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