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

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index 5972c62f028100b71b9007785af7c9d4600aaeb4..6d0a116ac4d0d5d1bb2b8cf97f1ea5a1b5126fef 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -10,8 +10,55 @@
 #include "chimerabellerophoncommand.h"
 #include "bellerophon.h"
 
+//**********************************************************************************************************************
+vector<string> ChimeraBellerophonCommand::getValidParameters(){        
+       try {
+               string AlignArray[] =  {"fasta","filter","correction","processors","window","increment","outputdir","inputdir"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraBellerophonCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraBellerophonCommand::getRequiredParameters(){     
+       try {
+               string AlignArray[] =  {"fasta"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraBellerophonCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraBellerophonCommand::getRequiredFiles(){  
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraBellerophonCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ChimeraBellerophonCommand::ChimeraBellerophonCommand(){        
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["chimera"] = tempOutNames;
+               outputTypes["accnos"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
+               exit(1);
+       }
+}
 //***************************************************************************************************************
-
 ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
        try {
                abort = false;
@@ -35,6 +82,11 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["chimera"] = tempOutNames;
+                       outputTypes["accnos"] = 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 = "";          }
@@ -66,6 +118,17 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                                                        fastaFileNames[i] = tryPath;
                                                }
                                        }
+                                       
+                                       //if you can't open it, try default location
+                                       if (ableToOpen == 1) {
+                                               if (m->getOutputDir() != "") { //default path is set
+                                                       string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       fastaFileNames[i] = tryPath;
+                                               }
+                                       }
+                                       
                                        in.close();
 
                                        if (ableToOpen == 1) { 
@@ -156,7 +219,7 @@ int ChimeraBellerophonCommand::execute(){
                        
                        chimera->getChimeras();
                        
-                       if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0;     }
+                       if (m->control_pressed) { delete chimera; for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } outputTypes.clear(); return 0;        }
                        
                #ifdef USE_MPI
                        MPI_File outMPI;
@@ -192,12 +255,12 @@ int ChimeraBellerophonCommand::execute(){
                        
                #endif
                        
-                       if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } delete chimera;       return 0;       }
+                       if (m->control_pressed) { remove(accnosFileName.c_str()); remove(outputFileName.c_str()); for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } outputTypes.clear(); delete chimera;  return 0;       }
                        
                        m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
                        
-                       outputNames.push_back(outputFileName);
-                       outputNames.push_back(accnosFileName);
+                       outputNames.push_back(outputFileName);  outputTypes["chimera"].push_back(outputFileName);
+                       outputNames.push_back(accnosFileName);  outputTypes["accnos"].push_back(accnosFileName);
                        
                        delete chimera;
                }