clustercommand.cpp

   1 /*
   2  *  clustercommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "clustercommand.h"
  11
  12 //**********************************************************************************************************************
  13 //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
  14 ClusterCommand::ClusterCommand(){
  15         try{
  16                 globaldata = GlobalData::getInstance();
  17
  18                 if(globaldata->gSparseMatrix != NULL)   {       matrix = new SparseMatrix(*globaldata->gSparseMatrix);          }
  19         //  Not sure if we want the address or an entire new memory allocation.  Might be nice to have new memory so data
  20         //  doesn't need to be re-read, but then again, it could suck up a ton of memory.  Dunno.
  21         //      if(globaldata->getSparseMatrix() != NULL)       {       matrix = globaldata->getSparseMatrix();         }
  22
  23                 if(globaldata->gListVector != NULL){
  24                         list = new ListVector(*globaldata->gListVector);
  25                         rabund = new RAbundVector(list->getRAbundVector());
  26                         //rabund->print(cout);
  27                 }
  28
  29                 if(globaldata->getMethod() != "")       {       method = globaldata->getMethod();               }
  30                 //if no method given use furthest, initialized in globaldata
  31                 if(method == "furthest")        {       cluster = new CompleteLinkage(rabund, list, matrix);    tag = "fn";     }
  32                 else if(method == "nearest"){   cluster = new SingleLinkage(rabund, list, matrix);              tag = "nn";     }
  33                 else if(method == "average"){   cluster = new AverageLinkage(rabund, list, matrix);             tag = "an";     }
  34                 else                                            {       cout << "error - not recognized method" << endl;                                                                                        }
  35
  36                 if(globaldata->getPrecision() != ""){
  37                         convert(globaldata->getPrecision(), precision);
  38                 }
  39
  40                 //saves precision legnth for formatting below
  41                 length = globaldata->getPrecision().length();
  42
  43                 if(globaldata->getCutOff() != ""){
  44                         convert(globaldata->getCutOff(), cutoff);
  45                         cutoff += (5 / (precision * 10.0));
  46                 }
  47
  48                 fileroot = getRootName(globaldata->getFileRoot());
  49
  50                 openOutputFile(fileroot+ tag + ".sabund",       sabundFile);
  51                 openOutputFile(fileroot+ tag + ".rabund",       rabundFile);
  52                 openOutputFile(fileroot+ tag + ".list",         listFile);
  53         }
  54         catch(exception& e) {
  55                 cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function ClusterCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  56                 exit(1);
  57         }
  58         catch(...) {
  59                 cout << "An unknown error has occurred in the ClusterCommand class function ClusterCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  60                 exit(1);
  61         }
  62 }
  63 //**********************************************************************************************************************
  64
  65 ClusterCommand::~ClusterCommand(){
  66         delete cluster;
  67         delete matrix;
  68         delete list;
  69         delete rabund;
  70 }
  71
  72 //**********************************************************************************************************************
  73
  74 int ClusterCommand::execute(){
  75         try {
  76                 float previousDist = 0.00000;
  77                 float rndPreviousDist = 0.00000;
  78                 oldRAbund = *rabund;
  79                 oldList = *list;
  80
  81                 float x;
  82                 x=0.1;
  83                 toString(x, 2);
  84
  85                 while(matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
  86                         cluster->update();
  87                         float dist = matrix->getSmallDist();
  88                         float rndDist = roundDist(dist, precision);
  89
  90                         if(previousDist <= 0.0000 && dist != previousDist){
  91                                 printData("unique");
  92                         }
  93                         else if(rndDist != rndPreviousDist){
  94                                 printData(toString(rndPreviousDist,  length-1));
  95                         }
  96
  97                         previousDist = dist;
  98                         rndPreviousDist = rndDist;
  99                         oldRAbund = *rabund;
 100                         oldList = *list;
 101                 }
 102
 103                 if(previousDist <= 0.0000){
 104                         printData("unique");
 105                 }
 106                 else if(rndPreviousDist<cutoff){
 107                         printData(toString(rndPreviousDist, length-1));
 108                 }
 109
 110                 //delete globaldata's copy of the sparsematrix and listvector to free up memory
 111                 delete globaldata->gSparseMatrix;  globaldata->gSparseMatrix = NULL;
 112                 delete globaldata->gListVector;  globaldata->gListVector = NULL;
 113
 114                 //saves .list file so you can do the collect, rarefaction and summary commands without doing a read.list
 115                 if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
 116                 else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); }
 117
 118                 globaldata->setListFile(fileroot+ tag + ".list");
 119                 globaldata->setNameFile("");
 120                 globaldata->setFormat("list");
 121
 122                 return 0;
 123         }
 124         catch(exception& e) {
 125                 cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 126                 exit(1);
 127         }
 128         catch(...) {
 129                 cout << "An unknown error has occurred in the ClusterCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 130                 exit(1);
 131         }
 132
 133 }
 134
 135 //**********************************************************************************************************************
 136
 137 void ClusterCommand::printData(string label){
 138         try {
 139                 oldRAbund.setLabel(label);
 140                 oldRAbund.getSAbundVector().print(cout);
 141                 oldRAbund.print(rabundFile);
 142                 oldRAbund.getSAbundVector().print(sabundFile);
 143
 144                 oldList.setLabel(label);
 145                 oldList.print(listFile);
 146         }
 147         catch(exception& e) {
 148                 cout << "Standard Error: " << e.what() << " has occurred in the ClusterCommand class Function printData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 149                 exit(1);
 150         }
 151         catch(...) {
 152                 cout << "An unknown error has occurred in the ClusterCommand class function printData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 153                 exit(1);
 154         }
 155
 156 }
 157 //**********************************************************************************************************************