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/*
* formatphylip.cpp
* Mothur
*
* Created by westcott on 1/13/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "formatphylip.h"
#include "progress.hpp"
/***********************************************************************/
FormatPhylipMatrix::FormatPhylipMatrix(string df) : filename(df) {
m->openInputFile(filename, fileHandle);
}
/***********************************************************************/
//not using nameMap
int FormatPhylipMatrix::read(NameAssignment* nameMap){
try {
float distance;
int square, nseqs;
string name;
ofstream out;
string numTest;
fileHandle >> numTest >> name;
if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
else { convert(numTest, nseqs); }
if(nameMap == NULL){
list = new ListVector(nseqs);
list->set(0, name);
}
else{
list = new ListVector(nameMap->getListVector());
if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
}
char d;
while((d=fileHandle.get()) != EOF){
if(isalnum(d)){ //you are square
square = 1;
fileHandle.close(); //reset file
//open and get through numSeqs, code below formats rest of file
m->openInputFile(filename, fileHandle);
fileHandle >> nseqs; m->gobble(fileHandle);
distFile = filename + ".rowFormatted";
m->openOutputFile(distFile, out);
break;
}
if(d == '\n'){
square = 0;
break;
}
}
Progress* reading;
reading = new Progress("Formatting matrix: ", nseqs * nseqs);
//lower triangle, so must go to column then formatted row file
if(square == 0){
int index = 0;
ofstream outTemp;
string tempFile = filename + ".temp";
m->openOutputFile(tempFile, outTemp);
//convert to square column matrix
for(int i=1;i<nseqs;i++){
fileHandle >> name;
if(nameMap == NULL){ list->set(i, name); }
else { if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
}
for(int j=0;j<i;j++){
if (m->control_pressed) { outTemp.close(); m->mothurRemove(tempFile); fileHandle.close(); delete reading; return 0; }
fileHandle >> distance;
if (distance == -1) { distance = 1000000; }
if(distance < cutoff){
outTemp << i << '\t' << j << '\t' << distance << endl;
outTemp << j << '\t' << i << '\t' << distance << endl;
}
index++;
reading->update(index);
}
}
outTemp.close();
//format from square column to rowFormatted
//sort file by first column so the distances for each row are together
string outfile = m->getRootName(tempFile) + "sorted.dist.temp";
//use the unix sort
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
string command = "sort -n " + tempFile + " -o " + outfile;
system(command.c_str());
#else //sort using windows sort
string command = "sort " + tempFile + " /O " + outfile;
system(command.c_str());
#endif
if (m->control_pressed) { m->mothurRemove(tempFile); m->mothurRemove(outfile); delete reading; return 0; }
//output to new file distance for each row and save positions in file where new row begins
ifstream in;
m->openInputFile(outfile, in);
distFile = outfile + ".rowFormatted";
m->openOutputFile(distFile, out);
rowPos.resize(nseqs, -1);
int currentRow;
int first, second;
float dist;
map<int, float> rowMap;
map<int, float>::iterator itRow;
//get first currentRow
in >> first;
currentRow = first;
string firstString = toString(first);
for(int k = 0; k < firstString.length(); k++) { in.putback(firstString[k]); }
while(!in.eof()) {
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); m->mothurRemove(distFile); m->mothurRemove(outfile); delete reading; return 0; }
in >> first >> second >> dist; m->gobble(in);
if (first != currentRow) {
//save position in file of each new row
rowPos[currentRow] = out.tellp();
out << currentRow << '\t' << rowMap.size() << '\t';
for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
out << itRow->first << '\t' << itRow->second << '\t';
}
out << endl;
currentRow = first;
rowMap.clear();
//save row you just read
rowMap[second] = dist;
index++;
reading->update(index);
}else{
rowMap[second] = dist;
}
}
//print last Row
//save position in file of each new row
rowPos[currentRow] = out.tellp();
out << currentRow << '\t' << rowMap.size() << '\t';
for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
out << itRow->first << '\t' << itRow->second << '\t';
}
out << endl;
in.close();
out.close();
m->mothurRemove(tempFile);
m->mothurRemove(outfile);
if (m->control_pressed) { m->mothurRemove(distFile); delete reading; return 0; }
}
else{ //square matrix convert directly to formatted row file
int index = nseqs;
map<int, float> rowMap;
map<int, float>::iterator itRow;
rowPos.resize(nseqs, -1);
for(int i=0;i<nseqs;i++){
fileHandle >> name;
if(nameMap == NULL){ list->set(i, name); }
else { if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
}
for(int j=0;j<nseqs;j++){
if (m->control_pressed) { fileHandle.close(); out.close(); m->mothurRemove(distFile); delete reading; return 0; }
fileHandle >> distance;
if (distance == -1) { distance = 1000000; }
if((distance < cutoff) && (j != i)){
rowMap[j] = distance;
}
index++;
reading->update(index);
}
m->gobble(fileHandle);
//save position in file of each new row
rowPos[i] = out.tellp();
//output row to file
out << i << '\t' << rowMap.size() << '\t';
for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
out << itRow->first << '\t' << itRow->second << '\t';
}
out << endl;
//clear map for new row's info
rowMap.clear();
}
}
reading->finish();
delete reading;
fileHandle.close();
out.close();
