deleted read.shared command and added its functionality to read.otu.

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 189be88de11e4160b4e185727e324a581063727f..58f73f34e45b61b30e5355ebd38cfa63f988448d 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -15,22 +15,23 @@
 RareFactSharedCommand::RareFactSharedCommand(){
        try {
                globaldata = GlobalData::getInstance();
-               string fileNameRoot, groups;
+               string fileNameRoot;
                fileNameRoot = getRootName(globaldata->inputFileName);
-               groupmap = globaldata->gGroupmap;
-               
-               //initialize groups for label
-               groups = "";
-               for (int i = 0; i < groupmap->namesOfGroups.size(); i++) {
-                       groups = groups + groupmap->namesOfGroups[i];
-               }
-               
+               format = globaldata->getFormat();
+               validCalculator = new ValidCalculators();
+                               
                int i;
-               for (i=0; i<globaldata->sharedRareEstimators.size(); i++) {
-                       if (globaldata->sharedRareEstimators[i] == "sharedobserved") { 
-                               rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"r_shared.observed", groups)));
+               for (i=0; i<globaldata->Estimators.size(); i++) {
+                       if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) { 
+                               if (globaldata->Estimators[i] == "sharedobserved") { 
+                                       rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
+                               }
                        }
                }
+               
+               //reset calc for next command
+               globaldata->setCalc("");
+
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -57,12 +58,28 @@ RareFactSharedCommand::~RareFactSharedCommand(){
 int RareFactSharedCommand::execute(){
        try {
                int count = 1;
-               read = new ReadPhilFile(globaldata->inputFileName);     
-               read->read(&*globaldata); 
                
-               input = globaldata->ginput;
-               SharedList = globaldata->gSharedList;
-               order = SharedList->getSharedOrderVector();
+               //if the users entered no valid calculators don't execute command
+               if (rDisplays.size() == 0) { return 0; }
+
+               if (format == "sharedfile") {
+                       read = new ReadPhilFile(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->read(&*globaldata); 
+               
+                       input = globaldata->ginput;
+                       SharedList = globaldata->gSharedList;
+                       order = SharedList->getSharedOrderVector();
+               }
+               
+               //set users groups
+               setGroups();
                
                while(order != NULL){
                
@@ -78,17 +95,27 @@ int RareFactSharedCommand::execute(){
                                cout << order->getLabel() << '\t' << count << endl;
                        }
                        
-                       SharedList = input->getSharedListVector(); //get new list vector to process
-                       if (SharedList != NULL) {
-                               order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
-                               count++;
+                       //get next line to process
+                       if (format == "sharedfile") {
+                               order = input->getSharedOrderVector();
                        }else {
-                               break;
+                               //you are using a list and a groupfile
+                               SharedList = input->getSharedListVector(); //get new list vector to process
+                               if (SharedList != NULL) {
+                                       order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
+                               }else {
+                                       break;
+                               }
                        }
-               
+                       
+                       count++;
                }
        
                for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }       
+               
+               //reset groups parameter
+               globaldata->Groups.clear();  globaldata->setGroups("");
+
                return 0;
        }
        catch(exception& e) {
@@ -103,3 +130,51 @@ int RareFactSharedCommand::execute(){
 
 
 //**********************************************************************************************************************
+
+void RareFactSharedCommand::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 RareFactSharedCommand class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the RareFactSharedCommand class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }               
+
+}
+/***********************************************************/
+