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

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index 56284811af853a6504cac1adf026d6b6e67f3214..e305f2203b52a11d0ac809be3f35dfaf578ab1b3 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -11,7 +11,7 @@
 #include "ace.h"
 #include "sobs.h"
 #include "chao1.h"
-#include "jackknife.h"
+//#include "jackknife.h"
 #include "sharedsobscollectsummary.h"
 #include "sharedchao1.h"
 #include "sharedace.h"
@@ -24,6 +24,7 @@ VennCommand::VennCommand(){
                globaldata = GlobalData::getInstance();
                format = globaldata->getFormat();
                validCalculator = new ValidCalculators();
+               util = new SharedUtil();
                
                int i;
                
@@ -39,8 +40,8 @@ VennCommand::VennCommand(){
                                                if(abund < 5)
                                                        abund = 10;
                                                vennCalculators.push_back(new Ace(abund));
-                                       }else if (globaldata->Estimators[i] == "jack") {        
-                                               vennCalculators.push_back(new Jackknife());
+                                       //}else if (globaldata->Estimators[i] == "jack") {      
+                                               //vennCalculators.push_back(new Jackknife());
                                        }
                                }
                        }
@@ -80,6 +81,7 @@ VennCommand::~VennCommand(){
        delete input;
        delete read;
        delete venn;
+       delete util;
 }
 
 //**********************************************************************************************************************
@@ -118,7 +120,8 @@ int VennCommand::execute(){
                
                if (format != "list") { 
                        
-                       setGroups();
+                       util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "venn");
+                       globaldata->setGroups("");
                        
                        while(order != NULL){
                
@@ -145,7 +148,7 @@ int VennCommand::execute(){
                        }
                        
                        //reset groups parameter
-                       globaldata->Groups.clear();  globaldata->setGroups("");
+                       globaldata->Groups.clear();  
                        
                }else{
                        while(ordersingle != NULL){
@@ -175,67 +178,4 @@ int VennCommand::execute(){
 }
 
 //**********************************************************************************************************************
-void VennCommand::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) { 
-                                       if (globaldata->gGroupmap->namesOfGroups.size() > 4) {
-                                               cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using the first four groups in your groupfile." << endl; 
-                                               for (int i = 0; i < 4; i++) {
-                                                       globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
-                                               }
-                                       }else {
-                                               cout << "When using the groups parameter you must have at least 1 valid group. 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]);
-                       }
-               }
-               
-               
-               //check to make sure their are only 3 groups
-               if (globaldata->Groups.size() > 4) {
-                       cout << "You may only use up to 4 groups at a time with this command.  I will choose the first four and disregard the rest." << endl;
-                       for (int i = 4; i < globaldata->Groups.size(); i++) {
-                               globaldata->Groups.erase(globaldata->Groups.begin()+i);
-                       }
-               }
-               
-       }
-       catch(exception& e) {
-               cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the VennCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }               
-
-}
-/***********************************************************/