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package align2;
import dna.AminoAcid;
import shared.KillSwitch;
import shared.Shared;
/**
* @author Jonathan Rood
* @date Jul 18, 2014
*
*/
public class BandedAlignerJNI extends BandedAligner{
static {
Shared.loadJNI();
}
private native int alignForwardJNI(byte[] query, byte[] ref, int qstart, int rstart, int maxEdits, boolean exact, int maxWidth, byte[] baseToNumber, int[] returnVals);
private native int alignForwardRCJNI(byte[] query, byte[] ref, int qstart, int rstart, int maxEdits, boolean exact, int maxWidth, byte[] baseToNumber, byte[] baseToComplementExtended, int[] returnVals);
private native int alignReverseJNI(byte[] query, byte[] ref, int qstart, int rstart, int maxEdits, boolean exact, int maxWidth, byte[] baseToNumber, int[] returnVals);
private native int alignReverseRCJNI(byte[] query, byte[] ref, int qstart, int rstart, int maxEdits, boolean exact, int maxWidth, byte[] baseToNumber, byte[] baseToComplementExtended, int[] returnVals);
public static void main(String[] args){
byte[] query=args[0].getBytes();
byte[] ref=args[1].getBytes();
int qstart=-1;
int rstart=-1;
int maxedits=big;
int width=5;
if(args.length>2){qstart=Integer.parseInt(args[2]);}
if(args.length>3){rstart=Integer.parseInt(args[3]);}
if(args.length>4){maxedits=Integer.parseInt(args[4]);}
if(args.length>4){width=Integer.parseInt(args[5]);}
BandedAlignerJNI ba=new BandedAlignerJNI(width);
int edits;
edits=ba.alignForward(query, ref, (qstart==-1 ? 0 : qstart), (rstart==-1 ? 0 : rstart), maxedits, true);
System.out.println("Forward: \tedits="+edits+", lastRow="+ba.lastRow+", score="+ba.score());
System.out.println("***********************\n");
//
// edits=ba.alignForwardRC(query, ref, (qstart==-1 ? query.length-1 : qstart), (rstart==-1 ? 0 : rstart), maxedits, true);
// System.out.println("ForwardRC: \tedits="+edits+", lastRow="+ba.lastRow+", score="+ba.score());
// System.out.println("***********************\n");
edits=ba.alignReverse(query, ref, (qstart==-1 ? query.length-1 : qstart), (rstart==-1 ? ref.length-1 : rstart), maxedits, true);
System.out.println("Reverse: \tedits="+edits+", lastRow="+ba.lastRow+", score="+ba.score());
System.out.println("***********************\n");
// edits=ba.alignReverseRC(query, ref, (qstart==-1 ? 0 : qstart), (rstart==-1 ? ref.length-1 : rstart), maxedits, true);
// System.out.println("ReverseRC: \tedits="+edits+", lastRow="+ba.lastRow+", score="+ba.score());
// System.out.println("***********************\n");
}
public BandedAlignerJNI(int width_){
super(width_);
assert(big>maxWidth/2);
}
/**
* @param query
* @param ref
* @param qstart
* @param rstart
* @return Edit distance
*/
@Override
public int alignForward(final byte[] query, final byte[] ref, final int qstart, final int rstart, final int maxEdits, final boolean exact){
int[] returnVals = KillSwitch.allocInt1D(5);
returnVals[0] = lastQueryLoc;
returnVals[1] = lastRefLoc;
returnVals[2] = lastRow;
returnVals[3] = lastEdits;
returnVals[4] = lastOffset;
int edits = alignForwardJNI(query,ref,qstart,rstart,maxEdits,exact,maxWidth,AminoAcid.baseToNumber,returnVals);
lastQueryLoc = returnVals[0];
lastRefLoc = returnVals[1];
lastRow = returnVals[2];
lastEdits = returnVals[3];
lastOffset = returnVals[4];
return edits;
}
/**
* @param query
* @param ref
* @param qstart
* @param rstart
* @return Edit distance
*/
@Override
public int alignForwardRC(final byte[] query, final byte[] ref, final int qstart, final int rstart, final int maxEdits, final boolean exact){
int[] returnVals = KillSwitch.allocInt1D(5);
returnVals[0] = lastQueryLoc;
returnVals[1] = lastRefLoc;
returnVals[2] = lastRow;
returnVals[3] = lastEdits;
returnVals[4] = lastOffset;
int edits = alignForwardRCJNI(query,ref,qstart,rstart,maxEdits,exact,maxWidth,AminoAcid.baseToNumber,AminoAcid.baseToComplementExtended,returnVals);
lastQueryLoc = returnVals[0];
lastRefLoc = returnVals[1];
lastRow = returnVals[2];
lastEdits = returnVals[3];
lastOffset = returnVals[4];
return edits;
}
/**
* @param query
* @param ref
* @param qstart
* @param rstart
* @return Edit distance
*/
@Override
public int alignReverse(final byte[] query, final byte[] ref, final int qstart, final int rstart, final int maxEdits, final boolean exact){
int[] returnVals = KillSwitch.allocInt1D(5);
returnVals[0] = lastQueryLoc;
returnVals[1] = lastRefLoc;
returnVals[2] = lastRow;
returnVals[3] = lastEdits;
returnVals[4] = lastOffset;
int edits = alignReverseJNI(query,ref,qstart,rstart,maxEdits,exact,maxWidth,AminoAcid.baseToNumber,returnVals);
lastQueryLoc = returnVals[0];
lastRefLoc = returnVals[1];
lastRow = returnVals[2];
lastEdits = returnVals[3];
lastOffset = returnVals[4];
return edits;
}
/**
* @param query
* @param ref
* @param qstart
* @param rstart
* @return Edit distance
*/
@Override
public int alignReverseRC(final byte[] query, final byte[] ref, final int qstart, final int rstart, final int maxEdits, final boolean exact){
int[] returnVals = KillSwitch.allocInt1D(5);
returnVals[0] = lastQueryLoc;
returnVals[1] = lastRefLoc;
returnVals[2] = lastRow;
returnVals[3] = lastEdits;
returnVals[4] = lastOffset;
int edits = alignReverseRCJNI(query,ref,qstart,rstart,maxEdits,exact,maxWidth,AminoAcid.baseToNumber,AminoAcid.baseToComplementExtended,returnVals);
lastQueryLoc = returnVals[0];
lastRefLoc = returnVals[1];
lastRow = returnVals[2];
lastEdits = returnVals[3];
lastOffset = returnVals[4];
return edits;
}
}
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