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/*
* readcolumn.cpp
* Mothur
*
* Created by Sarah Westcott on 4/21/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "readcolumn.h"
#include "progress.hpp"
/***********************************************************************/
ReadColumnMatrix::ReadColumnMatrix(string df) : distFile(df){
successOpen = m->openInputFile(distFile, fileHandle);
sim = false;
}
/***********************************************************************/
ReadColumnMatrix::ReadColumnMatrix(string df, bool s) : distFile(df){
successOpen = m->openInputFile(distFile, fileHandle);
sim = s;
}
/***********************************************************************/
int ReadColumnMatrix::read(NameAssignment* nameMap){
try {
string firstName, secondName;
float distance;
int nseqs = nameMap->size();
DMatrix->resize(nseqs);
list = new ListVector(nameMap->getListVector());
Progress* reading = new Progress("Reading matrix: ", nseqs * nseqs);
int lt = 1;
int refRow = 0; //we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose
int refCol = 0; //shows up later - Cell(refCol,refRow). If it does, then its a square matrix
//need to see if this is a square or a triangular matrix...
while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...
fileHandle >> firstName; m->gobble(fileHandle);
fileHandle >> secondName; m->gobble(fileHandle);
fileHandle >> distance; // get the row and column names and distance
if (m->debug) { cout << firstName << '\t' << secondName << '\t' << distance << endl; }
if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
map<string,int>::iterator itA = nameMap->find(firstName);
map<string,int>::iterator itB = nameMap->find(secondName);
if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1); }
if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1); }
if (distance == -1) { distance = 1000000; }
else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(distance < cutoff && itA != itB){
if(itA->second > itB->second){
PDistCell value(itA->second, distance);
if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
refRow = itA->second;
refCol = itB->second;
DMatrix->addCell(itB->second, value);
}
else if(refRow == itA->second && refCol == itB->second){
lt = 0;
}
else{
DMatrix->addCell(itB->second, value);
}
}
else if(itA->second < itB->second){
PDistCell value(itB->second, distance);
if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
refRow = itA->second;
refCol = itB->second;
DMatrix->addCell(itA->second, value);
}
else if(refRow == itB->second && refCol == itA->second){
lt = 0;
}
else{
DMatrix->addCell(itA->second, value);
}
}
reading->update(itA->second * nseqs);
}
m->gobble(fileHandle);
}
if(lt == 0){ // oops, it was square
fileHandle.close(); //let's start over
DMatrix->clear(); //let's start over
m->openInputFile(distFile, fileHandle); //let's start over
while(fileHandle){
fileHandle >> firstName; m->gobble(fileHandle);
fileHandle >> secondName; m->gobble(fileHandle);
fileHandle >> distance; // get the row and column names and distance
if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
map<string,int>::iterator itA = nameMap->find(firstName);
map<string,int>::iterator itB = nameMap->find(secondName);
if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1); }
if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1); }
if (distance == -1) { distance = 1000000; }
else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(distance < cutoff && itA->second > itB->second){
PDistCell value(itA->second, distance);
DMatrix->addCell(itB->second, value);
reading->update(itA->second * nseqs);
}
m->gobble(fileHandle);
}
}
if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
reading->finish();
fileHandle.close();
list->setLabel("0");
return 1;
}
catch(exception& e) {
m->errorOut(e, "ReadColumnMatrix", "read");
exit(1);
}
}
/***********************************************************************/
int ReadColumnMatrix::read(CountTable* countTable){
try {
string firstName, secondName;
float distance;
int nseqs = countTable->size();
DMatrix->resize(nseqs);
list = new ListVector(countTable->getListVector());
Progress* reading = new Progress("Reading matrix: ", nseqs * nseqs);
int lt = 1;
int refRow = 0; //we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose
int refCol = 0; //shows up later - Cell(refCol,refRow). If it does, then its a square matrix
//need to see if this is a square or a triangular matrix...
while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...
fileHandle >> firstName; m->gobble(fileHandle);
fileHandle >> secondName; m->gobble(fileHandle);
fileHandle >> distance; // get the row and column names and distance
if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
int itA = countTable->get(firstName);
int itB = countTable->get(secondName);
if (m->control_pressed) { exit(1); }
if (distance == -1) { distance = 1000000; }
else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(distance < cutoff && itA != itB){
if(itA > itB){
PDistCell value(itA, distance);
if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
refRow = itA;
refCol = itB;
DMatrix->addCell(itB, value);
}
else if(refRow == itA && refCol == itB){
lt = 0;
}
else{
DMatrix->addCell(itB, value);
}
}
else if(itA < itB){
PDistCell value(itB, distance);
if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
refRow = itA;
refCol = itB;
DMatrix->addCell(itA, value);
}
else if(refRow == itB && refCol == itA){
lt = 0;
}
else{
DMatrix->addCell(itA, value);
}
}
reading->update(itA * nseqs);
}
m->gobble(fileHandle);
}
if(lt == 0){ // oops, it was square
fileHandle.close(); //let's start over
DMatrix->clear(); //let's start over
m->openInputFile(distFile, fileHandle); //let's start over
while(fileHandle){
fileHandle >> firstName; m->gobble(fileHandle);
fileHandle >> secondName; m->gobble(fileHandle);
fileHandle >> distance; // get the row and column names and distance
if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
int itA = countTable->get(firstName);
int itB = countTable->get(secondName);
if (m->control_pressed) { exit(1); }
if (distance == -1) { distance = 1000000; }
else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
if(distance < cutoff && itA > itB){
PDistCell value(itA, distance);
DMatrix->addCell(itB, value);
reading->update(itA * nseqs);
}
m->gobble(fileHandle);
}
}
if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
reading->finish();
fileHandle.close();
list->setLabel("0");
return 1;
}
catch(exception& e) {
m->errorOut(e, "ReadColumnMatrix", "read");
exit(1);
}
}
/***********************************************************************/
ReadColumnMatrix::~ReadColumnMatrix(){}
/***********************************************************************/
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