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

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 30136505f2a2136028c392c8e3e346ce878e045d..2dccd498f6dd2e5fdf82a9b12665aaf7a523ad90 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -10,8 +10,54 @@
 #include "chimerapintailcommand.h"
 #include "pintail.h"
 
+//**********************************************************************************************************************
+vector<string> ChimeraPintailCommand::getValidParameters(){    
+       try {
+               string AlignArray[] =  {"fasta","filter","processors","window" ,"increment","template","conservation","quantile","mask","outputdir","inputdir"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraPintailCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ChimeraPintailCommand::ChimeraPintailCommand(){        
+       try {
+               vector<string> tempOutNames;
+               outputTypes["chimera"] = tempOutNames;
+               outputTypes["accnos"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraPintailCommand", "ChimeraPintailCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraPintailCommand::getRequiredParameters(){ 
+       try {
+               string AlignArray[] =  {"template","fasta"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraPintailCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraPintailCommand::getRequiredFiles(){      
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraPintailCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //***************************************************************************************************************
-
 ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
        try {
                abort = false;
@@ -35,6 +81,10 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       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 
                        inputDir = validParameter.validFile(parameters, "inputdir", false);             
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -94,6 +144,16 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                                                        fastaFileNames[i] = tryPath;
                                                }
                                        }
+                                       
+                                       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) { 
@@ -140,7 +200,17 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                                                        maskfile = tryPath;
                                        }
                                }
-                                       in.close();
+                               
+                               if (ableToOpen == 1) {
+                                               if (m->getOutputDir() != "") { //default path is set
+                                                       string tryPath = m->getOutputDir() + m->getSimpleName(maskfile);
+                                                       m->mothurOut("Unable to open " + maskfile + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       maskfile = tryPath;
+                                               }
+                               }
+                               
+                               in.close();
                                        
                                if (ableToOpen == 1) { 
                                                m->mothurOut("Unable to open " + maskfile + "."); m->mothurOutEndLine(); 
@@ -332,7 +402,7 @@ int ChimeraPintailCommand::execute(){
                                MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
                                MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
                                
-                               if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
+                               if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {      remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
 
                                if (pid == 0) { //you are the root process 
                                                                
@@ -352,7 +422,7 @@ int ChimeraPintailCommand::execute(){
                                        //do your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
                                        
-                                       if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  for (int j = 0; j < outputNames.size(); j++) { remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
+                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
                                        
                                }else{ //you are a child process
                                        MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
@@ -367,7 +437,7 @@ int ChimeraPintailCommand::execute(){
                                        //do your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
                                        
-                                       if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
+                                       if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {      remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
                                }
                                
                                //close files 
@@ -388,7 +458,7 @@ int ChimeraPintailCommand::execute(){
                
                                        numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
                                        
-                                       if (m->control_pressed) { remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
+                                       if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
                                        
                                }else{
                                        processIDS.resize(0);
@@ -413,7 +483,7 @@ int ChimeraPintailCommand::execute(){
                                        if (m->control_pressed) { 
                                                remove(outputFileName.c_str()); 
                                                remove(accnosFileName.c_str());
-                                               for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } 
+                                               for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } outputTypes.clear();
                                                for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
                                                delete chimera;
                                                return 0;
@@ -423,7 +493,7 @@ int ChimeraPintailCommand::execute(){
                        #else
                                numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
                                
-                               if (m->control_pressed) { remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
+                               if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
                        #endif
                        
                #endif  
@@ -431,8 +501,8 @@ int ChimeraPintailCommand::execute(){
                        delete chimera;
                        for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
                        
-                       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);
                        
                        m->mothurOutEndLine();
                        m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();