--- /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) {
+ openInputFile(filename, fileHandle);
+}
+/***********************************************************************/
+//not using nameMap
+void FormatPhylipMatrix::read(NameAssignment* nameMap){
+ try {
+
+ float distance;
+ int square, nseqs;
+ string name;
+ ofstream out;
+
+ fileHandle >> nseqs >> name;
+
+ 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
+ openInputFile(filename, fileHandle);
+ fileHandle >> nseqs; gobble(fileHandle);
+
+ distFile = filename + ".rowFormatted";
+ 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";
+ 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++){
+ 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 = getRootName(tempFile) + "sorted.dist.temp";
+
+ //use the unix sort
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ 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
+
+
+ //output to new file distance for each row and save positions in file where new row begins
+ ifstream in;
+ openInputFile(outfile, in);
+
+ distFile = outfile + ".rowFormatted";
+ 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()) {
+ in >> first >> second >> dist; 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();
+
+ remove(tempFile.c_str());
+ remove(outfile.c_str());
+ }
+ else{ //square matrix convert directly to formatted row file
+ int index = nseqs;
+ map<int, float> rowMap;
+ map<int, float>::iterator itRow;
+
+
+ for(int i=0;i<nseqs;i++){
+ fileHandle >> name;
+
+ list->set(i, name);
+
+ for(int j=0;j<nseqs;j++){
+ fileHandle >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+
+ if((distance < cutoff) && (j != i)){
+ rowMap[j] = distance;
+ }
+ index++;
+ reading->update(index);
+ }
+
+ //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;
+
+ list->setLabel("0");
+ fileHandle.close();
+ out.close();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "FormatPhylipMatrix", "read");
+ exit(1);
+ }
+}
+/***********************************************************************/
+FormatPhylipMatrix::~FormatPhylipMatrix(){}
+/***********************************************************************/
+
+
projects / mothur.git / blobdiff