Revert to previous commit

[mothur.git] / readcolumn.cpp

diff --git a/readcolumn.cpp b/readcolumn.cpp
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+++ b/readcolumn.cpp
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+/*
+ *  readcolumn.cpp
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 4/21/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "readcolumn.h"
+#include "progress.hpp"
+
+/***********************************************************************/
+
+ReadColumnMatrix::ReadColumnMatrix(string df) : distFile(df){
+       
+       successOpen = m->openInputFile(distFile, fileHandle);
+       sim = false;
+       
+}
+/***********************************************************************/
+
+ReadColumnMatrix::ReadColumnMatrix(string df, bool s) : distFile(df){
+       
+       successOpen = m->openInputFile(distFile, fileHandle);
+       sim = s;
+}
+
+/***********************************************************************/
+
+int ReadColumnMatrix::read(NameAssignment* nameMap){
+       try {           
+
+               string firstName, secondName;
+               float distance;
+               int nseqs = nameMap->size();
+
+               list = new ListVector(nameMap->getListVector());
+       
+               Progress* reading = new Progress("Reading matrix:     ", nseqs * nseqs);
+
+               int lt = 1;
+               int refRow = 0; //we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose
+               int refCol = 0; //shows up later - Cell(refCol,refRow).  If it does, then its a square matrix
+
+               //need to see if this is a square or a triangular matrix...
+       
+               while(fileHandle && lt == 1){  //let's assume it's a triangular matrix...
+
+               
+                       fileHandle >> firstName >> secondName >> distance;      // get the row and column names and distance
+                       
+                       if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+       
+                       map<string,int>::iterator itA = nameMap->find(firstName);
+                       map<string,int>::iterator itB = nameMap->find(secondName);
+                               
+                       if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
+                       if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
+
+                       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 && itA != itB){
+                               if(itA->second > itB->second){
+                                       PCell value(itA->second, itB->second, distance);
+                       
+                                       if(refRow == refCol){           // in other words, if we haven't loaded refRow and refCol...
+                                               refRow = itA->second;
+                                               refCol = itB->second;
+                                               D->addCell(value);
+                                       }
+                                       else if(refRow == itA->second && refCol == itB->second){
+                                               lt = 0;
+                                       }
+                                       else{
+                                               D->addCell(value);
+                                       }
+                               }
+                               else if(itA->second < itB->second){
+                                       PCell value(itB->second, itA->second, distance);
+                       
+                                       if(refRow == refCol){           // in other words, if we haven't loaded refRow and refCol...
+                                               refRow = itA->second;
+                                               refCol = itB->second;
+                                               D->addCell(value);
+                                       }
+                                       else if(refRow == itB->second && refCol == itA->second){
+                                               lt = 0;
+                                       }
+                                       else{
+                                               D->addCell(value);
+                                       }
+                               }
+                               reading->update(itA->second * nseqs);
+                       }
+                       m->gobble(fileHandle);
+               }
+
+               if(lt == 0){  // oops, it was square
+       
+                       fileHandle.close();  //let's start over
+                       D->clear();  //let's start over
+                  
+                       m->openInputFile(distFile, fileHandle);  //let's start over
+
+                       while(fileHandle){
+                               fileHandle >> firstName >> secondName >> distance;
+                               
+                               if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+               
+                               map<string,int>::iterator itA = nameMap->find(firstName);
+                               map<string,int>::iterator itB = nameMap->find(secondName);
+                               
+                               if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
+                               if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
+                               
+                               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 && itA->second > itB->second){
+                                       PCell value(itA->second, itB->second, distance);
+                                       D->addCell(value);
+                                       reading->update(itA->second * nseqs);
+                               }
+               
+                               m->gobble(fileHandle);
+                       }
+               }
+               
+               if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
+               
+               reading->finish();
+               fileHandle.close();
+
+               list->setLabel("0");
+               
+               return 1;
+
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ReadColumnMatrix", "read");
+               exit(1);
+       }
+}
+
+/***********************************************************************/
+
+ReadColumnMatrix::~ReadColumnMatrix(){
+       //delete D;
+       //delete list;
+}
+
+