+++ /dev/null
-/*
- * formatphylip.cpp
- * Mothur
- *
- * Created by westcott on 1/13/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "formatphylip.h"
-#include "progress.hpp"
-
-/***********************************************************************/
-FormatPhylipMatrix::FormatPhylipMatrix(string df) : filename(df) {
- m->openInputFile(filename, fileHandle);
-}
-/***********************************************************************/
-//not using nameMap
-int FormatPhylipMatrix::read(NameAssignment* nameMap){
- try {
-
- float distance;
- int square, nseqs;
- string name;
- ofstream out;
-
- 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); }
-
-
- list = new ListVector(nseqs);
- list->set(0, name);
-
- char d;
- while((d=fileHandle.get()) != EOF){
-
- if(isalnum(d)){ //you are square
- square = 1;
- fileHandle.close(); //reset file
-
- //open and get through numSeqs, code below formats rest of file
- m->openInputFile(filename, fileHandle);
- fileHandle >> nseqs; m->gobble(fileHandle);
-
- distFile = filename + ".rowFormatted";
- m->openOutputFile(distFile, out);
- break;
- }
- if(d == '\n'){
- square = 0;
- break;
- }
- }
-
- Progress* reading;
- reading = new Progress("Formatting matrix: ", nseqs * nseqs);
-
- //lower triangle, so must go to column then formatted row file
- if(square == 0){
- int index = 0;
-
- ofstream outTemp;
- string tempFile = filename + ".temp";
- m->openOutputFile(tempFile, outTemp);
-
- //convert to square column matrix
- for(int i=1;i<nseqs;i++){
-
- fileHandle >> name;
-
- list->set(i, name);
-
- for(int j=0;j<i;j++){
-
- if (m->control_pressed) { outTemp.close(); m->mothurRemove(tempFile); fileHandle.close(); delete reading; return 0; }
-
- fileHandle >> distance;
-
- if (distance == -1) { distance = 1000000; }
-
- if(distance < cutoff){
- outTemp << i << '\t' << j << '\t' << distance << endl;
- outTemp << j << '\t' << i << '\t' << distance << endl;
- }
- index++;
- reading->update(index);
- }
- }
- outTemp.close();
-
- //format from square column to rowFormatted
- //sort file by first column so the distances for each row are together
- string outfile = m->getRootName(tempFile) + "sorted.dist.temp";
-
- //use the unix sort
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- string command = "sort -n " + tempFile + " -o " + outfile;
- system(command.c_str());
- #else //sort using windows sort
- string command = "sort " + tempFile + " /O " + outfile;
- system(command.c_str());
- #endif
-
- if (m->control_pressed) { m->mothurRemove(tempFile); 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(tempFile); m->mothurRemove(distFile); 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
- rowMap[second] = dist;
-
- index++;
- reading->update(index);
- }else{
- 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();
-
- m->mothurRemove(tempFile);
- m->mothurRemove(outfile);
-
- if (m->control_pressed) { m->mothurRemove(distFile); delete reading; return 0; }
-
- }
- else{ //square matrix convert directly to formatted row file
- int index = nseqs;
- map<int, float> rowMap;
- map<int, float>::iterator itRow;
- rowPos.resize(nseqs, -1);
-
- for(int i=0;i<nseqs;i++){
- fileHandle >> name;
-
- list->set(i, name);
-
- for(int j=0;j<nseqs;j++){
- if (m->control_pressed) { fileHandle.close(); out.close(); m->mothurRemove(distFile); delete reading; return 0; }
-
- fileHandle >> distance;
-
- if (distance == -1) { distance = 1000000; }
-
- if((distance < cutoff) && (j != i)){
- rowMap[j] = distance;
- }
- index++;
- reading->update(index);
- }
-
- m->gobble(fileHandle);
-
- //save position in file of each new row
- rowPos[i] = out.tellp();
-
- //output row to file
- out << i << '\t' << rowMap.size() << '\t';
- for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {
- out << itRow->first << '\t' << itRow->second << '\t';
- }
- out << endl;
-
- //clear map for new row's info
- rowMap.clear();
- }
- }
- reading->finish();
- delete reading;
- fileHandle.close();
- out.close();
-
- if (m->control_pressed) { m->mothurRemove(distFile); return 0; }
-
- list->setLabel("0");
-
- return 1;
-
-
- }
- catch(exception& e) {
- m->errorOut(e, "FormatPhylipMatrix", "read");
- exit(1);
- }
-}
-/***********************************************************************/
-FormatPhylipMatrix::~FormatPhylipMatrix(){}
-/***********************************************************************/
-
-
projects / mothur.git / blobdiff