fix: fasta space issue; polish: readfas, readnex
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c32f318f85
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92
main.cpp
92
main.cpp
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@ -3,6 +3,7 @@
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#include <iostream>
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#include <sstream>
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#include <string>
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#include <vector>
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using namespace std;
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@ -77,48 +78,53 @@ Sample readFas(char* itn) {
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int ntax, nchar, lnum;
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ifstream matrixfile;
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matrixfile.open(itn);
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// use vector to read once use serveral times
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vector<string> file_content;
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// check line number and taxa number
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ntax = 0;
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string temln;
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for (lnum = 0; getline(matrixfile, temln); lnum++) {
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file_content.push_back(temln);
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if (temln[0] == '>') {
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ntax++;
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}
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}
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matrixfile.clear();
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matrixfile.seekg(0);
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matrixfile.close();
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// check the nchar
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string str_a, str_b;
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int r = lnum / ntax;
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string str_i;
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int r;
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if (file_content.size() != 0) {
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r = file_content.size() / ntax;
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} else {
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cout << "MiMi:\tInput file contains 0 line" << endl;
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exit(0);
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}
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for (int i = 0; i < r; i++) {
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getline(matrixfile, str_a);
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if (i > 0) {
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str_b = str_b + str_a;
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file_content[i] = del_space(file_content[i]);
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str_i = str_i + file_content[i];
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}
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}
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nchar = str_b.length();
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matrixfile.clear();
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matrixfile.seekg(0);
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nchar = str_i.length();
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// create class
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Sample sam(ntax, nchar);
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// get class
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string str_c;
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for (int a = 1, b = 0; a <= lnum; a++) {
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if (a % r == 1) {
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getline(matrixfile, sam.taxas[b]);
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for (int a = 0, b = 0; a < (int)file_content.size(); a++) {
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if ((a + 1) % r == 1) {
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sam.taxas[b] = file_content[a];
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sam.taxas[b].erase(0, 1);
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sam.taxas[b] = rep_space(sam.taxas[b]);
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}
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if (a % r > 1) {
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getline(matrixfile, str_c);
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sam.chars[b] = sam.chars[b] + str_c;
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if ((a + 1) % r > 1) {
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file_content[a] = del_space(file_content[a]);
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sam.chars[b] = sam.chars[b] + file_content[a];
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}
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if (a % r == 0) {
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getline(matrixfile, str_c);
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sam.chars[b] = sam.chars[b] + str_c;
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if ((a + 1) % r == 0) {
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file_content[a] = del_space(file_content[a]);
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sam.chars[b] = sam.chars[b] + file_content[a];
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b++;
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}
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}
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matrixfile.close();
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return sam;
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}
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@ -164,15 +170,21 @@ Sample readNex(char* itn) {
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// open file
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ifstream matrixfile;
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matrixfile.open(itn);
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// some tem
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// some var
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string snall, stri, str_a, str_b;
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bool found_ntax = false, found_nchar = false, found_equal = false;
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char x = '=';
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// get line number and read line to vector
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int lnum;
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unsigned int eulnum;
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vector<string> file_content;
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while (getline(matrixfile, snall)) {
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file_content.push_back(snall);
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}
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matrixfile.close();
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// getline line by line
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for (lnum = 0; getline(matrixfile, snall); lnum++) {
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str_a = to_lower(snall);
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for (lnum = 0; lnum < (int)file_content.size(); lnum++) {
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str_a = to_lower(file_content[lnum]);
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str_b = add_space(x, str_a);
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istringstream istr(str_b);
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// convert to words
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@ -202,25 +214,16 @@ Sample readNex(char* itn) {
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}
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}
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}
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// go back
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matrixfile.clear();
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matrixfile.seekg(0);
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// create class
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Sample sam(ntax, nchar);
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// some temp, z is line number, l is the string arrary number
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unsigned int z = 0;
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// read line by line, limit line number
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int l = 0;
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// read line by line
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while (getline(matrixfile, snall)) {
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for (unsigned int z = eulnum; z < (eulnum + sam.ntax); z++) {
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// convert to word
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istringstream istr(snall);
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// limit the read line number
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if ((z > (eulnum - 1)) && (z < (eulnum + sam.ntax))) {
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istr >> sam.taxas[l];
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istr >> sam.chars[l];
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l++;
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}
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z++;
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istringstream istr(file_content[z]);
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istr >> sam.taxas[l];
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istr >> sam.chars[l];
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l++;
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}
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return sam;
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}
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@ -293,6 +296,7 @@ void writeNex(class Sample sam, char* otn) {
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matrixfile << "#NEXUS\nBegin data;\n\tDimensions nchar=" << sam.nchar
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<< " ntax=" << sam.ntax << ";\n\tFormat datatype=" << datatype
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<< " missing=? gap=-;\n\tMatrix" << endl;
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for (unsigned int i2 = 0; i2 < sam.ntax; i2++) {
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matrixfile << "\t\t" << sam.taxas[i2] << "\t" << sam.chars[i2] << endl;
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}
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@ -456,18 +460,14 @@ Sample read_input(char* itn, int intype) {
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void write_output(class Sample sam, char* otn, int outype) {
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ofstream matrixfile(otn);
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if (matrixfile.is_open()) {
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for (unsigned int i = 0; i < sam.ntax; i++) {
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sam.chars[i] = del_space(sam.chars[i]);
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sam.taxas[i] = rep_space(sam.taxas[i]);
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}
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if (outype == 1) writeFas(sam, otn);
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if (outype == 2) writeNex(sam, otn);
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if (outype == 3) writePhy(sam, otn);
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if (outype == 4) writeTnt(sam, otn);
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} else {
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cout << "MiMi:\tOutput file can't be open" << endl;
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exit(0);
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}
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if (outype == 1) writeFas(sam, otn);
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if (outype == 2) writeNex(sam, otn);
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if (outype == 3) writePhy(sam, otn);
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if (outype == 4) writeTnt(sam, otn);
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}
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bool checkalign(class Sample sam) {
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