--- /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 = openInputFile(distFile, fileHandle);
+
+}
+
+/***********************************************************************/
+
+void 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(nameMap->count(firstName)==0){
+ cerr << "AError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
+ }
+ if(nameMap->count(secondName)==0){
+ cerr << "AError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
+ }
+
+ if (distance == -1) { distance = 1000000; }
+
+ if(distance < cutoff && nameMap->get(firstName) != nameMap->get(secondName)){
+ if(nameMap->get(firstName) > nameMap->get(secondName)){
+ PCell value(nameMap->get(firstName), nameMap->get(secondName), distance);
+
+ if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
+ refRow = nameMap->get(firstName);
+ refCol = nameMap->get(secondName);
+ D->addCell(value);
+ }
+ else if(refRow == nameMap->get(firstName) && refCol == nameMap->get(secondName)){
+ lt = 0;
+ }
+ else{
+ D->addCell(value);
+ }
+ }
+ else if(nameMap->get(firstName) < nameMap->get(secondName)){
+ PCell value(nameMap->get(secondName), nameMap->get(firstName), distance);
+
+ if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
+ refRow = nameMap->get(firstName);
+ refCol = nameMap->get(secondName);
+ D->addCell(value);
+ }
+ else if(refRow == nameMap->get(secondName) && refCol == nameMap->get(firstName)){
+ lt = 0;
+ }
+ else{
+ D->addCell(value);
+ }
+ }
+ reading->update(nameMap->get(firstName) * nseqs);
+ }
+ gobble(fileHandle);
+ }
+
+ if(lt == 0){ // oops, it was square
+ fileHandle.close(); //let's start over
+ D->clear(); //let's start over
+
+ openInputFile(distFile, fileHandle); //let's start over
+
+ while(fileHandle){
+ fileHandle >> firstName >> secondName >> distance;
+
+ if(nameMap->count(firstName)==0){
+ cerr << "BError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
+ }
+ if(nameMap->count(secondName)==0){
+ cerr << "BError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
+ }
+
+ if (distance == -1) { distance = 1000000; }
+
+ if(distance < cutoff && nameMap->get(firstName) > nameMap->get(secondName)){
+ PCell value(nameMap->get(firstName), nameMap->get(secondName), distance);
+ D->addCell(value);
+ reading->update(nameMap->get(firstName) * nseqs);
+ }
+
+ gobble(fileHandle);
+ }
+ }
+ // else if(lt == 0){
+ // while(fileHandle){
+ // fileHandle >> firstName >> secondName >> distance;
+ //
+ // if(nameMap->count(firstName)==0){
+ // cerr << "CError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
+ // }
+ // if(nameMap->count(secondName)==0){
+ // cerr << "CError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
+ // }
+ // if (distance == -1) { distance = 1000000; }
+
+ // if(distance < cutoff && (*nameMap)[firstName].second < (*nameMap)[secondName].second){
+ //// cout << (*nameMap)[secondName] << ' ' << (*nameMap)[firstName] << ' ' << distance << endl;
+ // D->addCell(Cell((*nameMap)[secondName].second, (*nameMap)[firstName].second, distance));
+ // reading->update((*nameMap)[secondName].second * nseqs);
+ // }
+ //
+ // gobble(fileHandle);
+ // }
+ // }
+ reading->finish();
+ fileHandle.close();
+
+ list->setLabel("0");
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadColumnMatrix class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReadColumnMatrix class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+/***********************************************************************/
+
+ReadColumnMatrix::~ReadColumnMatrix(){
+ delete D;
+ delete list;
+}
+
+
projects / mothur.git / blobdiff