INFO4017_22_23_UYI

Repository for TPE and TP coding

INFO4017_22_23_UYI

project structure

.INFO4017_22_23_UYI
├── DATA                                  # DATA FILE TASKS IMPLEMENTATION
├── FUNCTIONS                             # FUNCTION FILE TASKS IMPLEMENTATION
├── INCLUDES                              # HEADER FILE TASKS IMPLEMENTATION
├── LIBRARIES                             # USEFULL LIBRARIES
├── LOGS                                  # LOGS DIRECTORY
├── LICENCE                               # LICENCE DECLARATION OF CODE BASED IMPLEMENTATION
├── README.md                             # documentation file
├── Makefile                              # EXECUTION SCRIPTS FOR PRODUCTION
├── *.cpp                                 # TASKS GUI ENTRY POINT
├── setup                                 # EXECUTABLE GUI ENTRY POINT
└── setup.cpp                             # MAIN GUI ENTRY POINT

Tasks

• strassen.cpp implementation of matrix mult within DPR paradigm
• lcs.cpp implementation of LCS problem solving with PD paradigm
• setup.cpp implementation of user gui
• globalSequenceAlignment.cpp implementation of sequence global alignment within DP paradim

Program: GSA
    entries: X, Y string
            PD table de programmation dynamique orientée
    outputs: _GSA vector of alignment
begin:
    a := {(len(X),len(Y))}
    _X := {}
    _Y := {}
    while a != empty do
        local_X := {}
        local_Y := {}
        local_a := {}
        for all (i,j) in a do
            if exists only one arrows in (i,j) cell then
                if match or mismatch then 
                    for all xi in _X do 
                        local_X := local_X U X[i] +  xi 
                    endfor
                    for all yi in _Y do 
                        local_Y := local_Y U Y[j] +  yi 
                    endfor
                    local_a := local_a U (i-1,j-1)
                else if vertical gap then
                    for all xi in _X do 
                        local_X := local_X U '_' + xi 
                    endfor
                    for all yi in _Y do 
                        local_Y := local_Y U Y[j] + yi 
                    endfor
                    local_a := local_a U (i,j-1)
                else if horizontal gap then
                    for all xi in _X do 
                        local_X := local_X U X[i] +  xi 
                    endfor
                    for all yi in _Y do 
                        local_Y := local_Y U '_' +  yi 
                    endfor
                    local_a := local_a U (i-1,j)
                else 
                    if i == 0 and j > 0 then
                        for all xi in _X do 
                            local_X := local_X U '_' +  xi 
                        endfor
                        for all yi in _Y do 
                            local_Y := local_Y U Y[j] +  yi 
                        endfor
                    else if j == 0 and i > 0 then
                        for all xi in _X do 
                            local_X := local_X U X[i] +  xi 
                        endfor
                        for all yi in _Y do 
                            local_Y := local_Y U '_' +  yi 
                        endfor
                    sinon 
                        for all xi in _X do 
                            local_X := local_X U xi 
                        endfor
                        for all yi in _Y do 
                            local_Y := local_Y U yi 
                        endfor
                    endif
                endif
            else
                if exists more than one arrows in (i,j) cell then
                    if match or mismatch then 
                        for all xi in _X do 
                            local_X := local_X U X[i] +  xi 
                        endfor
                        for all yi in _Y do 
                            local_Y := local_Y U Y[j] +  yi 
                        endfor  
                        local_a := local_a U (i-1,j-1)
                    endif
                    if vertical gap then
                        for all xi in _X do 
                            local_X := local_X U '_' + xi 
                        endfor
                        for all yi in _Y do 
                            local_Y := local_Y U Y[j] + yi 
                        endfor
                        local_a := local_a U (i,j-1)
                    endif
                    if horizontal gap then
                        for all xi in _X do 
                            local_X := local_X U X[i] +  xi 
                        endfor
                        for all yi in _Y do 
                            local_Y := local_Y U '_' +  yi 
                        endfor
                        local_a := local_a U (i-1,j)
                    endif
                endif
            endif
        endfor
        _X := local_X
        _Y := local_Y
        a := local_a
    endwhile
endprog

n*m	word 1 (n)	word 2 (m)	solution	time ms	number of alignments
4*4	here	here	here	0	3
10*4	here	here	here	0	17
15*4	here	here	here	0	18
15*10	here	here	here	0	54
20*4	here	here	here	0	31
20*10	here	here	here	0	45
20*15	here	here	here	25000	3114
25*4	here	here	here	0	4
25*10	here	here	here	0	39
25*15	here	here	here	1000	59
25*20	here	here	here	26000	1691
30*4	here	here	here	1000	33
30*10	here	here	here	0	14
30*15	here	here	here	1000	479
30*20	here	here	here	0	84
30*25	here	here	here	4000	140
45*50	here	here	here	137000	1520

