Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 12]

Align	Namespace including the functions of the kernel architecture
FindMax	Namespace related to functions used to find the maximum elements in in the score matrix
Fixed	This namespace contains functions to define the core architectures used in the fixed banding alignment kernel
Rectangular	This namespace contains functions to define the core architectures used in the non-banding alignment kernel
ALIGN_TYPE	This namespace contains the functions that is required to be implemented by the user. ALIGN_TYPE itself is a macro, and is supposed to be defined as the kernel name in params.h
Helper
PE
Traceback	The namespace for the customized function related to the traceback
CLUtils
KernelOperator
KernelWrapper
Compat
DebugUtils
Translate
HostUtils
Generate
IO
Sequence
PE
Random
SolutionUtils
Profile
Testbench
Traceback
Utils
Array
Init
Kernel
Matrix
AHRunner
Container
score_info
InitialValues
LoggerData
LoopCounter
LoopLogger
ScorePack	A structure to hold score and index information
ShiftRegister
ShiftRegisterBlock