set java_exe="C:\j2sdk1.4.2_08\bin\java"
set directory="D:\papers\GR2007_Supplemental\pph1"
%java_exe% -classpath %directory%\pph1.jar;%directory%\jars\colt.jar;%directory%\jars\sun_parser;%directory%\jars\xml4j_1_1_9.jar;%directory%\jars\patbinfree153.jar  pph1.PphAlign %1 %2 %3