One of the standard libraries for ECG software analysis is WFDB and PhysioNet: http://www.physionet.org/physiotools/wag/wag.htm
Two American national standards, ANSI / AAMI EC38: 1998 (ambulatory electrocardiographs) and ANSI / AAMI EC57: 1998 (test results and heart rate results and ST segment measurement algorithms) require the use of several WFDB applications to evaluate specific devices and algorithms.
Wrappers will be written, so you can use Java to access the code: http://www.physionet.org/physiotools/wfdb-swig.shtml
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