--- /dev/null
+/*
+ * readphylip.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 4/21/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "readphylip.h"
+#include "progress.hpp"
+
+/***********************************************************************/
+
+ReadPhylipMatrix::ReadPhylipMatrix(string distFile){
+
+ successOpen = m->openInputFile(distFile, fileHandle);
+ sim=false;
+
+}
+/***********************************************************************/
+
+ReadPhylipMatrix::ReadPhylipMatrix(string distFile, bool s){
+
+ successOpen = m->openInputFile(distFile, fileHandle);
+ sim=s;
+}
+
+
+/***********************************************************************/
+
+int ReadPhylipMatrix::read(NameAssignment* nameMap){
+ try {
+
+ float distance;
+ int square, nseqs;
+ string name;
+ vector<string> matrixNames;
+
+ 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); }
+
+ 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){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
+ }
+
+ char d;
+ while((d=fileHandle.get()) != EOF){
+
+ if(isalnum(d)){
+ square = 1;
+ fileHandle.putback(d);
+ for(int i=0;i<nseqs;i++){
+ fileHandle >> distance;
+ }
+ break;
+ }
+ if(d == '\n'){
+ square = 0;
+ break;
+ }
+ }
+
+ Progress* reading;
+
+ if(square == 0){
+
+ reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
+
+ int index = 0;
+
+ for(int i=1;i<nseqs;i++){
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ fileHandle >> 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++){
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+
+ fileHandle >> distance;
+
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ PCell value(i, j, distance);
+ D->addCell(value);
+ }
+ index++;
+ reading->update(index);
+ }
+
+ }
+ else{
+ if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
+
+ for(int j=0;j<i;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { delete reading; fileHandle.close(); return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
+ D->addCell(value);
+ }
+ index++;
+ reading->update(index);
+ }
+ }
+ }
+ }
+ else{
+
+ reading = new Progress("Reading matrix: ", nseqs * nseqs);
+
+ int index = nseqs;
+
+ for(int i=1;i<nseqs;i++){
+ fileHandle >> name;
+ matrixNames.push_back(name);
+
+
+
+ if(nameMap == NULL){
+ list->set(i, name);
+ for(int j=0;j<nseqs;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && j < i){
+ PCell value(i, j, distance);
+ D->addCell(value);
+ }
+ index++;
+ reading->update(index);
+ }
+
+ }
+ else{
+ if(nameMap->count(name)==0){ m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
+
+ for(int j=0;j<nseqs;j++){
+ fileHandle >> distance;
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && j < i){
+ PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
+ D->addCell(value);
+ }
+ index++;
+ reading->update(index);
+ }
+ }
+ }
+ }
+
+ if (m->control_pressed) { fileHandle.close(); delete reading; return 0; }
+
+ reading->finish();
+ delete reading;
+
+ list->setLabel("0");
+ fileHandle.close();
+
+ /* if(nameMap != NULL){
+ for(int i=0;i<matrixNames.size();i++){
+ nameMap->erase(matrixNames[i]);
+ }
+ if(nameMap->size() > 0){
+ //should probably tell them what is missing if we missed something
+ m->mothurOut("missed something\t" + toString(nameMap->size())); m->mothurOutEndLine();
+ }
+ } */
+
+ return 1;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadPhylipMatrix", "read");
+ exit(1);
+ }
+ }
+
+/***********************************************************************/
+
+ReadPhylipMatrix::~ReadPhylipMatrix(){
+ // delete D;
+ // delete list;
+}
projects / mothur.git / blobdiff