+++ /dev/null
-/*
- * readphylip.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 4/21/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "readphylip.h"
-#include "progress.hpp"
-
-/***********************************************************************/
-
-ReadPhylipMatrix::ReadPhylipMatrix(string distFile){
-
- successOpen = m->openInputFile(distFile, fileHandle);
- sim=false;
-
-}
-/***********************************************************************/
-
-ReadPhylipMatrix::ReadPhylipMatrix(string distFile, bool s){
-
- successOpen = m->openInputFile(distFile, fileHandle);
- sim=s;
-}
-
-
-/***********************************************************************/
-
-int ReadPhylipMatrix::read(NameAssignment* nameMap){
- try {
-
- float distance;
- int square, nseqs;
- string name;
- vector<string> matrixNames;
-
- 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); }
-
- matrixNames.push_back(name);
-
- 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)){
- square = 1;
- fileHandle.putback(d);
- for(int i=0;i<nseqs;i++){
- fileHandle >> distance;
- }
- break;
- }
- if(d == '\n'){
- square = 0;
- break;
- }
- }
-
- Progress* reading;
-
- if(square == 0){
-
- reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
-
- int index = 0;
-
- for(int i=1;i<nseqs;i++){
- if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
-
- fileHandle >> name;
- matrixNames.push_back(name);
-
-
- //there's A LOT of repeated code throughout this method...
- if(nameMap == NULL){
- list->set(i, name);
-
- for(int j=0;j<i;j++){
-
- if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
-
- fileHandle >> distance;
-
-
- 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){
- PCell value(i, j, distance);
- D->addCell(value);
- }
- index++;
- reading->update(index);
- }
-
- }
- 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++){
- fileHandle >> distance;
-
- if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
-
- 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){
- PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
- D->addCell(value);
- }
- index++;
- reading->update(index);
- }
- }
- }
- }
- else{
-
- reading = new Progress("Reading matrix: ", nseqs * nseqs);
-
- int index = nseqs;
-
- for(int i=1;i<nseqs;i++){
- fileHandle >> name;
- matrixNames.push_back(name);
-
-
-
- if(nameMap == NULL){
- list->set(i, name);
- for(int j=0;j<nseqs;j++){
- fileHandle >> distance;
-
- if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
-
- 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 && j < i){
- PCell value(i, j, distance);
- D->addCell(value);
- }
- index++;
- reading->update(index);
- }
-
- }
- 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++){
- fileHandle >> distance;
-
- if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
-
- 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 && j < i){
- PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
- D->addCell(value);
- }
- index++;
- reading->update(index);
- }
- }
- }
- }
-
- if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
-
- reading->finish();
- delete reading;
-
- list->setLabel("0");
- fileHandle.close();
-
- /* if(nameMap != NULL){
- for(int i=0;i<matrixNames.size();i++){
- nameMap->erase(matrixNames[i]);
- }
- if(nameMap->size() > 0){
- //should probably tell them what is missing if we missed something
- m->mothurOut("missed something\t" + toString(nameMap->size())); m->mothurOutEndLine();
- }
- } */
-
- return 1;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ReadPhylipMatrix", "read");
- exit(1);
- }
- }
-
-/***********************************************************************/
-
-ReadPhylipMatrix::~ReadPhylipMatrix(){
- // delete D;
- // delete list;
-}
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