Aqil 13518002

.vscode/settings.json

@@ -0,0 +1,44 @@
+{
+    "files.associations": {
+        "ostream": "cpp",
+        "cctype": "cpp",
+        "cmath": "cpp",
+        "concepts": "cpp",
+        "cstddef": "cpp",
+        "cstdint": "cpp",
+        "cstdio": "cpp",
+        "cstdlib": "cpp",
+        "cstring": "cpp",
+        "cwchar": "cpp",
+        "exception": "cpp",
+        "fstream": "cpp",
+        "initializer_list": "cpp",
+        "ios": "cpp",
+        "iosfwd": "cpp",
+        "iostream": "cpp",
+        "istream": "cpp",
+        "limits": "cpp",
+        "map": "cpp",
+        "memory": "cpp",
+        "new": "cpp",
+        "stdexcept": "cpp",
+        "streambuf": "cpp",
+        "string": "cpp",
+        "system_error": "cpp",
+        "tuple": "cpp",
+        "type_traits": "cpp",
+        "typeinfo": "cpp",
+        "utility": "cpp",
+        "xfacet": "cpp",
+        "xiosbase": "cpp",
+        "xlocale": "cpp",
+        "xlocinfo": "cpp",
+        "xlocnum": "cpp",
+        "xmemory": "cpp",
+        "xstddef": "cpp",
+        "xstring": "cpp",
+        "xtr1common": "cpp",
+        "xtree": "cpp",
+        "xutility": "cpp"
+    }
+}

NormalScore.txt

@@ -0,0 +1,5 @@
+# A C G T
+T -1 -1 -1 1
+G -1 -1 1
+C -1 1
+A 1

PAM250.txt

@@ -0,0 +1,21 @@
+# A R N D C Q E G H I L K M F P S T W Y V
+V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -5 -2 4
+Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10
+W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17
+T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -2 0 1 3
+S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 3
+P 1 0 -1 -1 -3 0 -1 -1 0 -2 -3 -1 -2 -5 6
+F -4 -4 -4 -6 -4 -5 -5 -5 -2 1 2 -5 0 9
+M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6
+K -1 3 1 0 -5 1 0 -2 0 -2 -3 5
+L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6
+I -1 -2 -2 -2 -2 -2 -2 -3 -2 5
+H -1 2 2 1 -3 3 1 -2 6
+G 1 -3 0 1 -3 -1 0 5
+E 0 -1 1 3 -5 2 4
+Q 0 1 1 2 -5 4
+C -2 -4 -4 -5 4
+D 0 -1 2 4
+N 0 0 2
+R 2 6
+A 2

