#include "sharedmorisitahorn.h"
#include "sharedbraycurtis.h"
#include "sharedjackknife.h"
-#include "sharedwhittaker.h"
+#include "whittaker.h"
//**********************************************************************************************************************
openOutputFile(outputFileName, outputFileHandle);
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
- util = new SharedUtil();
mult = false;
int i;
SummarySharedCommand::~SummarySharedCommand(){
delete input;
delete read;
- delete util;
}
//**********************************************************************************************************************
int SummarySharedCommand::execute(){
try {
int count = 1;
-
+
//if the users entered no valid calculators don't execute command
if (sumCalculators.size() == 0) { return 0; }
//check if any calcs can do multiples
}
}
+ //read first line
read = new ReadOTUFile(globaldata->inputFileName);
read->read(&*globaldata);
input = globaldata->ginput;
- order = input->getSharedOrderVector();
-
- //set users groups
- util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary");
+ lookup = input->getSharedRAbundVectors();
+ vector<SharedRAbundVector*> lastLookup = lookup;
//output estimator names as column headers
outputFileHandle << "label" <<'\t' << "comparison" << '\t';
outputFileHandle << endl;
//create file and put column headers for multiple groups file
- if (mult = true) {
+ if (mult == true) {
outAllFileName = ((getRootName(globaldata->inputFileName)) + "sharedmultiple.summary");
openOutputFile(outAllFileName, outAll);
outAll << endl;
}
- while(order != NULL){
+ if (lookup.size() < 2) {
+ cout << "I cannot run the command without at least 2 valid groups.";
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+ //close files and clean up
+ outputFileHandle.close(); remove(outputFileName.c_str());
+ if (mult == true) { outAll.close(); remove(outAllFileName.c_str()); }
+ return 0;
+ //if you only have 2 groups you don't need a .sharedmultiple file
+ }else if ((lookup.size() == 2) && (mult == true)) {
+ mult = false;
+ outAll.close();
+ remove(outAllFileName.c_str());
+ }
+
+ //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+ set<string> processedLabels;
+ set<string> userLabels = globaldata->labels;
+ set<int> userLines = globaldata->lines;
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
-
- cout << order->getLabel() << '\t' << count << endl;
- util->getSharedVectors(globaldata->Groups, lookup, order); //fills group vectors from order vector. //fills group vectors from order vector.
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+ process(lookup);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ userLines.erase(count);
+ }
+
+ if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ process(lastLookup);
+
+ processedLabels.insert(lastLookup[0]->getLabel());
+ userLabels.erase(lastLookup[0]->getLabel());
+ }
+
+
+ //prevent memory leak
+ if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
+ lastLookup = lookup;
+ //get next line to process
+ lookup = input->getSharedRAbundVectors();
+ count++;
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ cout << "Your file does not include the label "<< *it;
+ if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
+ cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ needToRun = true;
+ }else {
+ cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ }
+ }
+
+ //run last line if you need to
+ if (needToRun == true) {
+ cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+ process(lastLookup);
+ }
+
+ for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; }
+
+ //reset groups parameter
+ globaldata->Groups.clear(); globaldata->setGroups("");
+
+ //close files
+ outputFileHandle.close();
+ if (mult == true) { outAll.close(); }
+
+ return 0;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************/
+void SummarySharedCommand::process(vector<SharedRAbundVector*> thisLookup) {
+ try {
//loop through calculators and add to file all for all calcs that can do mutiple groups
- if (mult = true) {
+ if (mult == true) {
//output label
- outAll << order->getLabel() << '\t';
+ outAll << thisLookup[0]->getLabel() << '\t';
//output groups names
string outNames = "";
- for (int j = 0; j < lookup.size(); j++) {
- outNames += lookup[j]->getGroup() + "-";
+ for (int j = 0; j < thisLookup.size(); j++) {
+ outNames += thisLookup[j]->getGroup() + "-";
}
outNames = outNames.substr(0, outNames.length()-1); //rip off extra '-';
outAll << outNames << '\t';
for(int i=0;i<sumCalculators.size();i++){
if (sumCalculators[i]->getMultiple() == true) {
- sumCalculators[i]->getValues(lookup);
+ sumCalculators[i]->getValues(thisLookup);
outAll << '\t';
sumCalculators[i]->print(outAll);
}
}
outAll << endl;
}
-
+
int n = 1;
vector<SharedRAbundVector*> subset;
- for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
- for (int l = n; l < lookup.size(); l++) {
+ for (int k = 0; k < (thisLookup.size() - 1); k++) { // pass cdd each set of groups to commpare
+ for (int l = n; l < thisLookup.size(); l++) {
- outputFileHandle << order->getLabel() << '\t';
+ outputFileHandle << thisLookup[0]->getLabel() << '\t';
subset.clear(); //clear out old pair of sharedrabunds
//add new pair of sharedrabunds
- subset.push_back(lookup[k]); subset.push_back(lookup[l]);
+ subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
//sort groups to be alphanumeric
- if (lookup[k]->getGroup() > lookup[l]->getGroup()) {
- outputFileHandle << (lookup[l]->getGroup() +'\t' + lookup[k]->getGroup()) << '\t'; //print out groups
+ if (thisLookup[k]->getGroup() > thisLookup[l]->getGroup()) {
+ outputFileHandle << (thisLookup[l]->getGroup() +'\t' + thisLookup[k]->getGroup()) << '\t'; //print out groups
}else{
- outputFileHandle << (lookup[k]->getGroup() +'\t' + lookup[l]->getGroup()) << '\t'; //print out groups
+ outputFileHandle << (thisLookup[k]->getGroup() +'\t' + thisLookup[l]->getGroup()) << '\t'; //print out groups
}
for(int i=0;i<sumCalculators.size();i++) {
+
sumCalculators[i]->getValues(subset); //saves the calculator outputs
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
}
n++;
}
- }
-
- //get next line to process
- order = input->getSharedOrderVector();
- count++;
- }
-
- //reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
- return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the SummarySharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the SummarySharedCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
}
-/***********************************************************/
+/***********************************************************/
\ No newline at end of file
projects / mothur.git / blobdiff