finishing the container classes, combining read.otu and read.list commands. some...

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index b9fd08debd294870af590f5be48fdc4a7c7ba890..347ed0446c5e7c72cba1fac4dbab452b2992a606 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "summarysharedcommand.h"
+#include "sharedsobs.h"
 #include "sharedchao1.h"
 #include "sharedace.h"
 #include "sharedjabund.h"
@@ -27,7 +28,9 @@ SummarySharedCommand::SummarySharedCommand(){
                
                int i;
                for (i=0; i<globaldata->sharedSummaryEstimators.size(); i++) {
-                       if (globaldata->sharedSummaryEstimators[i] == "sharedChao") { 
+                       if (globaldata->sharedSummaryEstimators[i] == "sharedSobs") { 
+                               sumCalculators.push_back(new SharedSobs());
+                       }else if (globaldata->sharedEstimators[i] == "sharedChao") { 
                                sumCalculators.push_back(new SharedChao1());
                        }else if (globaldata->sharedSummaryEstimators[i] == "sharedAce") { 
                                sumCalculators.push_back(new SharedAce());
@@ -70,21 +73,21 @@ SummarySharedCommand::~SummarySharedCommand(){
 
 int SummarySharedCommand::execute(){
        try {
-               outputFileName = ((getRootName(globaldata->inputFileName)) + "sharedSummary");
+               outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
                openOutputFile(outputFileName, outputFileHandle);
        
                read = new ReadPhilFile(globaldata->inputFileName);     
                read->read(&*globaldata); 
                
-               outputFileHandle << '\t' << '\t' << '\t' << '\t'; //pads file for labels and groupnames
+               outputFileHandle << "label" <<'\t' << "comparison" << '\t'; 
                for(int i=0;i<sumCalculators.size();i++){
                        outputFileHandle << '\t' << sumCalculators[i]->getName();
                }
                outputFileHandle << endl;
                
-               list = globaldata->glist;
+               SharedList = globaldata->gSharedList;
                input = globaldata->ginput;
-               order = list->getSharedOrderVector();
+               order = SharedList->getSharedOrderVector();
                getGroupComb();
                
                int count = 1;
@@ -101,7 +104,7 @@ 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' << groupComb[n-1] << '\t'; //print out label and group
+                                               outputFileHandle << order->getLabel() << '\t' << groupComb[n-1] << '\t' << '\t'; //print out label and group
                                                for(int i=0;i<sumCalculators.size();i++){
                                                        sumCalculators[i]->getValues(lookup[k], lookup[l]); //saves the calculator outputs
                                                        outputFileHandle << '\t';
@@ -113,9 +116,9 @@ int SummarySharedCommand::execute(){
                                }
                        }
                
-                       list = input->getListVector(); //get new list vector to process
-                       if (list != NULL) {
-                               order = list->getSharedOrderVector(); //gets new order vector with group info.
+                       SharedList = input->getSharedListVector(); //get new list vector to process
+                       if (SharedList != NULL) {
+                               order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
                                count++;
                        }else {
                                break;