5 * Created by Sarah Westcott on 1/2/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "summarycommand.h"
14 #include "bootstrap.h"
16 #include "npshannon.h"
18 #include "jackknife.h"
20 //**********************************************************************************************************************
22 SummaryCommand::SummaryCommand(){
24 globaldata = GlobalData::getInstance();
25 validCalculator = new ValidCalculators();
28 for (i=0; i<globaldata->Estimators.size(); i++) {
29 if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) {
30 if(globaldata->Estimators[i] == "sobs"){
31 sumCalculators.push_back(new Sobs());
32 }else if(globaldata->Estimators[i] == "chao"){
33 sumCalculators.push_back(new Chao1());
34 }else if(globaldata->Estimators[i] == "ace"){
35 convert(globaldata->getAbund(), abund);
38 sumCalculators.push_back(new Ace(abund));
39 }else if(globaldata->Estimators[i] == "jack"){
40 sumCalculators.push_back(new Jackknife());
41 }else if(globaldata->Estimators[i] == "shannon"){
42 sumCalculators.push_back(new Shannon());
43 }else if(globaldata->Estimators[i] == "npshannon"){
44 sumCalculators.push_back(new NPShannon());
45 }else if(globaldata->Estimators[i] == "simpson"){
46 sumCalculators.push_back(new Simpson());
47 }else if(globaldata->Estimators[i] == "bootstrap"){
48 sumCalculators.push_back(new Bootstrap());
53 //reset calc for next command
54 globaldata->setCalc("");
58 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
62 cout << "An unknown error has occurred in the SummaryCommand class function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
66 //**********************************************************************************************************************
68 SummaryCommand::~SummaryCommand(){
74 //**********************************************************************************************************************
76 int SummaryCommand::execute(){
79 //if the users entered no valid calculators don't execute command
80 if (sumCalculators.size() == 0) { return 0; }
82 outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
83 openOutputFile(outputFileName, outputFileHandle);
84 outputFileHandle << "label";
86 read = new ReadPhilFile(globaldata->inputFileName);
87 read->read(&*globaldata);
89 for(int i=0;i<sumCalculators.size();i++){
90 if(sumCalculators[i]->getCols() == 1){
91 outputFileHandle << '\t' << sumCalculators[i]->getName();
94 outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
97 outputFileHandle << endl;
99 sabund = globaldata->sabund;
100 input = globaldata->ginput;
102 while(sabund != NULL){
104 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
106 cout << sabund->getLabel() << '\t' << count << endl;
108 outputFileHandle << sabund->getLabel();
109 for(int i=0;i<sumCalculators.size();i++){
110 vector<double> data = sumCalculators[i]->getValues(sabund);
111 outputFileHandle << '\t';
112 sumCalculators[i]->print(outputFileHandle);
114 outputFileHandle << endl;
117 sabund = input->getSAbundVector();
123 catch(exception& e) {
124 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
128 cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
133 //**********************************************************************************************************************