BinaryDataFile.java

package evoker;

import java.io.File;
import java.io.IOException;
import java.io.BufferedInputStream;
import java.io.FileInputStream;
import java.math.BigInteger;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
import java.util.ArrayList;

public abstract class BinaryDataFile extends BinaryData{

    File file;
    protected boolean compressed;

    BinaryDataFile(String filename, int numInds, MarkerData md, String collection, String chromosome){
        super(numInds,md,collection, chromosome);
        this.file = new File(filename);
    }

    /**
     * Checks whether the file is of a valid format
     * 
     * @param headers
     * @throws IOException 
     */
    public void checkFile(byte[] headers) throws IOException{

        if (file != null){
        	
        	BigInteger fileSize       = BigInteger.valueOf(file.length());
        	BigInteger checkSize      = BigInteger.valueOf(new Long(numSNPs)).multiply(BigInteger.valueOf(new Long(bytesPerRecord)));
        	
        	if (!fileSize.equals(checkSize.add(BigInteger.valueOf(new Long(headers.length))))) {
        		if (fileSize.equals(checkSize.add(new BigInteger("8")))){
        			//alternate Oxford format
                    //Change headers byte[] to be a new byte[] of the correct things as specified by numSNPs and numInds.
                    ByteBuffer buf = ByteBuffer.allocate(8);
                    buf.order(ByteOrder.LITTLE_ENDIAN);
                    // in the case of remote data we need to compare the total snps as this is the value in the header
                    buf.putInt(this.totNumSNPs); 
                    if (file.getName().endsWith("bed") || file.getName().endsWith("gen.bin") ){
                    	// the inds value in the header is the number of columns--three values per ind
                        buf.putInt(this.numInds*3);
                    }else if (file.getName().endsWith("bnt") || file.getName().endsWith("int.bin")){
                    	// the inds value in the header is the number of columns--two values per ind
                    	buf.putInt(this.numInds*2);
                    }
                    buf.clear();
                    headers = new byte[8];
                    buf.get(headers, 0, 8);
                    
                    bntHeaderOffset = 8;
                    bedHeaderOffset = 8;
        		} else{
        			throw new IOException(file + " is not properly formatted.\n(Incorrect length.)");
        		}
        	}
        } else{
            //this is a useless message, but it implies badness 10000
            throw new IOException("File is null?!?");
        }
                
       	//are the headers acceptable for this file?
       	BufferedInputStream binaryIS = new BufferedInputStream(new FileInputStream(file),8192);
       	byte[] fromFile = new byte[headers.length];
       	binaryIS.read(fromFile,0,headers.length);
         
       	for (int i = 0; i < headers.length; i++){
       		if (fromFile[i] != headers[i]){
       			throw new IOException(file +
       			" is not properly formatted.\n(Magic number is incorrect.)");
       		}
       	} 
    }
    
    public void checkFile(byte[] headers, boolean zipped) throws IOException{
    	//TODO: method for checking if compressed files are valid evoker files
    	// get the uncompressed size of the file - for gzip files that where originally smaller than 4gb you can read the last 4 bytes of the file
    	// at the moment we can assume this type of file is Oxford format
    }
    
    public ArrayList getRecord(String markerName){
        //do some checks on getting the data and handle errors centrally
        int snpIndex;
        try {
            if((snpIndex = md.getIndex(markerName,md.getSampleCollectionIndex(collection))) >= 0) {
                return getRecord(snpIndex);
            }
        }catch(IOException ioe) {
            //TODO: handle me
            //TODO: I don't know anything about that SNP?
        }
        return(null);
    }
    
    public boolean isCompressed(){
		return compressed;
    }

    abstract ArrayList getRecord(long index) throws IOException;
    
}