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package fr.inserm.umr915.core.bio.fasta;

import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.RandomAccessFile;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import java.util.regex.Pattern;



import org.lindenb.io.IOUtils;
import org.lindenb.util.StringUtils;
import fr.inserm.umr915.core.bio.SequenceProvider;


/**
 * IndexedGenome
 *
 */
public class IndexedGenome
	implements SequenceProvider
	{
	private Map<String, FastaIndex> name2index=new HashMap<String, FastaIndex>();
	private Map<File, RandomAccessFile> file2stream=new HashMap<File, RandomAccessFile>();
	
	public IndexedGenome()
		{
		
		}
	public void addAll(Collection<FastaIndex> indexes)
		{
		for(FastaIndex i:indexes) add(i);
		}
	
	public void add(FastaIndex index)
		{
		for(String name:index.getNames())
			{
			if(name2index.containsKey(name))
				{
				throw new IllegalArgumentException("Sequence "+index+" indexed twice.");
				}
			}
		for(String name:index.getNames())
			{
			this.name2index.put(name, index);
			}
		}
	
	@Override
	public void close()
		{
		for(File f:file2stream.keySet())
			{
			RandomAccessFile  io= file2stream.get(f);
			if(io!=null)
				{
				try { io.close(); } catch(IOException err) {}
				}
			}
		file2stream.clear();
		}
	
	@Override
	public byte[] getSequence(String chromosome,int start,int length) throws IOException
		{
		FastaIndex index=name2index.get(chromosome);
		if(index==null) throw new IOException("Sequence \""+chromosome+"\" was not indexed");
		RandomAccessFile io=file2stream.get(index.getFile());
		if(io==null)
			{
			io=new RandomAccessFile(index.getFile(), "r");
			file2stream.put(index.getFile(), io);
			}
		return index.getSequence(io, start, length);
		}
	
	
	public static IndexedGenome readIndex(File file) throws IOException
		{
		IndexedGenome genome=new IndexedGenome();
		genome.addAll(FastaIndexer.readIndex(file));
		return genome;
		}
	
	private static void _echo(String name,int start,int length,byte seq[],int lineLength)
		{
		System.out.print(">");
		System.out.print(name);
		System.out.print('|');
		System.out.print(""+start+"-"+(start+length));
		
		for(int i=0;i< seq.length;++i)
			{
			if(i%lineLength==0) System.out.println();
			System.out.print((char)seq[i]);
			}
		System.out.println();
		}
	private static void _run(IndexedGenome genome,BufferedReader in,int lineLength) throws IOException
		{
		Pattern TAB=Pattern.compile("[\t]");
		String line;
		while((line=in.readLine())!=null)
			{
			if(StringUtils.isBlank(line) || line.startsWith("#")) continue;
			String tokens[]=TAB.split(line);
			FastaIndex index=genome.name2index.get(tokens[0]);
			if(index==null)
				{
				System.err.println("Not indexed:\""+tokens[0]+"\"");
				continue;
				}
			if(tokens.length<3)
				{
				_echo(tokens[0], 0, index.getLength(),genome.getSequence(tokens[0], 0, index.getLength()),lineLength);
				}
			else
				{
				int start=Integer.parseInt(tokens[1]);
				int end=Integer.parseInt(tokens[2]);
				if(end<start)
					{
					System.err.println("Bad start/end in "+line);
					continue;
					}

				_echo(tokens[0],start,end-start,genome.getSequence(tokens[0], start,end-start),lineLength);
				}
			}
		}
	
	public static void main(String[] args)
		{
		try {
			int fastaLineLength=50;
			File indexFile=null;
			int optind=0;
			while(optind<args.length)
				{
				if(args[optind].equals("-h"))
					{
					System.err.println("-f <xml-index-file> REQUIRED");
					System.err.println("-n <int> fasta line length:"+fastaLineLength);
					System.err.println("(stdin|file) with ");
					System.err.println(" seqname\n OR");
					System.err.println(" seqname(tab)start(end)end");
					return;
					}
				else if(args[optind].equals("-f"))
					{
					indexFile=new File(args[++optind]);
					}
				else if(args[optind].equals("-n"))
					{
					fastaLineLength=Integer.parseInt(args[++optind]);
					if(fastaLineLength<=0)
						{
						System.err.println("Bad fasta line size "+fastaLineLength);
						return;
						}
					}
				else if(args[optind].equals("--"))
					{
					optind++;
					break;
					}
				else if(args[optind].startsWith("-"))
					{
					System.err.println("Unnown option: "+args[optind]);
					return;
					}
				else
					{
					break;
					}
				++optind;
				}
			
			if(indexFile==null)
				{
				System.err.println("XML Index file missing");
				return;
				}
			IndexedGenome index= IndexedGenome.readIndex(indexFile);
			if(optind==args.length)
				{
				_run(index,new BufferedReader(new InputStreamReader(System.in)),fastaLineLength);
				}
			else
				{
				while(optind< args.length)
					{
					String inputName=args[optind++];
					BufferedReader in=IOUtils.openReader(inputName);
					_run(index,new BufferedReader(new InputStreamReader(System.in)),fastaLineLength);
					in.close();
					}
				}
			index.close();
		} catch (Exception e) {
			e.printStackTrace();
		}
		}
	}