broke apart read matrix file

[mothur.git] / readphylip.cpp

diff --git a/readphylip.cpp b/readphylip.cpp
new file mode 100644 (file)
index 0000000..174b7e3
--- /dev/null
+++ b/readphylip.cpp
@@ -0,0 +1,186 @@
+/*
+ *  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 = openInputFile(distFile, fileHandle);
+       
+}
+
+/***********************************************************************/
+
+void ReadPhylipMatrix::read(NameAssignment* nameMap){
+       try {
+       
+                       float distance;
+                       int square, nseqs;
+                       string name;
+                       vector<string> matrixNames;
+       
+                       fileHandle >> nseqs >> 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){    cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
+                       }
+       
+                       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++){
+                                       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++){
+                                                       fileHandle >> distance;
+                                               
+                                                       if (distance == -1) { distance = 1000000; }
+                                               
+                                                       if(distance < cutoff){
+                                                               PCell value(i, j, distance);
+                                                               D->addCell(value);
+                                                       }
+                                                       index++;
+                                                       reading->update(index);
+                                               }
+                               
+                                       }
+                                       else{
+                                               if(nameMap->count(name)==0){    cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
+                               
+                                               for(int j=0;j<i;j++){
+                                                       fileHandle >> distance;
+                               
+                                                       if (distance == -1) { distance = 1000000; }
+                                                       
+                                                       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 (distance == -1) { distance = 1000000; }
+                                                       
+                                                       if(distance < cutoff && j < i){
+                                                               PCell value(i, j, distance);
+                                                               D->addCell(value);
+                                                       }
+                                                       index++;
+                                                       reading->update(index);
+                                               }
+                                       
+                                       }
+                                       else{
+                                               if(nameMap->count(name)==0){    cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
+                               
+                                               for(int j=0;j<nseqs;j++){
+                                                       fileHandle >> distance;
+                       
+                                                       if (distance == -1) { distance = 1000000; }
+                                                       
+                                                       if(distance < cutoff && j < i){
+                                                               PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
+                                                               D->addCell(value);
+                                                       }
+                                                       index++;
+                                                       reading->update(index);
+                                               }
+                                       }
+                               }
+                       }
+                       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
+                                       cout << "missed something" << '\t' << nameMap->size() << endl;
+                               }
+                       }
+
+               }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ReadPhylipMatrix class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ReadPhylipMatrix class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+
+ReadPhylipMatrix::~ReadPhylipMatrix(){
+       delete D;
+       delete list;
+}
+