2 * collectsharedcommand.cpp
5 * Created by Sarah Westcott on 1/2/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "collectsharedcommand.h"
11 #include "sharedsobscollectsummary.h"
12 #include "sharedchao1.h"
13 #include "sharedace.h"
14 #include "sharedjabund.h"
15 #include "sharedsorabund.h"
16 #include "sharedjclass.h"
17 #include "sharedsorclass.h"
18 #include "sharedjest.h"
19 #include "sharedsorest.h"
20 #include "sharedthetayc.h"
21 #include "sharedthetan.h"
24 //**********************************************************************************************************************
26 CollectSharedCommand::CollectSharedCommand(){
28 globaldata = GlobalData::getInstance();
30 fileNameRoot = getRootName(globaldata->inputFileName);
31 format = globaldata->getFormat();
32 validCalculator = new ValidCalculators();
35 for (i=0; i<globaldata->Estimators.size(); i++) {
36 if (validCalculator->isValidCalculator("shared", globaldata->Estimators[i]) == true) {
37 if (globaldata->Estimators[i] == "sharedchao") {
38 cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
39 }else if (globaldata->Estimators[i] == "sharedsobs") {
40 cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
41 }else if (globaldata->Estimators[i] == "sharedace") {
42 cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
43 }else if (globaldata->Estimators[i] == "sharedjabund") {
44 cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund")));
45 }else if (globaldata->Estimators[i] == "sharedsorensonabund") {
46 cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund")));
47 }else if (globaldata->Estimators[i] == "sharedjclass") {
48 cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass")));
49 }else if (globaldata->Estimators[i] == "sharedsorclass") {
50 cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass")));
51 }else if (globaldata->Estimators[i] == "sharedjest") {
52 cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest")));
53 }else if (globaldata->Estimators[i] == "sharedsorest") {
54 cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest")));
55 }else if (globaldata->Estimators[i] == "sharedthetayc") {
56 cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc")));
57 }else if (globaldata->Estimators[i] == "sharedthetan") {
58 cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
63 //reset calc for next command
64 globaldata->setCalc("");
68 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
72 cout << "An unknown error has occurred in the CollectSharedCommand class function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
78 //**********************************************************************************************************************
80 CollectSharedCommand::~CollectSharedCommand(){
87 //**********************************************************************************************************************
89 int CollectSharedCommand::execute(){
93 //if the users entered no valid calculators don't execute command
94 if (cDisplays.size() == 0) { return 0; }
96 if (format == "sharedfile") {
97 read = new ReadPhilFile(globaldata->inputFileName);
98 read->read(&*globaldata);
100 input = globaldata->ginput;
101 order = input->getSharedOrderVector();
103 //you are using a list and a groupfile
104 read = new ReadPhilFile(globaldata->inputFileName);
105 read->read(&*globaldata);
107 input = globaldata->ginput;
108 SharedList = globaldata->gSharedList;
109 order = SharedList->getSharedOrderVector();
111 set<string> orderList;
116 while(order != NULL){
117 orderList.insert(order->getLabel());
118 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
119 //create collectors curve
120 cCurve = new Collect(order, cDisplays);
121 convert(globaldata->getFreq(), freq);
122 cCurve->getSharedCurve(freq);
126 cout << order->getLabel() << '\t' << count << endl;
129 //get next line to process
130 if (format == "sharedfile") {
131 order = input->getSharedOrderVector();
133 //you are using a list and a groupfile
134 SharedList = input->getSharedListVector(); //get new list vector to process
135 if (SharedList != NULL) {
136 order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
144 set<string>::iterator i;
145 for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
146 if(orderList.count(*i) == 0)
147 cout << "'" << *i << "'" << " is not a valid label.\n";
148 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
150 //reset groups parameter
151 globaldata->Groups.clear(); globaldata->setGroups("");
155 catch(exception& e) {
156 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
160 cout << "An unknown error has occurred in the CollectSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
166 //**********************************************************************************************************************
167 void CollectSharedCommand::setGroups() {
169 //if the user has not entered specific groups to analyze then do them all
170 if (globaldata->Groups.size() != 0) {
171 if (globaldata->Groups[0] != "all") {
172 //check that groups are valid
173 for (int i = 0; i < globaldata->Groups.size(); i++) {
174 if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
175 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
176 // erase the invalid group from globaldata->Groups
177 globaldata->Groups.erase(globaldata->Groups.begin()+i);
181 //if the user only entered invalid groups
182 if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) {
183 cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
184 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
185 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
188 }else{//user has enter "all" and wants the default groups
189 globaldata->Groups.clear();
190 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
191 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
193 globaldata->setGroups("");
196 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
197 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
202 catch(exception& e) {
203 cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
207 cout << "An unknown error has occurred in the CollectSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
212 /***********************************************************/