Blatt 4 Aufgabe 4 C++

Schreiben Sie eine Funktion void makeSTARAlignment(const std::vector<Alignment>& alignments) welche aus einer Liste von paarweisen Alignments das multiple Sequenzalignment mit dem STAR-Algorithmus berechnet.

Die Funktion soll hierzu das multiple Sequenzalignment auf der Konsole ausgeben.

Verwenden Sie C++11

Scaffold Head: #include <algorithm> #include <string> #include <vector> #include <iostream> #include <cmath> #include <fstream> #include <cassert> struct Alignment{ std::string s1aligned; std::string s2aligned; const std::string& operator[](int i) const{ if(i == 0){ return s1aligned; }else{ return s2aligned; } } };
Scaffold Foot: int main(int argc, char** argv){ if(argc < 2){ std::cout << "error missing input argument" << std::endl; return 0; } std::ifstream input(argv[1]); if(input){ int numalignments = 0; while(input >> numalignments){ std::string s1, s2; std::vector<Alignment> alignments; for(int i = 0; i < numalignments; i++){ input >> s1 >> s2; alignments.emplace_back(Alignment{s1,s2}); } makeSTARAlignment(alignments); std::cout << "---------------------------" << std::endl; } }else{ std::cout << "error could not open input file" << std::endl; } return 0; }

Start time:: Do 17 Okt 2019 12:00:00
End time:: Mi 20 Nov 2019 11:00:00

General test timeout:: 10.0 seconds

Tests

Command line arguments	`input.txt`
Comment prefix	`#`
Given input	4 T-AGCTAGCA TGA-CTAGCT -TAG-CTAGCA ATCGACGAGC- TAGCTAGC-A --GC-AGCGA TAGCT-AG-C--A- CA-CACAGTCACAC 4 CTCC-T GTGAGT -CTCCT TCTAC- CT-CCT ATAGCT CTCC-T GTCCAG 4 GTTTATACATATAGAATCAAGTGTACATTAGGGATCAAAAGGTATCG-TTTTTAGAGTTATAG-TTG---TAATTAAG-TTTTA-AACCGAGTGAAA-TAACT-CTGCCGACACA AACCA-AGATCTAGAGTC---T-TA-AT-ATTGTTCATCGGGTTTTGCTTTTTGCAATTTTAGCCGGCCCCAACTATGAATCAATAAGC-AGCAAAATTAAGTGCAACAAAAA-A -GTT-TATACATA-TAGA-ATCAAGTGTACATTAGGGATCA--AAAGGTATCGTTTTTAGAGTTATA-GTTGTAATTAAG-TT-TTAAACCGAGT-GAAATAACT-CTGCCGA---CACA ACTTGCATAAAAACT-GACA-CAGTTCTA-ATT-GT-ACCACTGAAG-T-T-GTTTGCA---TTACACGTAGTAA--AAGATTATTTATTGGAATACAAATA-CTCCTGAAAATTGGAGA -GTTTATACATATAGAA-TCAAGTGTACATTAGGGATCAAAAGGTATCGTTTTTAGAGTTATAGTT-GTA-A-TTAAGTTTTAAAC-CGAG-TGAAAT-A-ACTCTGCCGACACA TGTGTCTTC-TA-ACAAGGAAACACTACTTT-GGCTT-ATAAGATG-CGGTTGCGGT-TTA-AGTTCTTATACTCAA-TCATACACATGAGATCAAGTCATATTC-GACTCCAAA -G--TTTATACATA-TAGAATCAAGTGTACATTAGGGATCA-AAAGGTATCGTTTTTAG-AGTTATAGTTGTAATTAAGTTTTAAACCGA--GTGAAATA-ACTCTG-CCGACACA AGAACTTAAAC-TACTAC--TCGA-TGTT-ATAAGCC-TAAGTAATATTTCCTTCTTAGAAGACACAAA-GCCA--AAGACTCATATGGACTTTGGC-TACACCATGAAAGCTTTG
Expected output	-T-AG-CT-AG-C--A- -TGA--CT-AG-C--T- AT-CGACG-AG-C---- ----G-C--AG-CG-A- -C-A--CACAGTCACAC --------------------------- -CT-CC-T -GT-GAGT TCT-AC-- -ATAGC-T -GT-CCAG --------------------------- -G--TT-TATACATA-TAGA-A-TCAAGTGTACATTAGGGATCA--AAAGGTATCG-TTTTTAG-AGTTATA-G-TT-G---TA-A-TTAAG-TT-TTA-AAC-CGA--G-T-GAAA-T-A-ACT-CTG-CCGA---CACA -A--AC-CA-AGATC-TAGA-G-TC---T-TA-AT-ATTGTTCA--TCGGGTTTTGCTTTTTGC-AATTTTA-GCCG-GCCCCA-A-CTATGAAT-CAATAAG-C-A--G-C-AAAATT-A-AGTGCAA-CAAA---AA-A AC--TTGCATAAAAACT-GACA--CAGTTCTA-ATT-GT-ACCACTGAAG-T-T-G-TTTGCA----TTACACG-TA-G---TA-A---AAGATTATTT-ATT-GGA--A-TACAAA-T-A--CTCCTG-AAAATTGGAGA TG--TG-TCTTC-TA--ACA-AGGAAACACTACTTT-GGCTT-A--TAAGATG-CG-GTTGCGG-T-TTA-A-G-TTCT---TATACTCAA--TC-ATA-CACATGA--GAT-CAAG-TCATATT-C-G-ACTC---CAAA AGAACT-TAAAC-TACTAC----TCGA-TGTT-ATAAGCC-TAAG-TAATATTTCC-TTCTTAGAAGACACA-A-A--G---CC-A---AAG-AC-TCA-TAT-GGACTT-T-GGC--T-ACACC-ATGAAAGC---TTTG ---------------------------

Blatt 4 Aufgabe 4 C++ Assignment

Tests