added sharedbraycurtis, sharedmorisirahorn, sharedkulczynski, sharedkulczynskicody...

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index b3f798145bc4de3abe460aa0e8dbccd8825178c6..6ee2943777f4053bb89f6d86e400269f3af30789 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -19,6 +19,14 @@
 #include "sharedsorest.h"
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
+#include "sharednseqs.h"
+#include "sharedochiai.h"
+#include "sharedanderberg.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
 
 
 //**********************************************************************************************************************
@@ -56,6 +64,22 @@ CollectSharedCommand::CollectSharedCommand(){
                                        cDisplays.push_back(new CollectDisplay(new SharedThetaYC(), new SharedOneColumnFile(fileNameRoot+"shared.thetayc")));
                                }else if (globaldata->Estimators[i] == "sharedthetan") { 
                                        cDisplays.push_back(new CollectDisplay(new SharedThetaN(), new SharedOneColumnFile(fileNameRoot+"shared.thetan")));
+                               }else if (globaldata->Estimators[i] == "sharednseqs") { 
+                                       cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
+                               }else if (globaldata->Estimators[i] == "sharedochiai") { 
+                                       cDisplays.push_back(new CollectDisplay(new SharedOchiai(), new SharedOneColumnFile(fileNameRoot+"shared.ochiai")));
+                               }else if (globaldata->Estimators[i] == "sharedanderberg") { 
+                                       cDisplays.push_back(new CollectDisplay(new SharedAnderberg(), new SharedOneColumnFile(fileNameRoot+"shared.anderberg")));
+                               }else if (globaldata->Estimators[i] == "sharedkulczynski") { 
+                                       cDisplays.push_back(new CollectDisplay(new SharedKulczynski(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynski")));
+                               }else if (globaldata->Estimators[i] == "sharedkulczynskicody") { 
+                                       cDisplays.push_back(new CollectDisplay(new SharedKulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"shared.kulczynskicody")));
+                               }else if (globaldata->Estimators[i] == "sharedlennon") { 
+                                       cDisplays.push_back(new CollectDisplay(new SharedLennon(), new SharedOneColumnFile(fileNameRoot+"shared.lennon")));
+                               }else if (globaldata->Estimators[i] == "sharedmorisitahorn") { 
+                                       cDisplays.push_back(new CollectDisplay(new SharedMorHorn(), new SharedOneColumnFile(fileNameRoot+"shared.morisitahorn")));
+                               }else if (globaldata->Estimators[i] == "sharedbraycurtis") { 
+                                       cDisplays.push_back(new CollectDisplay(new SharedBrayCurtis(), new SharedOneColumnFile(fileNameRoot+"shared.braycurtis")));
                                }
                        }
                }
@@ -109,6 +133,9 @@ int CollectSharedCommand::execute(){
                        order = SharedList->getSharedOrderVector();
                }
                set<string> orderList;
+               
+               //set users groups
+               setGroups();
 
                while(order != NULL){
                        orderList.insert(order->getLabel());
@@ -142,8 +169,11 @@ int CollectSharedCommand::execute(){
                for(i = globaldata->labels.begin(); i != globaldata->labels.end(); ++i)
                        if(orderList.count(*i) == 0)
                                cout << "'" << *i << "'" << " is not a valid label.\n";
-               globaldata->clearLabels();
                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }       
+               
+               //reset groups parameter
+               globaldata->Groups.clear();  globaldata->setGroups("");
+               
                return 0;
        }
        catch(exception& e) {
@@ -158,3 +188,50 @@ int CollectSharedCommand::execute(){
 
 
 //**********************************************************************************************************************
+void CollectSharedCommand::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 CollectSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the CollectSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+
+}
+/***********************************************************/
+