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add: check aligned

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This commit is contained in:
kuoi 2023-03-20 04:09:09 +08:00
parent f01844d2a8
commit c080629b63
1 changed files with 50 additions and 2 deletions
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52
main.cpp
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@ -39,7 +39,9 @@ void writeTnt(class Sample sam);
void writeNex(class Sample sam); void writeNex(class Sample sam);
bool isNum(string strnum); bool isNum(string strnum);
string to_lower(string stri); string to_lower(string stri);
string add_space (char x, string str_old); string add_space(char x, string str_old);
string checktype(string str);
int countfre(string str, char c);
Sample readPhy(){ Sample readPhy(){
//read file //read file
@ -298,6 +300,8 @@ void writePhy(class Sample sam){
void writeNex(class Sample sam){ void writeNex(class Sample sam){
ofstream outputFile(otn); ofstream outputFile(otn);
string datatype;
datatype = checktype(sam.chars[0]);
if (outputFile.is_open()) { if (outputFile.is_open()) {
outputFile << "#NEXUS" << endl; outputFile << "#NEXUS" << endl;
// outputFile << "Begin TAXA;" << endl << "\tDimensions ntax=" << sam.ntax << ";" << endl << "\tTaxLabels"; // outputFile << "Begin TAXA;" << endl << "\tDimensions ntax=" << sam.ntax << ";" << endl << "\tTaxLabels";
@ -305,7 +309,7 @@ void writeNex(class Sample sam){
// outputFile << " " << sam.taxas[i1]; // outputFile << " " << sam.taxas[i1];
// } // }
// outputFile << ";" << endl << "End;" << endl << endl; // outputFile << ";" << endl << "End;" << endl << endl;
outputFile << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax << ";" << endl << "\tFormat datatype=dna missing=? gap=-;" << endl << "\tMatrix" << endl; outputFile << "Begin data;" << endl << "\tDimensions nchar=" << sam.nchar << " ntax=" << sam.ntax << ";" << endl << "\tFormat datatype=" << datatype << " missing=? gap=-;" << endl << "\tMatrix" << endl;
for(int i2=0;i2<sam.ntax;i2++){ for(int i2=0;i2<sam.ntax;i2++){
outputFile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl; outputFile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
} }
@ -316,6 +320,38 @@ void writeNex(class Sample sam){
outputFile.close(); outputFile.close();
} }
string checktype(string str){
float a, c, t, g, zero, one, two, dna, standard;
char ca='a', cc='c', ct='t', cg='g', czero='0', cone='1', ctwo='2';
string datatype;
a = countfre(str, ca);
c = countfre(str, cc);
t = countfre(str, ct);
g = countfre(str, cg);
zero = countfre(str, czero);
one = countfre(str, cone);
two = countfre(str, ctwo);
dna = a+c+t+g;
standard = zero+one+two;
if((dna/str.length())>0.7){
datatype = "dna";
} else if ((standard/str.length())>0.7){
datatype = "standard";
} else {
datatype = "protein";
}
return datatype;
}
int countfre(string str, char c){
int num;
str = to_lower(str);
num = count(str.begin(),str.end(),c);
return num;
}
void writeTnt(class Sample sam){ void writeTnt(class Sample sam){
ofstream outputFile(otn); ofstream outputFile(otn);
if (outputFile.is_open()) { if (outputFile.is_open()) {
@ -398,6 +434,18 @@ void write_output (class Sample sam){
if (outype==4) writeTnt(sam); if (outype==4) writeTnt(sam);
} }
bool checkalign(class Sample sam){
int a=0, b=0;
a = sam.chars[0].length();
bool aligned = true;
for(int i=1;i<(sam.ntax-1)&&aligned;i++){
b = sam.chars[i].length();
aligned = (a==b);
}
return aligned;
}
int main(int argc, char **argv){ int main(int argc, char **argv){
procargs (argc, argv); procargs (argc, argv);
if(intype!=0&&outype!=0){ if(intype!=0&&outype!=0){