changed pruning algorithm as per RMG meeting May 26, 2010
changed pruning algorithm as per RMG meeting May 26, 2010

now, we use the first point that the core inclusion threshold is exceeded to determine which species to add; however, we still integrate til termination tolerance to decide whether we can prune species

connie/RMG-Java,connie/RMG-Java,rwest/RMG-Java,faribas/RMG-Java,KEHANG/RMG-Java,jwallen/RMG-Java,rwest/RMG-Java,KEHANG/RMG-Java,keceli/RMG-Java,connie/RMG-Java,keceli/RMG-Java,keceli/RMG-Java,faribas/RMG-Java,KEHANG/RMG-Java,KEHANG/RMG-Java,jwallen/RMG-Java,enochd/RMG-Java,enochd/RMG-Java,jwallen/RMG-Java,enochd/RMG-Java,rwest/RMG-Java,nyee/RMG-Java,connie/RMG-Java,keceli/RMG-Java,ReactionMechanismGenerator/RMG-Java,KEHANG/RMG-Java,nyee/RMG-Java,jwallen/RMG-Java,nyee/RMG-Java,faribas/RMG-Java,nyee/RMG-Java,faribas/RMG-Java,nyee/RMG-Java,rwest/RMG-Java,enochd/RMG-Java,ReactionMechanismGenerator/RMG-Java,nyee/RMG-Java,rwest/RMG-Java,ReactionMechanismGenerator/RMG-Java,enochd/RMG-Java,KEHANG/RMG-Java,jwallen/RMG-Java,enochd/RMG-Java,jwallen/RMG-Java,connie/RMG-Java,keceli/RMG-Java,keceli/RMG-Java,ReactionMechanismGenerator/RMG-Java,ReactionMechanismGenerator/RMG-Java