• pgcb.cpp implementation of the most big white square

fonction PGCB(n)
 pour x = 1 à n
    pour y = 1 à n
        si (x,y) est noir
           pgcb[x,y] = 0
        sinon si x = 1 ou y = 1
            pgcb[x,y] = 1
        sinon
           pgcb[x,y] = 1 + min{pgcb(x-1,y-1),pgcb(x,y-1),pgcb(x-1,y)}

Programme PGCB
    données:    A matrice binaire représentant l'image chromatique
                n la taille de la matrice binaire
    resultats: (_c,_x,_y) 
    variables:  _pgcb un tableau,
                _c,_x,_y des d'entier
Debut
    // cette version de l'algorithme de pgcb retourne à la fois la taille _c des plus grand carré blanc 
    // et deux vecteur _x,_y représentation conjointement les différentes position de pixels
    // en bas à droit de ses grand carré blanc

    // tout d'abord redimensionner _pgcd suivant la taille de l'image prise en paramètre
    redim(_pgcb,n);

    // initialisons la taille maximal du plus grand carré
    _c = -1;

    // contruction
    pour i de 1 à n faire
        pour j de 1 à n faire 
            _pgcb[i][j] = 0
        finpour
    finpour
    // remplissage du tableau de programmation dynamique
    pour i de 1 à n faire
        pour j de 1 à n faire 
            si A[i][j] == 0 alors // où 0 matérialise le blanc dans notre image chromatique
                si i == 0 ou j == 0 alors
                    _pgcb[i][j] = 1
                    si _c < 1 alors
                        vider(_x)
                        vider(_y)
                        _c = 1
                        _x.ajouter(i)
                        _y.ajouter(j)
                    sinon
                        si _c == 1 alors 
                            _x.ajouter(i)
                            _y.ajouter(j)
                        finsi
                    finsi
                sinon
                    _pgcb[i][j] = min(_pgcb[i-1][j-1],min(_pgcb[i][j-1],_pgcb[i-1][j]))
                    si _c < _pgcb[i][j] alors
                        vider(_x)
                        vider(_y)
                        _c = _pgcb[i][j]
                        _x.ajouter(i)
                        _y.ajouter(j)
                    sinon
                        si _c == _pgcb[i][j] alors 
                            _x.ajouter(i)
                            _y.ajouter(j)
                        finsi
                    finsi
                finsi
            finsi
        finpour
    finpour
    // retourner la solution
    retourner (_c,_x,_y)
fin

• karatsuba.cpp implementation of polynom mult within DPR paradigm
• sac_a_dos.cpp implementation of whole backpack problem within PD paradigm
• tree.cpp implementation of tree methods such as pre-fixed, post-fixed and in-fixed, deep route, ...
• graph.cpp implementation of tree methods such as prim, kuuskal, ...
• knn.cpp implementation of k nearest neighbors method, for k 2,3, ...
• sort.cpp implementation of sort method, such as fusion sort, bubble sort, ...
• fibonacci.cpp implementation of fibonacci method
• market_traveling.cpp implementation of market traveling problem
• sequence_alignment.cpp implementation of sequence alignment problem in genetic, ...

Scripts d'installation

clone project

• https link

git clone https://github.com/VictorNico/INFO4017_22_23_UYI.git

• ssh link

git clone [email protected]:VictorNico/INFO4017_22_23_UYI.git

• github command

gh repo clone VictorNico/INFO4017_22_23_UYI

change directory of task

cd INFO4017_22_23_UYI/task

usage

• reset

make clean

• compile

make

• execute

without debugging flag

./setup

with debugging flags

./setup -g 

Notice : -g is use to show some methods progression along the time execution.