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//
// optimatrix.cpp
// Mothur
//
// Created by Sarah Westcott on 4/20/16.
// Copyright (c) 2016 Schloss Lab. All rights reserved.
//
#include "optimatrix.h"
#include "counttable.h"
/***********************************************************************/
OptiMatrix::OptiMatrix(vector< set<long long> > close, vector<string> name, vector<string> single, double c) : OptiData(c) {
closeness = close;
nameMap = name;
singletons = single;
}
/***********************************************************************/
OptiMatrix::OptiMatrix(string d, string nc, string f, string df, double c, bool s) : distFile(d), distFormat(df), format(f), sim(s), OptiData(c) {
if (format == "name") { namefile = nc; countfile = ""; }
else if (format == "count") { countfile = nc; namefile = ""; }
else { countfile = ""; namefile = ""; }
if (distFormat == "phylip") { readPhylip(); }
else if (distFormat == "column") { readColumn(); }
}
/***********************************************************************/
int OptiMatrix::readPhylip(){
try {
nameMap.clear();
float distance;
long long nseqs;
bool square = false;
string name;
map<long long, long long> singletonIndexSwap;
ifstream fileHandle;
string numTest;
Utils util; util.openInputFile(distFile, fileHandle);
fileHandle >> numTest >> name;
nameMap.push_back(name);
singletonIndexSwap[0] = 0;
if (!util.isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting.\n"); exit(1); }
else { convert(numTest, nseqs); }
//square test
char d;
while((d=fileHandle.get()) != EOF){
if(isalnum(d)){ square = true; fileHandle.putback(d); for(int i=0;i<nseqs;i++){ fileHandle >> distance; } break; }
if(d == '\n'){ square = false; break; }
}
vector<bool> singleton; singleton.resize(nseqs, true);
///////////////////// Read to eliminate singletons ///////////////////////
if(square){
for(long long i=1;i<nseqs;i++){
if (m->getControl_pressed()) { fileHandle.close(); return 0; }
fileHandle >> name; nameMap.push_back(name); singletonIndexSwap[i] = i;
for(long long j=0;j<i;j++){
fileHandle >> distance;
if (util.isEqual(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){
singleton[i] = false;
singleton[j] = false;
}
}
}
}else{
for(long long i=1;i<nseqs;i++){
if (m->getControl_pressed()) { fileHandle.close(); return 0; }
fileHandle >> name; nameMap.push_back(name); singletonIndexSwap[i] = i;
for(long long j=0;j<nseqs;j++){
fileHandle >> distance;
if (util.isEqual(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 && j < i){
singleton[i] = false;
singleton[j] = false;
}
}
}
}
fileHandle.close();
//////////////////////////////////////////////////////////////////////////
long long nonSingletonCount = 0;
for (long long i = 0; i < singleton.size(); i++) {
if (!singleton[i]) { //if you are not a singleton
singletonIndexSwap[i] = nonSingletonCount;
nonSingletonCount++;
}else { singletons.push_back(nameMap[i]); }
}
singleton.clear();
closeness.resize(nonSingletonCount);
map<string, string> names;
if (namefile != "") {
util.readNames(namefile, names);
for (long long i = 0; i < singletons.size(); i++) {
singletons[i] = names[singletons[i]];
}
}
ifstream in; util.openInputFile(distFile, in);
in >> nseqs >> name;
if (namefile != "") { name = names[name]; } //redundant names
nameMap[singletonIndexSwap[0]] = name;
string line = "";
if(square){
int index = 0;
for(long long i=1;i<nseqs;i++){
if (m->getControl_pressed()) { in.close(); return 0; }
in >> name; gobble(in);
if (namefile != "") { name = names[name]; } //redundant names
nameMap[singletonIndexSwap[i]] = name;
for(long long j=0;j<i;j++){
in >> distance; gobble(in);
if (util.isEqual(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){
long long newB = singletonIndexSwap[j];
long long newA = singletonIndexSwap[i];
closeness[newA].insert(newB);
closeness[newB].insert(newA);
}
index++;
}
}
}else{
long long index = nseqs;
for(long long i=0;i<nseqs;i++){ in >> distance; } gobble(in);
for(long long i=1;i<nseqs;i++){
if (m->getControl_pressed()) { in.close(); return 0; }
in >> name; gobble(in);
if (namefile != "") { name = names[name]; } //redundant names
nameMap[singletonIndexSwap[i]] = name;
for(long long j=0;j<nseqs;j++){
in >> distance; gobble(in);
if (util.isEqual(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 && j < i){
long long newB = singletonIndexSwap[j];
