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#include "TestChromosomeNTdata.h"
TestChromosomeNTdata::TestChromosomeNTdata(const char* testInputChrFileN, const char* testOutputChrFileN)
{
cout << "Start TestChromosomeNTdata" << endl;
bool bFasta = true;
unsigned int ntPerLine = 96; // TODO manually test
generateTestInput(testInputChrFileN);
cout << "generateTestInput" << endl;
CchromosomeNTdata* chr = new CchromosomeNTdata(testInputChrFileN, bFasta);
cout << "Got Chr" << endl;
outputFasta(testOutputChrFileN, ntPerLine, chr->caChromosome);
cout << "end" << endl;
delete chr;
}
TestChromosomeNTdata::~TestChromosomeNTdata(void)
{
}
int TestChromosomeNTdata::outputFasta(const char* filename, unsigned int ntPerLine, const char* ntStr)
{
int lineCounter = 0;
ofstream ofile(filename);
int length = (int)strlen(ntStr);
for(int ntCount = strlen(ntStr); ntCount > 0; ntCount = ntCount - ntPerLine) {
for(int i = 0; i < ntPerLine; i++) {
int index = lineCounter * ntPerLine + i;
char c = ntStr[index];
if( c != EOF && c != '\0' && index != length) {
ofile << c;
} else {
ofile << "\n";
break;
}
}
ofile << endl;
lineCounter ++;
}
ofile.close();
return(0);
}
int TestChromosomeNTdata::generateTestInput(const char* filename)
{
// defaultNtPerLine = 48;
int lineNo = 500000;
const char* line = "ACGTNNAnaCGTNNCnACGTNNGnAcGTNNTnACGTNNAnACgTNNCnACGtNNGnaCGTNNTnAcGTNNAnACgTNNCnACgTNNGnACGtNNTn";
ofstream ofile(filename);
ofile << ">Test Ref" << endl;
for(int i = 0; i < lineNo; i++) {
ofile << line << endl;
}
ofile.close();
return(0);
}
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