if (m->control_pressed) { m->mothurRemove(distFile); return 0; }
list->setLabel("0");
return 1;
}
catch(exception& e) {
m->errorOut(e, "FormatPhylipMatrix", "read");
exit(1);
}
}
/***********************************************************************/
//not using nameMap
int FormatPhylipMatrix::read(CountTable* nameMap){
try {
float distance;
int square, nseqs;
string name;
ofstream out;
string numTest;
fileHandle >> numTest >> name;
if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
else { convert(numTest, nseqs); }
if(nameMap == NULL){
list = new ListVector(nseqs);
list->set(0, name);
}
else{
list = new ListVector(nameMap->getListVector());
nameMap->get(name);
}
char d;
while((d=fileHandle.get()) != EOF){
if(isalnum(d)){ //you are square
square = 1;
fileHandle.close(); //reset file
//open and get through numSeqs, code below formats rest of file
m->openInputFile(filename, fileHandle);
fileHandle >> nseqs; m->gobble(fileHandle);
distFile = filename + ".rowFormatted";
m->openOutputFile(distFile, out);
break;
}
if(d == '\n'){
square = 0;
break;
}
}
Progress* reading;
reading = new Progress("Formatting matrix: ", nseqs * nseqs);
//lower triangle, so must go to column then formatted row file
if(square == 0){
int index = 0;
ofstream outTemp;
string tempFile = filename + ".temp";
m->openOutputFile(tempFile, outTemp);
//convert to square column matrix
for(int i=1;i<nseqs;i++){
fileHandle >> name;
if(nameMap == NULL){ list->set(i, name); }
else { nameMap->get(name); }
for(int j=0;j<i;j++){
if (m->control_pressed) { outTemp.close(); m->mothurRemove(tempFile); fileHandle.close(); delete reading; return 0; }
fileHandle >> distance;
if (distance == -1) { distance = 1000000; }
if(distance < cutoff){
outTemp << i << '\t' << j << '\t' << distance << endl;
outTemp << j << '\t' << i << '\t' << distance << endl;
}
index++;
reading->update(index);
}
}
outTemp.close();
//format from square column to rowFormatted
//sort file by first column so the distances for each row are together
string outfile = m->getRootName(tempFile) + "sorted.dist.temp";
//use the unix sort
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
string command = "sort -n " + tempFile + " -o " + outfile;
system(command.c_str());
#else //sort using windows sort
string command = "sort " + tempFile + " /O " + outfile;
system(command.c_str());
#endif
if (m->control_pressed) { m->mothurRemove(tempFile); m->mothurRemove(outfile); delete reading; return 0; }
//output to new file distance for each row and save positions in file where new row begins
ifstream in;
m->openInputFile(outfile, in);
distFile = outfile + ".rowFormatted";
m->openOutputFile(distFile, out);
rowPos.resize(nseqs, -1);
int currentRow;
int first, second;
float dist;
map<int, float> rowMap;
map<int, float>::iterator itRow;
//get first currentRow
in >> first;
currentRow = first;
string firstString = toString(first);
for(int k = 0; k < firstString.length(); k++) { in.putback(firstString[k]); }
while(!in.eof()) {
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); m->mothurRemove(distFile); m->mothurRemove(outfile); delete reading; return 0; }
in >> first >> second >> dist; m->gobble(in);
if (first != currentRow) {
//save position in file of each new row
rowPos[currentRow] = out.tellp();
out << currentRow << '\t' << rowMap.size() << '\t';
for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
out << itRow->first << '\t' << itRow->second << '\t';
}
out << endl;
currentRow = first;
rowMap.clear();
//save row you just read
rowMap[second] = dist;
index++;
reading->update(index);
}else{
rowMap[second] = dist;
}
}
//print last Row
//save position in file of each new row
rowPos[currentRow] = out.tellp();
out << currentRow << '\t' << rowMap.size() << '\t';
for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
out << itRow->first << '\t' << itRow->second << '\t';
}
out << endl;
in.close();
out.close();
m->mothurRemove(tempFile);
m->mothurRemove(outfile);
if (m->control_pressed) { m->mothurRemove(distFile); delete reading; return 0; }
}
else{ //square matrix convert directly to formatted row file
int index = nseqs;
map<int, float> rowMap;
map<int, float>::iterator itRow;
rowPos.resize(nseqs, -1);
for(int i=0;i<nseqs;i++){
fileHandle >> name;
if(nameMap == NULL){ list->set(i, name); }
else { nameMap->get(name); }
for(int j=0;j<nseqs;j++){
if (m->control_pressed) { fileHandle.close(); out.close(); m->mothurRemove(distFile); delete reading; return 0; }
fileHandle >> distance;
if (distance == -1) { distance = 1000000; }
if((distance < cutoff) && (j != i)){
rowMap[j] = distance;
}
index++;
reading->update(index);
}
m->gobble(fileHandle);
//save position in file of each new row
rowPos[i] = out.tellp();
//output row to file
out << i << '\t' << rowMap.size() << '\t';
for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
out << itRow->first << '\t' << itRow->second << '\t';
}
out << endl;
//clear map for new row's info
rowMap.clear();
}
}
reading->finish();
delete reading;
fileHandle.close();
out.close();
if (m->control_pressed) { m->mothurRemove(distFile); return 0; }
list->setLabel("0");
return 1;
}
catch(exception& e) {
m->errorOut(e, "FormatPhylipMatrix", "read");
exit(1);
}
}
/***********************************************************************/
FormatPhylipMatrix::~FormatPhylipMatrix(){}
/***********************************************************************/
|
