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

[mothur.git] / clearcutcommand.cpp

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index c76de383fce839d31dd95e56bb7288a6df617d3c..0d2da75284049cd377d9cf209de5d0eb44b4034c 100644 (file)
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -10,7 +10,54 @@
 #include "clearcutcommand.h"
 #include "clearcut.h"
 
-
+//**********************************************************************************************************************
+vector<string> ClearcutCommand::getValidParameters(){  
+       try {
+               string AlignArray[] =  {"fasta","phylip","version","verbose","quiet","seed","norandom","shuffle","neighbor","expblen",
+                                                               "expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","outputdir","inputdir"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClearcutCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ClearcutCommand::ClearcutCommand(){    
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["tree"] = tempOutNames;
+               outputTypes["matrixout"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClearcutCommand", "ClearcutCommand");
+               exit(1);
+       }
+}//**********************************************************************************************************************
+vector<string> ClearcutCommand::getRequiredParameters(){       
+       try {
+               string Array[] =  {"fasta","phylip","or"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClearcutCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ClearcutCommand::getRequiredFiles(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClearcutCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 /**************************************************************************************/
 ClearcutCommand::ClearcutCommand(string option)  {     
        try {
@@ -36,6 +83,11 @@ ClearcutCommand::ClearcutCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["tree"] = tempOutNames;
+                       outputTypes["matrixout"] = 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);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -177,6 +229,7 @@ int ClearcutCommand::execute() {
                
                //prepare filename
                string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
+               outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName);
                
                vector<char*> cPara;
                
@@ -226,6 +279,8 @@ int ClearcutCommand::execute() {
                        char* temp = new char[tempMatrix.length()];
                        strcpy(temp, tempMatrix.c_str());
                        cPara.push_back(temp);
+                       outputNames.push_back((outputDir + matrixout));
+                       outputTypes["matrixout"].push_back((outputDir + matrixout));
                }
 
                if (ntrees != "1")              {  
@@ -252,8 +307,7 @@ int ClearcutCommand::execute() {
                if (!stdoutWanted) {    
                        m->mothurOutEndLine();
                        m->mothurOut("Output File Names: "); m->mothurOutEndLine();
-                       m->mothurOut(outputName); m->mothurOutEndLine();
-                       if (matrixout != "")    {  m->mothurOut(outputDir+matrixout); m->mothurOutEndLine();  }
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
                        m->mothurOutEndLine();
                }