code: public void parse(InputStream inputStream) throws IOException {
  
  		currentMatrix = null;
  		currentRows = "";
  		currentCols = "";
  		max = Short.MIN_VALUE;
  		min = Short.MAX_VALUE;
  		inMatrix = false;
  
  		BufferedReader buf = new BufferedReader (new InputStreamReader (inputStream));
  		String line = null;
  		line = buf.readLine();
  
  		while (  line != null ) {
  
  			if ( line.startsWith("//")) {
  				finalizeMatrix();
  				inMatrix = false;
  
  			} else if ( line.startsWith("H ")){
  				// a new matric!
  				newMatrix(line);
  			} else if ( line.startsWith("D ")) {
  				currentMatrix.setDescription(line.substring(2));
  			} else if ( line.startsWith("M ")) {
  				initMatrix(line);
  				inMatrix = true;
  			} else if ( line.startsWith("  ")){
  				if ( inMatrix)
  					processScores(line);
  			}
  
  			line = buf.readLine();
  		}
  
  	}
docs: parse an inputStream that points to an AAINDEX database file
  
  @param inputStream
  @throws IOException