public static Alignable align_NPE(Matrix sim,StrucAligParameters params){
		//System.out.println("align_NPE");

		float gapOpen = params.getGapOpen();
		float gapExtension = params.getGapExtension();

		int rows = sim.getRowDimension();
		int cols = sim.getColumnDimension();

		Alignable al = new StrCompAlignment(rows,cols);
		al.setGapExtCol(gapExtension);
		al.setGapExtRow(gapExtension);
		al.setGapOpenCol(gapOpen);
		al.setGapOpenRow(gapOpen);
		//System.out.println("size of aligmat: " + rows+1 + " " + cols+1);
		//AligMatEl[][] aligmat = new AligMatEl[rows+1][cols+1];
		AligMatEl[][] aligmat = al.getAligMat();

		for (int i = 0; i < rows; i++) {
			for (int j = 0; j < cols; j++) {

				int e=0;
				//if ( ( i < rows) &&
				//        ( j < cols)) {
					//TODO: the ALIGFACTOR calc should be hidden in Gotoh!!

				e = (int)Math.round(Gotoh.ALIGFACTOR * sim.get(i,j));
				//}
				//System.out.println(e);
				AligMatEl am = new AligMatEl();
				am.setValue(e);
				//am.setTrack(new IndexPair((short)-99,(short)-99));
				aligmat[i+1][j+1] = am;

			}
		}
		//al.setAligMat(aligmat);

		 new Gotoh(al);

		return al;
	}
public static Alignable align_NPE ( Matrix sim , StrucAligParameters params ) { float gapOpen = params . getGapOpen ( ) ; float gapExtension = params . getGapExtension ( ) ; int rows = sim . getRowDimension ( ) ; int cols = sim . getColumnDimension ( ) ; Alignable al = new StrCompAlignment ( rows , cols ) ; al . setGapExtCol ( gapExtension ) ; al . setGapExtRow ( gapExtension ) ; al . setGapOpenCol ( gapOpen ) ; al . setGapOpenRow ( gapOpen ) ; AligMatEl [ ] [ ] aligmat = al . getAligMat ( ) ; for ( int i = 0 ; i < rows ; i ++ ) { for ( int j = 0 ; j < cols ; j ++ ) { int e = 0 ; e = ( int ) Math . round ( Gotoh . ALIGFACTOR * sim . get ( i , j ) ) ; AligMatEl am = new AligMatEl ( ) ; am . setValue ( e ) ; aligmat [ i + 1 ] [ j + 1 ] = am ; } } new Gotoh ( al ) ; return al ; }
Align without penalizing end-gaps. Return alignment and score

@param sim the similarity matrix
@param params the structure alignment parameters to be used
@return an Alignable