Wunsch.cpp

@@ -0,0 +1,218 @@
+// CPP program to implement sequence alignment 
+// problem. 
+// #include <bits/stdc++.h> 
+#include <iostream>
+#include <fstream>
+#include <string>
+#include <map>
+using namespace std; 
+
+// int match = 1;
+// int gap = -1;
+std::map<char,map<char,int>> scoring;
+char chars[20];
+
+
+
+
+
+void loadscorematrix(string name){
+    ifstream inp(name);
+    string line;
+    if (inp.is_open()){
+        getline(inp,line);
+        // cout << line;
+        // cout << line.find(' ') << endl;
+        line.erase(0,line.find(' ')+1);
+        // cout << "Hey";
+        int i = 0;
+        while (line.size() > 0){
+            char c = line[0];
+            chars[i] = c;
+            // cout << c << endl;
+            if (line.size() > 2){
+                // cout << line << endl;
+                line.erase(0,line.find(' ')+1);
+                }
+            else{
+                // cout << line.find(' ') << endl;
+                line.erase(0,line.size()+1);
+            }
+            i++;
+        }
+        i = 0;
+        int j;
+        while (getline(inp,line)){
+            line.erase(0,2);
+            j = 0;
+            while(line.size() > 2){
+                // cout << chars[20-i-1] << " " << chars[j] << endl;
+                int score = stoi(line.substr(0,line.find(' ')+1));
+                scoring[chars[20-i-1]][chars[j]] = score;
+                scoring[chars[j]][chars[20-i-1]] = score;
+                // cout << score << endl;
+                j++;
+                line.erase(0,line.find(' ')+1);
+            }
+            // cout << chars[20-i-1] << "HERE" << endl;
+            scoring[chars[20-i-1]][chars[j]] = stoi(line);
+            // cout << stoi(line) << endl;
+            i++;
+        }
+    }else{
+        cout << "File not found" << endl;
+    }
+}
+
+void writeToFile(string str, string name){
+    string res = "result/" + name + ".txt";
+
+
+}
+
+
+
+void needleman(string seq1, string seq2,string name, string name2, int gap){
+    int x,y;
+    x = seq1.size();
+    y = seq2.size();
+    // printf("halo");
+    // cout << x << " " << y ;
+    // int **matrix = new int[x+1][y+1];
+    // int matrix[x+1][y+1];
+    cout << x << " " << y;
+    int **matrix = new int*[x+1];
+    for (int i = 0; i <= x; i++){
+        matrix[i] = new int[y+1];
+        // cout << i << endl;
+    }
+    for (int i=0; i<=x;i++){
+        for (int j = 0; j<=y;j++){
+            matrix[i][j] = 0;
+            // cout << "Tes";
+        }
+    }
+
+    for (int i=0; i <= x; i++){
+        matrix[i][0] = i * gap;
+    }
+    for (int i=0; i <= y; i++){
+        matrix[0][i] = i * gap;
+    }
+
+    for (int i=1; i<= x; i++){
+        for (int j =1 ; j <= y; j++){
+            // if (seq1[i-1] == seq2[j-1]){
+            //     matrix[i][j] = scoring[seq1[i-1]][seq2[j-1]] + matrix[i-1][j-1];
+            // }
+            // else{
+                // cout << "Tes" << endl;
+                int top, left, diag, little;
+                top = matrix[i-1][j] + gap;
+                left = matrix[i][j-1] + gap;
+                diag = matrix[i-1][j-1] + scoring[seq1[i-1]][seq2[j-1]];
+                if (top < left){
+                    if (left < diag){
+                        little = diag;
+                    }
+                    else{
+                        little = left;
+                    }
+                }else{
+                    if (top < diag){
+                        little = diag;
+                    }
+                    else{
+                        little = top;
+                    }
+                }
+                matrix[i][j] = little;
+            // }
+        }
+    }
+
+    string xend = "",yend = "";
+    int i = x;
+    int j = y;
+
+    while ( i != 0 || j != 0){
+        if (i == 0 && j != 0){
+            xend = "_" + xend;
+            yend = seq2[j-1] + yend;
+            j--;
+        }else if (j == 0 && i != 0){
+            yend = "_" + yend;
+            xend = seq1[i-1] + xend;
+            i--;
+        }
+        else if (j != 0 && i != 0){
+            if (matrix[i-1][j] + gap == matrix[i][j]){
+                xend  = seq1[i-1] + xend;
+                yend = "_" + yend;
+                i--;
+            }
+            else if (matrix[i][j-1] + gap == matrix[i][j]){
+                xend = "_" + xend;
+                yend = seq2[j-1] + yend;
+                j--;
+            }   
+            else{
+                xend = seq1[i-1] + xend;
+                yend = seq2[j-1] + yend;
+                i--;
+                j--;
+            }
+        }
+    }
+    cout << "Best Score : " << matrix[x][y] << endl;
+    cout << xend << endl;
+    cout << yend << endl;
+    // for (int i =0; i <= x; i++){
+    //     for (int j = 0 ; j <= y ; j ++){
+    //         cout << matrix[i][j] << " ";
+    //     }
+    //     cout << endl;
+    // }
+
+}
+
+void withNamaFile(string nama1, string nama2, int gap){
+    string str1="",str2="";
+    ifstream inp(nama1);
+    string line;
+    if (inp.is_open()){
+        getline(inp,line);
+        cout << "First sequence : " << line << endl;
+        while (getline(inp,line)){
+            str1 = str1+line;
+        }
+    }
+    else{
+        cout << "File 1 not found" << endl;
+    }
+    ifstream inp2(nama2);
+    if (inp2.is_open()){
+        getline(inp2,line);
+        cout << "Second sequence : " << line << endl;
+        while(getline(inp2,line)){
+            // cout << line;
+            str2 = str2 + line;
+        }
+    }
+    // cout << str1 << endl;
+    // cout << str2 << endl;
+    return needleman(str1,str2,nama1,nama2,gap);
+}
+
+
+
+int main(int argc, char* argv[]){
+    if (argc < 2)
+        cout << "Maaf kurang argumen, berikan file yang ingin dialign, lalu scoring matrix diakhir, lalu nilai jika terjadi gap" << endl;
+    else{
+        loadscorematrix(argv[argc-2]);
+        int gap = stoi(argv[argc-1]);
+        // needleman(argv[1],argv[2],-1);
+        withNamaFile(argv[1],argv[2],-1);
+    }
+}

data/nucleotide/MT019529.1.fasta

@@ -426,4 +426,4 @@ GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT
 TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC
 GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT
 TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAA
+AAAAAAAAA

data/nucleotide/MT044258.1.fasta

@@ -425,4 +425,4 @@ ATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTA
 CATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCTTTAATCAGTGTGTAACATTAGGGA
 GGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTACGATCGAGTGTACAGTGAACAATGC
 TAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAATTTTAGTAGTGCTATCCCCATGTGA
-TTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAA
+TTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAA

data/protein/AGP04929.1.fasta

@@ -18,4 +18,4 @@ ILARLDTVEQEAQIDRLINGRLTSLNAFVAQQLVRTEAAARSAQLAQDKVNECVKSQSKRNGFCGTGTHI
 VSFAINAPNGLYFFHVGYQPTSHVNATAAYGLCNTENPQKCIAPIDGYFVLNQTTSTVADSDQQWYYTGS
 SFFHPEPITEANSKYVSMDVKFENLTNRLPPPLLSNSTDLDFKEELEEFFKNVSSQGPNFQEISKINTTL
 LNLNTELMVLSEVVKQLNESYIDLKELGNYTFYQKWPWYIWLGFIAGLVALALCVFFILCCTGCGTSCLG
-KLKCNRCCDSYDEYEVEKIHIH
+KLKCNRCCDSYDEYEVEKIHIH

data/protein/AYN64561.1.fasta

@@ -18,4 +18,4 @@ FGAISSSLQEILSRLDNLEAQVQIDRLINGRLTALNAYVSQQLSDITLIKAGASRAIEKVNECVKSQSPR
 INFCGNGNHILSLVQNAPYGLLFIHFSYKPTSFKTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSS
 YYYPEPISDKNVVFMNSCSVNFTKAPFIYLNNSIPNLSDFEAEFSLWFKNHTSIAPNLTFNSHINATFLD
 LYYEMNVIQESIKSLNSSFINLKEIGTYEMYVKWPWYIWLLIVILFIIFLMILFFICCCTGCGSACFSKC
-HNCCDEYGGHNDFVIKASHDD
+HNCCDEYGGHNDFVIKASHDD