Here is a list of all file members with links to the files they belong to:

- a -

• aligned_coords_t : scoreAlignment2.cpp

- c -

• checkCollinear() : scoreAlignment2.cpp
• comp_filter : scoreAlignment2.cpp
• compareAlignments() : scoreAlignment2.cpp
• computeIndelAccuracy() : scoreAlignment2.cpp
• computeLCBaccuracy() : scoreAlignment2.cpp
• constructCoordList() : scoreAlignment2.cpp
• constructIndelList() : scoreAlignment2.cpp
• CREATE_EXCEPTION() : Alignment.h
• CreateSeed() : twister.h, twister.c

- d -

• debugCheckingLevel() : Alignment.h, Alignment.cpp
• debugChecks() : Alignment.h, Alignment.cpp
• DONOR_ID : Alignment.cpp

- e -

• exponentialSample() : Mutator.cpp

- f -

• filterGaps() : Alignment.cpp
• findFirstCorrectlyAlignedPair() : scoreAlignment2.cpp
• findLcb() : scoreAlignment2.cpp

- g -

• GappedIntervalSequence : Alignment.h
• genrand_int31() : twister.c
• genrand_int32() : twister.c
• genrand_real1() : twister.c
• genrand_real2() : twister.c
• genrand_real3() : twister.c
• genrand_res53() : twister.c

- h -

• homogenizeParity() : scoreAlignment2.cpp

- i -

• indel_map_t : scoreAlignment2.cpp
• indel_t : scoreAlignment2.cpp
• init_by_array() : twister.c
• init_genrand() : twister.c

- l -

• LOWER_MASK : twister.c

- m -

• M : twister.c
• main() : sgEvolver.cpp, scoreAlignment2.cpp, mfaToMultiFiles.cpp, maf2xmfa.cpp
• markAllCorrectlyAlignedLcbs() : scoreAlignment2.cpp
• MATRIX_A : twister.c
• mt : twister.c
• mti : twister.c

- n -

• N : twister.c
• NELEMS : sgEvolver.cpp
• NO_INDEL : scoreAlignment2.cpp

- p -

• poissonSample() : Mutator.cpp
• print_usage() : sgEvolver.cpp
• printIndel() : scoreAlignment2.cpp

- r -

• recursiveInvert() : Alignment.cpp
• rndu() : twister.h, twister.c

- s -

• sanityCheck() : scoreAlignment2.cpp
• SetSeed() : twister.h, twister.c

- t -

• TARGET_ID : Alignment.cpp

- u -

• uniformSample() : Mutator.cpp
• UPPER_MASK : twister.c

- w -

• warn_count : scoreAlignment2.cpp
• WARN_MAX : scoreAlignment2.cpp
• warn_missing : scoreAlignment2.cpp

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