finished wrapper for catchall

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 390f47f9fac6f255ce6e30fec4c7b2264e25cdad..2ea9377f8e559cc21e107724de4c30b0b1ba9c47 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -19,7 +19,54 @@
 #include "sharedmorisitahorn.h"
 #include "sharedbraycurtis.h"
 
-
+//**********************************************************************************************************************
+vector<string> MatrixOutputCommand::getValidParameters(){      
+       try {
+               string Array[] =  {"label","calc","groups","outputdir","inputdir", "output"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MatrixOutputCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+MatrixOutputCommand::MatrixOutputCommand(){    
+       try {
+               abort = true;
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["phylip"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> MatrixOutputCommand::getRequiredParameters(){   
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MatrixOutputCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> MatrixOutputCommand::getRequiredFiles(){        
+       try {
+               string Array[] =  {"shared"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "MatrixOutputCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 MatrixOutputCommand::MatrixOutputCommand(string option)  {
@@ -49,10 +96,14 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["phylip"] = tempOutNames;
+                       
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
-                               outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it       
                        }
                        
                        //make sure the user has already run the read.otu command
@@ -66,7 +117,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
@@ -82,7 +133,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
-                               splitAtDash(groups, Groups);
+                               m->splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                                
@@ -91,7 +142,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        else { 
                                 if (calc == "default")  {  calc = "jclass-thetayc";  }
                        }
-                       splitAtDash(calc, Estimators);
+                       m->splitAtDash(calc, Estimators);
 
                        if (abort == false) {
                        
@@ -199,7 +250,7 @@ int MatrixOutputCommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                
-                       if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
+                       if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
                
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
                                m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
@@ -209,7 +260,7 @@ int MatrixOutputCommand::execute(){
                                userLabels.erase(lookup[0]->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                string saveLabel = lookup[0]->getLabel();
                                
                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
@@ -232,7 +283,7 @@ int MatrixOutputCommand::execute(){
                        lookup = input->getSharedRAbundVectors();
                }
                
-               if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
+               if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -247,7 +298,7 @@ int MatrixOutputCommand::execute(){
                        }
                }
                
-               if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
+               if (m->control_pressed) { outputTypes.clear(); delete read; delete input; globaldata->ginput = NULL;  for (int i = 0; i < outputNames.size(); i++) {    remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
 
                //run last label if you need to
                if (needToRun == true)  {
@@ -259,7 +310,7 @@ int MatrixOutputCommand::execute(){
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } 
                }
                
-               if (m->control_pressed) { delete read; delete input; globaldata->ginput = NULL;  for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
+               if (m->control_pressed) { outputTypes.clear();  delete read; delete input; globaldata->ginput = NULL;  for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0;  }
                
                //reset groups parameter
                globaldata->Groups.clear();  
@@ -347,9 +398,9 @@ int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
                                                }
                                        }
                                        
-                                       exportFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
-                                       openOutputFile(exportFileName, out);
-                                       outputNames.push_back(exportFileName);
+                                       exportFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
+                                       m->openOutputFile(exportFileName, out);
+                                       outputNames.push_back(exportFileName); outputTypes["phylip"].push_back(exportFileName);
                                        
                                        printSims(out);
                                        out.close();