5 * Created by Sarah Westcott on 1/2/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "summarycommand.h"
15 #include "bootstrap.h"
17 #include "npshannon.h"
19 #include "jackknife.h"
23 #include "bergerparker.h"
26 //**********************************************************************************************************************
28 SummaryCommand::SummaryCommand(){
30 globaldata = GlobalData::getInstance();
31 validCalculator = new ValidCalculators();
34 for (i=0; i<globaldata->Estimators.size(); i++) {
35 if (validCalculator->isValidCalculator("summary", globaldata->Estimators[i]) == true) {
36 if(globaldata->Estimators[i] == "sobs"){
37 sumCalculators.push_back(new Sobs());
38 }else if(globaldata->Estimators[i] == "chao"){
39 sumCalculators.push_back(new Chao1());
40 }else if(globaldata->Estimators[i] == "geom"){
41 sumCalculators.push_back(new Geom());
42 }else if(globaldata->Estimators[i] == "logsd"){
43 sumCalculators.push_back(new LogSD());
44 }else if(globaldata->Estimators[i] == "qstat"){
45 sumCalculators.push_back(new QStat());
46 }else if(globaldata->Estimators[i] == "bergerparker"){
47 sumCalculators.push_back(new BergerParker());
48 }else if(globaldata->Estimators[i] == "bstick"){
49 sumCalculators.push_back(new BStick());
50 }else if(globaldata->Estimators[i] == "ace"){
51 convert(globaldata->getAbund(), abund);
54 sumCalculators.push_back(new Ace(abund));
55 }else if(globaldata->Estimators[i] == "jack"){
56 sumCalculators.push_back(new Jackknife());
57 }else if(globaldata->Estimators[i] == "shannon"){
58 sumCalculators.push_back(new Shannon());
59 }else if(globaldata->Estimators[i] == "npshannon"){
60 sumCalculators.push_back(new NPShannon());
61 }else if(globaldata->Estimators[i] == "simpson"){
62 sumCalculators.push_back(new Simpson());
63 }else if(globaldata->Estimators[i] == "bootstrap"){
64 sumCalculators.push_back(new Bootstrap());
65 }else if (globaldata->Estimators[i] == "nseqs") {
66 sumCalculators.push_back(new NSeqs());
71 //reset calc for next command
72 globaldata->setCalc("");
76 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
80 cout << "An unknown error has occurred in the SummaryCommand class function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
84 //**********************************************************************************************************************
86 SummaryCommand::~SummaryCommand(){
92 //**********************************************************************************************************************
94 int SummaryCommand::execute(){
97 //if the users entered no valid calculators don't execute command
98 if (sumCalculators.size() == 0) { return 0; }
100 outputFileName = ((getRootName(globaldata->inputFileName)) + "summary");
101 openOutputFile(outputFileName, outputFileHandle);
102 outputFileHandle << "label";
104 read = new ReadPhilFile(globaldata->inputFileName);
105 read->read(&*globaldata);
107 for(int i=0;i<sumCalculators.size();i++){
108 if(sumCalculators[i]->getCols() == 1){
109 outputFileHandle << '\t' << sumCalculators[i]->getName();
112 outputFileHandle << '\t' << sumCalculators[i]->getName() << "\t" << sumCalculators[i]->getName() << "_lci\t" << sumCalculators[i]->getName() << "_hci";
115 outputFileHandle << endl;
117 sabund = globaldata->sabund;
118 input = globaldata->ginput;
120 while(sabund != NULL){
122 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(sabund->getLabel()) == 1){
124 cout << sabund->getLabel() << '\t' << count << endl;
126 outputFileHandle << sabund->getLabel();
127 for(int i=0;i<sumCalculators.size();i++){
128 vector<double> data = sumCalculators[i]->getValues(sabund);
129 outputFileHandle << '\t';
130 sumCalculators[i]->print(outputFileHandle);
133 outputFileHandle << endl;
135 sabund = input->getSAbundVector();
141 catch(exception& e) {
142 cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
146 cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
151 //**********************************************************************************************************************