long long newA = singletonIndexSwap[i];
closeness[newA].insert(newB);
closeness[newB].insert(newA);
}
index++;
}
}
}
in.close();
return 0;
}
catch(exception& e) {
m->errorOut(e, "OptiMatrix", "readPhylip");
exit(1);
}
}
/***********************************************************************/
int OptiMatrix::readColumn(){
try {
Utils util;
map<string, long long> nameAssignment;
if (namefile != "") { util.readNames(namefile, nameAssignment); }
else {
CountTable ct; ct.readTable(countfile, false, true);
map<string, int> temp = ct.getNameMap();
for (map<string, int>::iterator it = temp.begin(); it!= temp.end(); it++) { nameAssignment[it->first] = it->second; }
}
long long count = 0;
for (map<string, long long>::iterator it = nameAssignment.begin(); it!= nameAssignment.end(); it++) {
it->second = count; count++;
nameMap.push_back(it->first);
}
string firstName, secondName;
float distance;
///////////////////// Read to eliminate singletons ///////////////////////
ifstream fileHandle;
util.openInputFile(distFile, fileHandle);
vector<bool> singleton; singleton.resize(nameAssignment.size(), true);
map<long long, long long> singletonIndexSwap;
while(fileHandle){ //let's assume it's a triangular matrix...
fileHandle >> firstName; gobble(fileHandle);
fileHandle >> secondName; gobble(fileHandle);
fileHandle >> distance; gobble(fileHandle); // get the row and column names and distance
if (m->getDebug()) { cout << firstName << '\t' << secondName << '\t' << distance << endl; }
if (m->getControl_pressed()) { fileHandle.close(); return 0; }
if (util.isEqual(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){
map<string,long long>::iterator itA = nameAssignment.find(firstName);
map<string,long long>::iterator itB = nameAssignment.find(secondName);
if(itA == nameAssignment.end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the name or count file, please correct\n"); exit(1); }
if(itB == nameAssignment.end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the name or count file, please correct\n"); exit(1); }
long long indexA = (itA->second);
long long indexB = (itB->second);
singleton[indexA] = false;
singleton[indexB] = false;
singletonIndexSwap[indexA] = indexA;
singletonIndexSwap[indexB] = indexB;
}
}
fileHandle.close();
//////////////////////////////////////////////////////////////////////////
long long nonSingletonCount = 0;
for (long long i = 0; i < singleton.size(); i++) {
if (!singleton[i]) { //if you are a singleton
singletonIndexSwap[i] = nonSingletonCount;
nonSingletonCount++;
}else { singletons.push_back(nameMap[i]); }
}
singleton.clear();
closeness.resize(nonSingletonCount);
map<string, string> names;
if (namefile != "") {
util.readNames(namefile, names);
for (long long i = 0; i < singletons.size(); i++) {
singletons[i] = names[singletons[i]];
}
}
ifstream in; util.openInputFile(distFile, in);
while(in){ //let's assume it's a triangular matrix...
in >> firstName; gobble(in);
in >> secondName; gobble(in);
in >> distance; gobble(in); // get the row and column names and distance
if (m->getDebug()) { cout << firstName << '\t' << secondName << '\t' << distance << endl; }
if (m->getControl_pressed()) { in.close(); return 0; }
if (util.isEqual(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){
map<string,long long>::iterator itA = nameAssignment.find(firstName);
map<string,long long>::iterator itB = nameAssignment.find(secondName);
if(itA == nameAssignment.end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the name or count file, please correct\n"); exit(1); }
if(itB == nameAssignment.end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the name or count file, please correct\n"); exit(1); }
long long indexA = (itA->second);
long long indexB = (itB->second);
long long newB = singletonIndexSwap[indexB];
long long newA = singletonIndexSwap[indexA];
closeness[newA].insert(newB);
closeness[newB].insert(newA);
if (namefile != "") {
firstName = names[firstName]; //redundant names
secondName = names[secondName]; //redundant names
}
nameMap[newA] = firstName;
nameMap[newB] = secondName;
}
}
in.close();
nameAssignment.clear();
return 1;
}
catch(exception& e) {
m->errorOut(e, "OptiMatrix", "readColumn");
exit(1);
}
}
/***********************************************************************/
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