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

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 60e90500866673aa8e643e024c3c60b840140dce..ce8aeb74dcd8a83b9a48b9923be219eb06edfa97 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -15,7 +15,54 @@
 #include "onegapignore.h"
 
 //**********************************************************************************************************************
-
+vector<string> DistanceCommand::getValidParameters(){  
+       try {
+               string Array[] =  {"fasta","oldfasta","column", "output", "calc", "countends", "cutoff", "processors", "outputdir","inputdir","compress"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DistanceCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+DistanceCommand::DistanceCommand(){    
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["phylip"] = tempOutNames;
+               outputTypes["column"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DistanceCommand", "DistanceCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> DistanceCommand::getRequiredParameters(){       
+       try {
+               string Array[] =  {"fasta"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChopSeqsCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> DistanceCommand::getRequiredFiles(){    
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "DistanceCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 DistanceCommand::DistanceCommand(string option) {
        try {
                abort = false;
@@ -41,6 +88,11 @@ DistanceCommand::DistanceCommand(string option) {
                                if (validParameter.isValidParameter(it2->first, myArray, it2->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["phylip"] = tempOutNames;
+                       outputTypes["column"] = 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 = "";          }
@@ -213,11 +265,12 @@ int DistanceCommand::execute(){
                                
                if (output == "lt") { //does the user want lower triangle phylip formatted file 
                        outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
-                       remove(outputFile.c_str());
+                       remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
                        
                        //output numSeqs to phylip formatted dist file
                }else if (output == "column") { //user wants column format
                        outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
+                       outputTypes["column"].push_back(outputFile);
                        
                        //so we don't accidentally overwrite
                        if (outputFile == column) { 
@@ -229,6 +282,7 @@ int DistanceCommand::execute(){
                }else { //assume square
                        outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
                        remove(outputFile.c_str());
+                       outputTypes["phylip"].push_back(outputFile);
                }
                
 
@@ -270,11 +324,11 @@ int DistanceCommand::execute(){
                                
                                driverMPI(start, end, outMPI, cutoff); 
                                
-                               if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
+                               if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
                        
                                //wait on chidren
                                for(int i = 1; i < processors; i++) { 
-                                       if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
+                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
                                        
                                        char buf[5];
                                        MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status); 
@@ -283,7 +337,7 @@ int DistanceCommand::execute(){
                                //do your part
                                driverMPI(start, end, outMPI, cutoff); 
                                
-                               if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
+                               if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
                        
                                char buf[5];
                                strcpy(buf, "done"); 
@@ -303,7 +357,7 @@ int DistanceCommand::execute(){
                                if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
                                else { driverMPI(start, end, outputFile, mySize, output); }
        
-                               if (m->control_pressed) {  delete distCalculator;  return 0; }
+                               if (m->control_pressed) {  outputTypes.clear();  delete distCalculator;  return 0; }
                                
                                int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
                                MPI_File outMPI;
@@ -322,7 +376,7 @@ int DistanceCommand::execute(){
                                for(int b = 1; b < processors; b++) { 
                                        unsigned long int fileSize;
                                        
-                                       if (m->control_pressed) { MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
+                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&outMPI);  delete distCalculator;  return 0; }
                                        
                                        MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status); 
                                        
@@ -398,7 +452,7 @@ int DistanceCommand::execute(){
        #endif
        
 #endif
-               if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
                
                #ifdef USE_MPI
                        MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
@@ -441,7 +495,7 @@ int DistanceCommand::execute(){
                        }
                #endif
                
-               if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear();  delete distCalculator; remove(outputFile.c_str()); return 0; }
                
                delete distCalculator;
                
@@ -456,7 +510,8 @@ int DistanceCommand::execute(){
                        m->mothurOut("Compressing..."); m->mothurOutEndLine();
                        m->mothurOut("(Replacing " + outputFile + " with " + outputFile + ".gz)"); m->mothurOutEndLine();
                        system(("gzip -v " + outputFile).c_str());
-               }
+                       outputNames.push_back(outputFile + ".gz");
+               }else { outputNames.push_back(outputFile); }
 
                return 0;