code: private void initMatrix(String line) {
  		String[] spl = line.split(" ");
  
  		// trim off the final , character
  		currentRows = spl[3].substring(0, spl[3].length()-1);
  		currentCols = spl[6];
  		currentRowPos = -1;
  
  		int nrRows = currentRows.length();
  		int nrCols = currentCols.length();
  
  		matrix = new short[nrRows][nrCols];
  
  		rows = new ArrayList<AminoAcidCompound>();
  		cols = new ArrayList<AminoAcidCompound>();
  
  
  		//System.out.println(">" + currentRows+"<");
  		AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
  		for ( int i = 0 ; i < currentRows.length() ; i ++){
  			char c = currentRows.charAt(i);
  			AminoAcidCompound aa = compoundSet.getCompoundForString(String.valueOf(c));
  
  			rows.add(aa);
  		}
  
  		for ( int i = 0 ; i < currentCols.length() ; i ++){
  			char c = currentRows.charAt(i);
  			AminoAcidCompound aa = compoundSet.getCompoundForString(String.valueOf(c));
  
  			cols.add(aa);
  		}
  
  
  
  
  
  		currentMatrix.setScale(scale);
  	}
docs: process a line of type >M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV<