started shared utilities, updates to venn and heatmap added tree.groups command

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 526cd8292e2082eccf96c2c25f82c8a4709267e5..bebdf2637edad951b4b766760d4d96ee86281f69 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -40,6 +40,7 @@ SummarySharedCommand::SummarySharedCommand(){
                openOutputFile(outputFileName, outputFileHandle);
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
+               util = new SharedUtil();
                
                int i;
                for (i=0; i<globaldata->Estimators.size(); i++) {
@@ -109,6 +110,7 @@ SummarySharedCommand::SummarySharedCommand(){
 SummarySharedCommand::~SummarySharedCommand(){
        delete input;
        delete read;
+       delete util;
 }
 
 //**********************************************************************************************************************
@@ -137,7 +139,7 @@ int SummarySharedCommand::execute(){
                }
                
                //set users groups
-               setGroups();
+               util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "summary");
                
                //output estimator names as column headers
                outputFileHandle << "label" <<'\t' << "comparison" << '\t'; 
@@ -151,7 +153,7 @@ int SummarySharedCommand::execute(){
                        if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){                       
        
                                cout << order->getLabel() << '\t' << count << endl;
-                               getSharedVectors();  //fills group vectors from order vector.
+                               util->getSharedVectors(globaldata->Groups, lookup, order);  //fills group vectors from order vector.  //fills group vectors from order vector.
                                
                                //randomize group order
                                if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
@@ -159,7 +161,7 @@ int SummarySharedCommand::execute(){
                                int n = 1; 
                                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++) {
-                                               outputFileHandle << order->getLabel() << '\t' << (lookup[k]->getGroup() + lookup[l]->getGroup()) << '\t' << '\t'; //print out label and group
+                                               
                                                outputFileHandle << order->getLabel() << '\t';
                                                
                                                //sort groups to be alphanumeric
@@ -210,91 +212,4 @@ int SummarySharedCommand::execute(){
        }               
 }
 
-//**********************************************************************************************************************
-
-void SummarySharedCommand::getSharedVectors(){
-try {
-               lookup.clear();
-               //create and initialize vector of sharedvectors, one for each group
-               for (int i = 0; i < globaldata->Groups.size(); i++) { 
-                       SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
-                       temp->setLabel(order->getLabel());
-                       temp->setGroup(globaldata->Groups[i]);
-                       lookup.push_back(temp);
-               }
-               
-               int numSeqs = order->size();
-               //sample all the members
-               for(int i=0;i<numSeqs;i++){
-                       //get first sample
-                       individual chosen = order->get(i);
-                       int abundance; 
-                                       
-                       //set info for sharedvector in chosens group
-                       for (int j = 0; j < lookup.size(); j++) { 
-                               if (chosen.group == lookup[j]->getGroup()) {
-                                        abundance = lookup[j]->getAbundance(chosen.bin);
-                                        lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
-                                        break;
-                               }
-                       }
-               }
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SummarySharedCommand class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-
-}
-
-//**********************************************************************************************************************
-void SummarySharedCommand::setGroups() {
-       try {
-               //if the user has not entered specific groups to analyze then do them all
-               if (globaldata->Groups.size() != 0) {
-                       if (globaldata->Groups[0] != "all") {
-                               //check that groups are valid
-                               for (int i = 0; i < globaldata->Groups.size(); i++) {
-                                       if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
-                                               cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
-                                               // erase the invalid group from globaldata->Groups
-                                               globaldata->Groups.erase(globaldata->Groups.begin()+i);
-                                       }
-                               }
-                       
-                               //if the user only entered invalid groups
-                               if ((globaldata->Groups.size() == 0) || (globaldata->Groups.size() == 1)) { 
-                                       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; 
-                                       for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-                                               globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-                                       }
-                               }
-                       }else{//user has enter "all" and wants the default groups
-                               globaldata->Groups.clear();
-                               for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-                                       globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-                               }
-                               globaldata->setGroups("");
-                       }
-               }else {
-                       for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
-                               globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-                       }
-               }
-               
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the SummarySharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the SummarySharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
-
-}
 /***********************************************************/