+++ /dev/null
-/*
- * formatcolumn.cpp
- * Mothur
- *
- * Created by westcott on 1/13/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "formatcolumn.h"
-#include "progress.hpp"
-
-/***********************************************************************/
-FormatColumnMatrix::FormatColumnMatrix(string df) : filename(df){
- m->openInputFile(filename, fileHandle);
-}
-/***********************************************************************/
-
-int FormatColumnMatrix::read(NameAssignment* nameMap){
- try {
-
- string firstName, secondName;
- float distance;
- int nseqs = nameMap->size();
-
- list = new ListVector(nameMap->getListVector());
-
- Progress* reading = new Progress("Formatting 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...
-
- ofstream out;
- string tempOutFile = filename + ".temp";
- m->openOutputFile(tempOutFile, out);
-
- while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...
-
- if (m->control_pressed) { out.close(); m->mothurRemove(tempOutFile); fileHandle.close(); delete reading; return 0; }
-
- fileHandle >> firstName >> secondName >> distance; // get the row and column names and distance
-
- 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; }
-
- if((distance < cutoff) && (itA != itB)){
- if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
- refRow = itA->second;
- refCol = itB->second;
-
- //making it square
- out << itA->second << '\t' << itB->second << '\t' << distance << endl;
- out << itB->second << '\t' << itA->second << '\t' << distance << endl;
- }
- else if(refRow == itA->second && refCol == itB->second){ lt = 0; } //you are square
- else if(refRow == itB->second && refCol == itA->second){ lt = 0; } //you are square
- else{ //making it square
- out << itA->second << '\t' << itB->second << '\t' << distance << endl;
- out << itB->second << '\t' << itA->second << '\t' << distance << endl;
- }
-
- reading->update(itA->second * nseqs / 2);
- }
- m->gobble(fileHandle);
- }
- out.close();
- fileHandle.close();
-
- string squareFile;
- if(lt == 0){ // oops, it was square
- squareFile = filename;
- }else{ squareFile = tempOutFile; }
-
- //sort file by first column so the distances for each row are together
- string outfile = m->getRootName(squareFile) + "sorted.dist.temp";
-
- //use the unix sort
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- string command = "sort -n " + squareFile + " -o " + outfile;
- system(command.c_str());
- #else //sort using windows sort
- string command = "sort " + squareFile + " /O " + outfile;
- system(command.c_str());
- #endif
-
- if (m->control_pressed) { m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
-
- //output to new file distance for each row and save positions in file where new row begins
- ifstream in;
- m->openInputFile(outfile, in);
-
- distFile = outfile + ".rowFormatted";
- m->openOutputFile(distFile, out);
-
- rowPos.resize(nseqs, -1);
- int currentRow;
- int first, second;
- float dist;
- map<int, float> rowMap;
- map<int, float>::iterator itRow;
-
- //get first currentRow
- in >> first;
- currentRow = first;
-
- string firstString = toString(first);
- for(int k = 0; k < firstString.length(); k++) { in.putback(firstString[k]); }
-
- while(!in.eof()) {
-
- if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
-
- in >> first >> second >> dist; m->gobble(in);
-
- if (first != currentRow) {
- //save position in file of each new row
- rowPos[currentRow] = out.tellp();
-
- out << currentRow << '\t' << rowMap.size() << '\t';
-
- for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
- out << itRow->first << '\t' << itRow->second << '\t';
- }
- out << endl;
-
- currentRow = first;
- rowMap.clear();
-
- //save row you just read
- if (dist < cutoff) {
- rowMap[second] = dist;
- }
- }else{
- if (dist < cutoff) {
- rowMap[second] = dist;
- }
- }
- }
-
- //print last Row
- //save position in file of each new row
- rowPos[currentRow] = out.tellp();
-
- out << currentRow << '\t' << rowMap.size() << '\t';
-
- for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
- out << itRow->first << '\t' << itRow->second << '\t';
- }
- out << endl;
-
-
- in.close();
- out.close();
-
- if (m->control_pressed) { m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
-
- m->mothurRemove(tempOutFile);
- m->mothurRemove(outfile);
-
- reading->finish();
-
- delete reading;
- list->setLabel("0");
-
- if (m->control_pressed) { m->mothurRemove(distFile); return 0; }
-
- return 1;
-
- }
- catch(exception& e) {
- m->errorOut(e, "FormatColumnMatrix", "read");
- exit(1);
- }
-}
-
-/***********************************************************************/
-FormatColumnMatrix::~FormatColumnMatrix(){}
-/***********************************************************************/
-
-
-
projects / mothur.git / blobdiff