+++ /dev/null
-/*
- * 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();
-
- 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 >> secondName >> 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 != itB){
- if(itA->second > itB->second){
- PCell value(itA->second, itB->second, distance);
-
- if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
- refRow = itA->second;
- refCol = itB->second;
- D->addCell(value);
- }
- else if(refRow == itA->second && refCol == itB->second){
- lt = 0;
- }
- else{
- D->addCell(value);
- }
- }
- else if(itA->second < itB->second){
- PCell value(itB->second, itA->second, distance);
-
- if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
- refRow = itA->second;
- refCol = itB->second;
- D->addCell(value);
- }
- else if(refRow == itB->second && refCol == itA->second){
- lt = 0;
- }
- else{
- D->addCell(value);
- }
- }
- reading->update(itA->second * nseqs);
- }
- m->gobble(fileHandle);
- }
-
- if(lt == 0){ // oops, it was square
-
- fileHandle.close(); //let's start over
- D->clear(); //let's start over
-
- m->openInputFile(distFile, fileHandle); //let's start over
-
- while(fileHandle){
- fileHandle >> firstName >> secondName >> 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){
- PCell value(itA->second, itB->second, distance);
- D->addCell(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);
- }
-}
-
-/***********************************************************************/
-
-ReadColumnMatrix::~ReadColumnMatrix(){
- //delete D;
- //delete list;
-}
-
-
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