Winston C. Yang
winston@cs.wisc.edu
2003-07-26

The following files are Java translations of the C code written by
Athula Gunawardena.

Beam.java
Heap.java
Matrix.java
RowShapeMatrix.java
ShapeMatrix.java
ShapeMatrixComparator.java

Beam.java is the main class. It takes 1 argument, the input file
containing the intensity matrix. Usage:

	  java Beam input.map

Matrix.java is for input and output of the intensity and difference
matrices. It is called by Beam.java and does error checking, such as
checking that all rows in the intensity matrix in the input file have
the same number of columns. It trims the rows and columns of the
intensity matrix that are 0's; the Beam class works with the resulting
matrix.

Heap.java implements a heap of Objects and needs a Comparator so that
it can compare the objects. The Objects have type ShapeMatrix, and the
Comparator is in the short file ShapeMatrixComparator.java.

RowShapeMatrix.java is another short file; the class is used for
containing data.

Many of the classes have toString methods, for easy printing of
objects.