added pipeline commands which involved change to command factory and command class...

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 51e3c319f377b893224e1e2f2d7093b3665c0d8a..4a4e55e2c01788141dc6d1173e3e14ed768d1fec 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -10,6 +10,54 @@
 
 #include "pcacommand.h"
 
+//**********************************************************************************************************************
+vector<string> PCACommand::getValidParameters(){       
+       try {
+               string Array[] =  {"phylip", "outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PCACommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+PCACommand::PCACommand(){      
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["pcoa"] = tempOutNames;
+               outputTypes["loadings"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PCACommand", "PCACommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> PCACommand::getRequiredParameters(){    
+       try {
+               string Array[] =  {"phylip"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PCACommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> PCACommand::getRequiredFiles(){ 
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "PCACommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 PCACommand::PCACommand(string option)  {
@@ -47,7 +95,12 @@ PCACommand::PCACommand(string option)  {
                                        if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
                                }
                        }
-
+                       
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["pcoa"] = tempOutNames;
+                       outputTypes["loadings"] = tempOutNames;
+                       
                        //required parameters
                        phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
@@ -516,11 +569,13 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
                pcaData.setf(ios::fixed, ios::floatfield);
                pcaData.setf(ios::showpoint);   
                outputNames.push_back(fnameRoot+"pcoa");
+               outputTypes["pcoa"].push_back(fnameRoot+"pcoa");
                
                ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
                pcaLoadings.setf(ios::fixed, ios::floatfield);
                pcaLoadings.setf(ios::showpoint);
-               outputNames.push_back(fnameRoot+"pcoa.loadings");       
+               outputNames.push_back(fnameRoot+"pcoa.loadings");
+               outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings");   
                
                pcaLoadings << "axis\tloading\n";
                for(int i=0;i<rank;i++){