- a -

• add_branch() : ProbScan.cpp , ProbScan.h

- b -

• basestack() : ProbScan.cpp , ProbScan.h

- e -

• equal_within_tolerance() : thermodynamics.cpp
• errmsg() : RNA.cpp

- f -

• file_exists() : Multilign_object.cpp

- h -

• hairpin() : ProbScan.cpp , ProbScan.h

- i -

• internal_loop() : ProbScan.cpp , ProbScan.h
• isAlphabetRNA() : RNA.cpp

- m -

• main() : Dynalign_class.cpp , DynalignSMP_class.cpp , HybridRNA_class.cpp , OligoWalk_class.cpp , RNA_class.cpp
• multibranch_loop() : ProbScan.h , ProbScan.cpp

- p -

• pow() : design.h
• prev_val() : ProbScan.cpp

- s -

• show_bulge_loops() : ProbScan.cpp , ProbScan.h
• show_hairpins() : ProbScan.h , ProbScan.cpp
• show_internal_loops() : ProbScan.cpp , ProbScan.h
• show_mb_element_array() : ProbScan.h , ProbScan.cpp
• show_mbl() : ProbScan.h , ProbScan.cpp
• show_stacks() : ProbScan.cpp , ProbScan.h