added consensus.seqs command

[mothur.git] / catchallcommand.cpp

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 7f740bd4642f5f385562141e017a37bbe5e89042..8f2841358dd4bbb91b69c2a530b6332b8fc2d131 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -26,8 +26,8 @@ vector<string> CatchAllCommand::getValidParameters(){
 CatchAllCommand::CatchAllCommand(){    
        try {
                //initialize outputTypes
-               
-               //need to determine outputFIles and types
+               vector<string> tempOutNames;
+               outputTypes["csv"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "CatchAllCommand", "CatchAllCommand");
@@ -83,10 +83,9 @@ CatchAllCommand::CatchAllCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
-                       
                        //initialize outputTypes
-                       //need to determine outputFIles and types
-                       
+                       vector<string> tempOutNames;
+                       outputTypes["csv"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -199,10 +198,10 @@ int CatchAllCommand::execute() {
                                
                                        filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                                
-                                       outputNames.push_back(filename + "_Analysis.csv");
-                                       outputNames.push_back(filename + "_BestModelsAnalysis.csv");
-                                       outputNames.push_back(filename + "_BestModelsFits.csv");
-                                       outputNames.push_back(filename + "_BubblePlot.csv");
+                                       outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
+                                       outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
+                                       outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
+                                       outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
                                
                                                                                
                                        if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read;  delete input; globaldata->ginput = NULL; delete sabund;  return 0; }
@@ -234,11 +233,11 @@ int CatchAllCommand::execute() {
                                
                                        filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                                
-                                       outputNames.push_back(filename + "_Analysis.csv");
-                                       outputNames.push_back(filename + "_BestModelsAnalysis.csv");
-                                       outputNames.push_back(filename + "_BestModelsFits.csv");
-                                       outputNames.push_back(filename + "_BubblePlot.csv");
-
+                                       outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
+                                       outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
+                                       outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
+                                       outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");
+                               
                                        if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {remove(outputNames[i].c_str()); } delete read;  delete input; globaldata->ginput = NULL; delete sabund;  return 0; }
 
                                        processedLabels.insert(sabund->getLabel());
@@ -289,11 +288,10 @@ int CatchAllCommand::execute() {
                        
                        filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra .
                        
-                       outputNames.push_back(filename + "_Analysis.csv");
-                       outputNames.push_back(filename + "_BestModelsAnalysis.csv");
-                       outputNames.push_back(filename + "_BestModelsFits.csv");
-                       outputNames.push_back(filename + "_BubblePlot.csv");
-                       
+                       outputNames.push_back(filename + "_Analysis.csv"); outputTypes["csv"].push_back(filename + "_Analysis.csv");
+                       outputNames.push_back(filename + "_BestModelsAnalysis.csv"); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis.csv");
+                       outputNames.push_back(filename + "_BestModelsFits.csv"); outputTypes["csv"].push_back(filename + "_BestModelsFits.csv");
+                       outputNames.push_back(filename + "_BubblePlot.csv"); outputTypes["csv"].push_back(filename + "_BubblePlot.csv");                        
                        
                        delete sabund;
                }