more calculator edits and added coverage and whittaker

[mothur.git] / collectsharedcommand.cpp

diff --git a/collectsharedcommand.cpp b/collectsharedcommand.cpp
index 8c04545d61fc321382122526bc53e4c2892321eb..bc0609ef539e119addffbb531d7f8f54f44f747b 100644 (file)
--- a/collectsharedcommand.cpp
+++ b/collectsharedcommand.cpp
@@ -19,6 +19,17 @@
 #include "sharedsorest.h"
 #include "sharedthetayc.h"
 #include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "whittaker.h"
+#include "sharednseqs.h"
+#include "sharedochiai.h"
+#include "sharedanderbergs.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
+
 
 
 //**********************************************************************************************************************
@@ -30,6 +41,7 @@ CollectSharedCommand::CollectSharedCommand(){
                fileNameRoot = getRootName(globaldata->inputFileName);
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
+               util = new SharedUtil();
                
                int i;
                for (i=0; i<globaldata->Estimators.size(); i++) {
@@ -40,22 +52,42 @@ CollectSharedCommand::CollectSharedCommand(){
                                        cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
                                }else if (globaldata->Estimators[i] == "sharedace") { 
                                        cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
-                               }else if (globaldata->Estimators[i] == "sharedjabund") {        
-                                       cDisplays.push_back(new CollectDisplay(new SharedJAbund(), new SharedOneColumnFile(fileNameRoot+"shared.jabund")));
-                               }else if (globaldata->Estimators[i] == "sharedsorensonabund") { 
-                                       cDisplays.push_back(new CollectDisplay(new SharedSorAbund(), new SharedOneColumnFile(fileNameRoot+"shared.sorabund")));
-                               }else if (globaldata->Estimators[i] == "sharedjclass") { 
-                                       cDisplays.push_back(new CollectDisplay(new SharedJclass(), new SharedOneColumnFile(fileNameRoot+"shared.jclass")));
-                               }else if (globaldata->Estimators[i] == "sharedsorclass") { 
-                                       cDisplays.push_back(new CollectDisplay(new SharedSorClass(), new SharedOneColumnFile(fileNameRoot+"shared.sorclass")));
-                               }else if (globaldata->Estimators[i] == "sharedjest") { 
-                                       cDisplays.push_back(new CollectDisplay(new SharedJest(), new SharedOneColumnFile(fileNameRoot+"shared.jest")));
-                               }else if (globaldata->Estimators[i] == "sharedsorest") { 
-                                       cDisplays.push_back(new CollectDisplay(new SharedSorEst(), new SharedOneColumnFile(fileNameRoot+"shared.sorest")));
-                               }else if (globaldata->Estimators[i] == "sharedthetayc") { 
-                                       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] == "jabund") {      
+                                       cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
+                               }else if (globaldata->Estimators[i] == "sorabund") { 
+                                       cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
+                               }else if (globaldata->Estimators[i] == "jclass") { 
+                                       cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
+                               }else if (globaldata->Estimators[i] == "sorclass") { 
+                                       cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
+                               }else if (globaldata->Estimators[i] == "jest") { 
+                                       cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
+                               }else if (globaldata->Estimators[i] == "sorest") { 
+                                       cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
+                               }else if (globaldata->Estimators[i] == "thetayc") { 
+                                       cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
+                               }else if (globaldata->Estimators[i] == "thetan") { 
+                                       cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
+                               }else if (globaldata->Estimators[i] == "kstest") { 
+                                       cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
+                               }else if (globaldata->Estimators[i] == "whittaker") { 
+                                       cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
+                               }else if (globaldata->Estimators[i] == "sharednseqs") { 
+                                       cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
+                               }else if (globaldata->Estimators[i] == "ochiai") { 
+                                       cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
+                               }else if (globaldata->Estimators[i] == "anderberg") { 
+                                       cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
+                               }else if (globaldata->Estimators[i] == "skulczynski") { 
+                                       cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
+                               }else if (globaldata->Estimators[i] == "kulczynskicody") { 
+                                       cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
+                               }else if (globaldata->Estimators[i] == "lennon") { 
+                                       cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
+                               }else if (globaldata->Estimators[i] == "morisitahorn") { 
+                                       cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
+                               }else if (globaldata->Estimators[i] == "braycurtis") { 
+                                       cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
                                }
                        }
                }
@@ -82,6 +114,7 @@ CollectSharedCommand::~CollectSharedCommand(){
        delete input;
        delete cCurve;
        delete read;
+       delete util;
 }
 
 //**********************************************************************************************************************
@@ -94,14 +127,14 @@ int CollectSharedCommand::execute(){
                if (cDisplays.size() == 0) { return 0; }
                
                if (format == "sharedfile") {
-                       read = new ReadPhilFile(globaldata->inputFileName);     
+                       read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
                        
                        input = globaldata->ginput;
                        order = input->getSharedOrderVector();
                }else {
                        //you are using a list and a groupfile
-                       read = new ReadPhilFile(globaldata->inputFileName);     
+                       read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
                
                        input = globaldata->ginput;
@@ -109,6 +142,10 @@ int CollectSharedCommand::execute(){
                        order = SharedList->getSharedOrderVector();
                }
                set<string> orderList;
+               
+               //set users groups
+               util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
+               util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 
                while(order != NULL){
                        orderList.insert(order->getLabel());
@@ -143,6 +180,10 @@ int CollectSharedCommand::execute(){
                        if(orderList.count(*i) == 0)
                                cout << "'" << *i << "'" << " is not a valid label.\n";
                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }       
+               
+               //reset groups parameter
+               globaldata->Groups.clear();  globaldata->setGroups("");
+               
                return 0;
        }
        catch(exception& e) {
@@ -155,5 +196,5 @@ int CollectSharedCommand::execute(){
        }       
 }
 
+/***********************************************************/
 
-//**********************************************************************************************************************