring(1, 2);
						//System.out.println(annot);
						//System.out.println(pos);
						
					   // ann[1] = new Annotation(pos, "", ' ', 0f);
					   // ann[1].secondaryStructure = 'A';
					    //System.out.println(ann[1]);
					    
					   // toto.annotations=ann;
					    

					    
////						 Annotation[] els = new Annotation[seq.size()];
//						
//						//System.err.println(""+seq.size());
//					    Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
//					    String[] annot = new String[10000];
//					  
//						//Annotation[] ann = new Annotation[allbpsTmp.size()];
//						for (int i = 0; i < allbpsTmp.size(); i++) {
//						RNAMLParser.BPTemp bp = allbpsTmp.get(i);
//						//System.err.println("toto ="+bp);
//						int bp5 = bp.pos5;
//						annot[bp5]= "(";
//						//annot[bp5]= '(';
//						System.out.println(annot[bp5]);
//						//System.out.println("bp5 ="+bp5);
//						int bp3 = bp.pos3;
//					
//						annot[bp3]= ")";
//						System.out.println(annot[bp3]);
//						//System.out.println(annot.get(bp3));
//						
//						//String pos1 = annot.substring(bp5, bp5+1);
//						//String pos2 = annot.substring(bp3, bp3+1);
//						//ann[i] = new Annotation(pos1, "", ' ', 0f);
//						//ann[i+1] = new Annotation(pos2, "", ' ', 0f);
//						//System.out.println(pos1);
//						
//						//System.out.println("bp3 ="+bp3);
//						//ModeleBP newStyle = bp.createBPStyle(mb, part);
//						}	
//						Annotation[] ann = new Annotation[annot.length+1];
//						for(int i=0;i<annot.length;i++)
//						{		
//							if(annot[i]==null)
//							{
//								annot[i]=".";
//							}
//							
//							ann[i] = new Annotation(annot[i], "", ' ', 0f);
//						//System.out.print(annot[i]);
//						}
//						
//						AlignmentAnnotation toto = new AlignmentAnnotation("Secondary structure","",ann);
//						this.annotations.addElement(toto);
					
						// Creating empty structure of suitable size
//						int[] str = new int[seq.size()];
//						for (int i=0;i<str.length;i++)
//						{ str[i] = -1; }
//						Vector<RNAMLParser.BPTemp> allbpsTmp = rnaTmp.getStructure();
//						for (int i = 0; i < allbpsTmp.size(); i++) {
//							RNAMLParser.BPTemp bp = allbpsTmp.get(i);
//							//System.err.println("toto ="+bp);
//							int bp5 = bp.pos5;
//							//System.out.println("bp5 ="+bp5);
//							int bp3 = bp.pos3;
							//System.out.println("bp3 ="+bp3);
							//ModeleBP newStyle = bp.createBPStyle(mb, part);
//						}
						//Annotation ann;
					    //ann = new Annotation(bp5, "", ' ', 0f);
				
					//}

			

//				return result;
	  
}

	  
	  public static String print(SequenceI[] s)
	  {
	    return "not yet implemented";
	  }
	  
	  public String print()
	  {
		System.out.print("affiche :");
	    return print(getSeqsAsArray());
	  }
	  
	  /**
	   * make a friendly ID string.
	   * 
	   * @param dataName
	   * @return truncated dataName to after last '/'
	   */
	  private String safeName(String dataName)
	  {
	    int b = 0;
	    while ((b = dataName.indexOf("/")) > -1 && b < dataName.length() )
	    {	    	   
	    	dataName = dataName.substring(b + 1).trim();
	    	
	    }
	    int e = (dataName.length() - dataName.indexOf("."))+1;
	    dataName = dataName.substring(1,e).trim();
	    return dataName;
	  }
	  
	  public ArrayList getRNA()
	  {
		  return result;
	  }
	  
	  public Vector getAnnot()
	  {
		  return annotations;
	  }
}