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ChangeLog
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ChangeLog
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2017-08-23-v1.4.0 Lars Hahn <lhahn@biolgie.uni-goettingen.de>
* Main.cpp: Adjusted new rasbhari implementation function call.
'--help' and '--version' now parsed before rasbhari parameter parsing.
* rasopt.hpp: A new header for the new rasbhari options namespace.
* rasopt.cpp: A new namespace for all relevant rasbhari options to be set
global in its own namespace.
* rasbimp.hpp: A new header for the new rasbhari implementation namespace.
* rasbimp.cpp: A new namespace for an easier implementation of the rasbhari
functionality. Only Options have to be set and the correct function has
to be choosen.
* rasbhari.hpp: A new header for the new rasbhari class.
* rasbhari.cpp: A new class that comprises all necessary functions and
variables neccessary for the rasbhari approach. Stored is the
patternset, its coefficient (OC/Var) and its sensitivity (if calculated)
* rasbcomp.hpp: A new header for the new rasbhari computation namespace.
* rasbcomp.cpp: A new namespace that holds the entire algorithms for the
OverlaptComplexity and Variance. In its own namespace the overlap aspect
can be used in different approaches using only this namespace.
* speedsens.hpp: A new header for the new sensitivity calculation of SpEED.
* speedsens.cpp: Here the sensitivty calculation of SpEED is wrapped into
it's own namespace to show, that this part is done by the work of
Ilie&Ilie and extracted from their spaced seed optimisation program
SpEED.
* sensmem.hpp: A new header for the new sensitivity memory observation header.
* sensmem.hpp: A namespace that holds special unix functions to observe the
memory currently used. It was realised to stop the program from entering
the swap-memory and extremly slowing down without the users permission.
At this point, the user can save important data, if he wants to hardly
restart the operating system.
* patternset.hpp: A new header for the new approach of the patternset class.
* patternset.cpp: The patternset class has been completely redefined to a
new class, where the actual pattern are outsourced into a new pattern
class.
* pattern.hpp: A new header for the new pattern class.
* pattern.cpp: A new class that holds all neccessary functions that can/
have/should be executed on a pattern instance.
2016-10-19-v1.3.0 Lars Hahn <lhahn@biolgie.uni-goettingen.de>
* Main.cpp: Chaning maximum and minimum DC value print output.
Adding a 'version' and 'help' parameter and updating the help
output.
* Patternset.cpp
(CreateLengths): DC boundary calculation with intervals updated correctly.
(SetSeed): New function to set the seed for the random generator.
* Patternset.h:
(SetSeed): New function to set the seed for the random generator.
* Variance.cpp
(Init): New seed parameter added.
* Variance.h
(Init): New seed parameter added.
* Sensitivity.h: Adding new prototypes and instance variable memvalue.
Also new librarys.
(Init): New seed parameter added.
* Sensitivity.cpp
(CalculateSensitivity): Remove return value, using instance variable,
adding try-catch block for sensitivity calculation and
a special output for a time consuming calculation.
(AvailableMemory): A new function, which checks the amount of free
available memory (no swap) in total.
(CheckMemory): Overhead function which organizes the memory check and
and user interaction.
(MULTIPLE_SENSITIVITY2): Adding the CheckMemory function before each
'new' statement for the current memory usage.
(Init): New seed parameter added.
* Sensitivity.cpp
(CalculateSensitivity): Remove return value.
(Init): New seed parameter added.
2016-08-25-v1.2.1 Lars Hahn <lhahn@biolgie.uni-goettingen.de>
* Patternset.h:
Adding library <random>
* Patternset.cpp
(SetImprove): Changing pattern_improve create paramter
(VerifyPatternCondition): Resetting options for variable 'pattern_error'.
Solving read problem for file in correct format.
* Main.cpp:
Adding library <cstdint>
2016-05-12-v1.2.0 Lars Hahn <lhahn@biolgie.uni-goettingen.de>
* main.cpp
(sensitivity_obj): now generated on the stack, no heap pointer.
* variance.cpp
(Ctor): removed; initialization seperated;
(variance): Constructors extracted from 'Ctor', class variables setted.
(InitVarMatrix,InitVar): removed, separated to InitVariance,SetVariance.
(SetVariance): New function added.
(UpdateVariance): removed, integrated efficiently in 'improve' function.
(ReInitVariance): removed, integrated in 'ReInit' function.
(ImproveOC): removed, integraded in 'UpdateVariance' function and 'OC' bool.
(Gaus): removed, integrated into patternset.cpp
(SetPatOrder): removed, integrated in set 'variance_set' as sorted tree.
(GetL1,GetL2,GetLHom): removed, not necessary.
(Init): Initializtion removed from constructor, a new function.
* variance.h
(RandPatLength): removed, boolean in 'Init'.
(var_sum): changed to var_mat.
(pattern_order, pattern_order_sort): removed, integrated in set 'variance_set'.
(isInFile,isOutFile): new bool as file flag.
(pattern_set): now generated on the stack, no heap pointer.
(l1,l2,lhom): a new variable 'seq_leng';
* patternset.cpp
(SymbolRandPos,SymbolCalcPos,GetSymbol): removed, integrated in 'GetSymbolPos'.
(IsSetScore): removed.
(ValidatePatternFormat): removed, integrated in 'CheckParams'.
(ChangeBits): renamed in 'ChangeBitsRandom'.
(GetImprove): New function returns bool-vector.
(GetValue): removed and integrated to 'GetPattern';
(GetBidMode): New function for variable 'bitmode'.
(GetLengthMean): removed;
(CreateRandomPattern): renamed in 'CreatePattern'.
(UniqBit): new function.
* patternset.h
(bitmode): a new flag to change between bitmode or not, for pattern with
length more then 64.
* extkey.cpp:
removed; exchanged by set object
* extkey.h:
removed; exchanged by set object
2016-04-13-v1.1.0 Lars Hahn <lhahn@biolgie.uni-goettingen.de>
* main.cpp: variance, sensitivty and patternset structur extracted.
* sensitivity.cpp: a new class, contains functions for pattern sensitvity.
* sensitivity.h: a new class header, for 'sensitivity.cpp', implements 'variance.h'.
* variance.cpp: a new class, contains functions for pattern variance and OC.
* variance.h: a new class header, for 'variance.cpp', implements 'patternset.h'
and 'extkey.h'
* patternset.cpp: a new class, contains functions for pattern creation and
modification.
* patternset.h: a new class header, for 'variance.cpp'.
* extkey.cpp: a new class, elements consists of to entries and functions
implemented for external sorting.
* extkey.cpp: a new class header, for 'extkey.cpp'