--- /dev/null
+/*
+ * readcluster.cpp
+ * Mothur
+ *
+ * Created by westcott on 10/28/09.
+ * Copyright 2009 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "readcluster.h"
+
+/***********************************************************************/
+
+ReadCluster::ReadCluster(string distfile, float c){
+ distFile = distfile;
+ cutoff = c;
+}
+
+/***********************************************************************/
+
+void ReadCluster::read(NameAssignment* nameMap){
+ try {
+
+ if (format == "phylip") { convertPhylip2Column(nameMap); }
+ else { list = new ListVector(nameMap->getListVector()); }
+
+ createHClusterFile();
+
+ }
+ catch(exception& e) {
+ errorOut(e, "ReadCluster", "read");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+void ReadCluster::createHClusterFile(){
+ try {
+ string outfile = getRootName(distFile) + "sorted.dist";
+
+ //if you can, use the unix sort since its been optimized for years
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ string command = "sort -n -k +3 " + distFile + " -o " + outfile;
+ system(command.c_str());
+ #else //you are stuck with my best attempt...
+ //windows sort does not have a way to specify a column, only a character in the line
+ //since we cannot assume that the distance will always be at the the same character location on each line
+ //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
+
+ //read in file line by file and put distance first
+ string tempDistFile = distFile + ".temp";
+ ifstream input;
+ ofstream output;
+ openInputFile(distFile, input);
+ openOutputFile(tempDistFile, output);
+
+ string firstName, secondName;
+ float dist;
+ while (input) {
+ input >> firstName >> secondName >> dist;
+ output << dist << '\t' << firstName << '\t' << secondName << endl;
+ gobble(input);
+ }
+ input.close();
+ output.close();
+
+
+ //sort using windows sort
+ string tempOutfile = outfile + ".temp";
+ string command = "sort " + tempDistFile + " /O " + tempOutfile;
+ system(command.c_str());
+
+ //read in sorted file and put distance at end again
+ ifstream input2;
+ openInputFile(tempOutfile, input2);
+ openOutputFile(outfile, output);
+
+ while (input2) {
+ input2 >> dist >> firstName >> secondName;
+ output << firstName << '\t' << secondName << '\t' << dist << endl;
+ gobble(input2);
+ }
+ input2.close();
+ output.close();
+
+ //remove temp files
+ remove(tempDistFile.c_str());
+ remove(tempOutfile.c_str());
+ #endif
+
+ OutPutFile = outfile;
+ }
+ catch(exception& e) {
+ errorOut(e, "ReadCluster", "createHClusterFile");
+ exit(1);
+ }
+}
+
+
+/***********************************************************************/
+
+void ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
+ try {
+ //convert phylip file to column file
+ map<int, string> rowToName;
+ map<int, string>::iterator it;
+
+ ifstream in;
+ ofstream out;
+ string tempFile = distFile + ".column.temp";
+
+ openInputFile(distFile, in);
+ openOutputFile(tempFile, out);
+
+ float distance;
+ int square, nseqs;
+ string name;
+ vector<string> matrixNames;
+
+ in >> nseqs >> name;
+ rowToName[0] = name;
+ matrixNames.push_back(name);
+
+ if(nameMap == NULL){
+ list = new ListVector(nseqs);
+ list->set(0, name);
+ }
+ else{
+ list = new ListVector(nameMap->getListVector());
+ if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+ }
+
+ char d;
+ while((d=in.get()) != EOF){
+
+ if(isalnum(d)){
+ square = 1;
+ in.putback(d);
+ for(int i=0;i<nseqs;i++){
+ in >> distance;
+ }
+ break;
+ }
+ if(d == '\n'){
+ square = 0;
+ break;
+ }
+ }
+
+ if(square == 0){
+
+ for(int i=1;i<nseqs;i++){
+ in >> name;
+ rowToName[i] = name;
+ matrixNames.push_back(name);
+
+ //there's A LOT of repeated code throughout this method...
+ if(nameMap == NULL){
+ list->set(i, name);
+
+ for(int j=0;j<i;j++){
+ in >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+
+ if(distance < cutoff){
+ out << i << '\t' << j << '\t' << distance << endl;
+ }
+ }
+
+ }
+ else{
+ if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+
+ for(int j=0;j<i;j++){
+ in >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+
+ if(distance < cutoff){
+ out << i << '\t' << j << '\t' << distance << endl;
+ }
+ }
+ }
+ }
+ }
+ else{
+
+ for(int i=1;i<nseqs;i++){
+ in >> name;
+ rowToName[i] = name;
+ matrixNames.push_back(name);
+
+ if(nameMap == NULL){
+ list->set(i, name);
+ for(int j=0;j<nseqs;j++){
+ in >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+
+ if(distance < cutoff && j < i){
+ out << i << '\t' << j << '\t' << distance << endl;
+ }
+ }
+
+ }
+ else{
+ if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
+
+ for(int j=0;j<nseqs;j++){
+ in >> distance;
+
+ if (distance == -1) { distance = 1000000; }
+
+ if(distance < cutoff && j < i){
+ out << i << '\t' << j << '\t' << distance << endl;
+ }
+
+ }
+ }
+ }
+ }
+
+ list->setLabel("0");
+ in.close();
+ out.close();
+
+ if(nameMap == NULL){
+ for(int i=0;i<matrixNames.size();i++){
+ nameMap->push_back(matrixNames[i]);
+ }
+ }
+
+ ifstream in2;
+ ofstream out2;
+
+ string outputFile = getRootName(distFile) + "column.dist";
+ openInputFile(tempFile, in2);
+ openOutputFile(outputFile, out2);
+
+ int first, second;
+ float dist;
+
+ while (in2) {
+ in2 >> first >> second >> dist;
+ out2 << rowToName[first] << '\t' << rowToName[second] << '\t' << dist << endl;
+ gobble(in2);
+ }
+ in2.close();
+ out2.close();
+
+ remove(tempFile.c_str());
+ distFile = outputFile;
+ }
+ catch(exception& e) {
+ errorOut(e, "ReadCluster", "convertPhylip2Column");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+ReadCluster::~ReadCluster(){}
+/***********************************************************************/
+
projects / mothur.git / blobdiff