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/*
* readphylipvector.cpp
* mothur
*
* Created by westcott on 1/11/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "readphylipvector.h"
/***********************************************************************/
ReadPhylipVector::ReadPhylipVector(string d) {
try {
m = MothurOut::getInstance();
distFile = d;
}
catch(exception& e) {
m->errorOut(e, "ReadPhylipVector", "ReadPhylipVector");
exit(1);
}
}
/***********************************************************************/
vector<string> ReadPhylipVector::read(vector< vector<double> >& matrix) {
try {
vector<string> names;
ifstream in;
m->openInputFile(distFile, in);
//check whether matrix is square
char d;
int square = 1;
int numSeqs;
string name;
string numTest;
in >> numTest >> name;
if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ". I suspect you entered a column formatted file as a phylip file, quitting."); m->mothurOutEndLine(); exit(1); }
else { convert(numTest, numSeqs); }
while((d=in.get()) != EOF){
//is d a number meaning its square
if(isalnum(d)){
square = 1;
break;
}
//is d a line return meaning its lower triangle
if(d == '\n'){
square = 2;
break;
}
}
in.close();
//reopen and read now that you know whether you are square
ifstream f;
m->openInputFile(distFile, f);
int rank;
f >> rank;
names.resize(rank);
matrix.resize(rank);
if(square == 1){
for(int i=0;i<rank;i++)
matrix[i].resize(rank);
for(int i=0;i<rank;i++) {
f >> names[i];
for(int j=0;j<rank;j++) {
if (m->control_pressed) { return names; }
f >> matrix[i][j];
if (matrix[i][j] == -0.0000)
matrix[i][j] = 0.0000;
}
}
}
else if(square == 2){
for(int i=0;i<rank;i++){
matrix[i].resize(rank);
}
matrix[0][0] = 0.0000;
f >> names[0];
for(int i=1;i<rank;i++){
f >> names[i];
matrix[i][i]=0.0000;
for(int j=0;j<i;j++){
if (m->control_pressed) { return names; }
f >> matrix[i][j];
if (matrix[i][j] == -0.0000)
matrix[i][j] = 0.0000;
matrix[j][i]=matrix[i][j];
}
}
}
f.close();
return names;
}
catch(exception& e) {
m->errorOut(e, "ReadPhylipVector", "read");
exit(1);
}
}
/***********************************************************************/
vector<string> ReadPhylipVector::read(vector<seqDist>& matrix) {
try {
vector<string> names;
ifstream in;
m->openInputFile(distFile, in);
//check whether matrix is square
char d;
int square = 1;
int numSeqs;
string name;
in >> numSeqs >> name;
while((d=in.get()) != EOF){
//is d a number meaning its square
if(isalnum(d)){
square = 1;
break;
}
//is d a line return meaning its lower triangle
if(d == '\n'){
square = 2;
break;
}
}
in.close();
//reopen and read now that you know whether you are square
ifstream f;
m->openInputFile(distFile, f);
int rank;
float temp;
f >> rank;
names.resize(rank);
if(square == 1){
for(int i=0;i<rank;i++) {
f >> names[i];
for(int j=0;j<rank;j++) {
if (m->control_pressed) { return names; }
f >> temp;
if (j < i) { //only save lt
seqDist dist(i, j, temp);
matrix.push_back(dist);
}
}
}
}
else if(square == 2){
f >> names[0];
for(int i=1;i<rank;i++){
f >> names[i];
for(int j=0;j<i;j++){
if (m->control_pressed) { return names; }
f >> temp;
seqDist dist(i, j, temp);
matrix.push_back(dist);
}
}
}
f.close();
return names;
}
catch(exception& e) {
m->errorOut(e, "ReadPhylipVector", "read");
exit(1);
}
}
/***********************************************************************/
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