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

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index ccf5eebe68f42426f16f2465b68832beb413d2eb..b4af28a2990a44d69527d4c5cb7e5984d8b73033 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -27,10 +27,57 @@
 
 
 //**********************************************************************************************************************
-
+vector<string> AlignCommand::getValidParameters(){     
+       try {
+               string AlignArray[] =  {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> AlignCommand::getRequiredParameters(){  
+       try {
+               string AlignArray[] =  {"template","candidate"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> AlignCommand::getRequiredFiles(){       
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+AlignCommand::AlignCommand(){  
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["alignreport"] = tempOutNames;
+               outputTypes["accnos"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCommand", "AlignCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 AlignCommand::AlignCommand(string option)  {
        try {
-               
                abort = false;
        
                //allow user to run help
@@ -52,7 +99,13 @@ AlignCommand::AlignCommand(string option)  {
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
-
+                       
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+                       outputTypes["alignreport"] = tempOutNames;
+                       outputTypes["accnos"] = 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 = "";         }
                        
@@ -112,6 +165,17 @@ AlignCommand::AlignCommand(string option)  {
                                                        candidateFileNames[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(candidateFileNames[i]);
+                                                       m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       candidateFileNames[i] = tryPath;
+                                               }
+                                       }
+                                       
                                        in.close();                                     
 
                                        if (ableToOpen == 1) { 
@@ -165,7 +229,6 @@ AlignCommand::AlignCommand(string option)  {
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
 
 AlignCommand::~AlignCommand(){ 
@@ -225,10 +288,9 @@ int AlignCommand::execute(){
                        m->mothurOutEndLine();
                        alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
                }
-               vector<string> outputNames;
                
                for (int s = 0; s < candidateFileNames.size(); s++) {
-                       if (m->control_pressed) { return 0; }
+                       if (m->control_pressed) { outputTypes.clear(); return 0; }
                        
                        m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
                        
@@ -277,7 +339,7 @@ int AlignCommand::execute(){
                                MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
                                MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
                                
-                               if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
+                               if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
                                
                                if (pid == 0) { //you are the root process 
                                        
@@ -297,7 +359,7 @@ int AlignCommand::execute(){
                                        //align your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
                                        
-                                       if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
+                                       if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 
                                        for (int i = 1; i < processors; i++) {
                                                bool tempResult;
@@ -319,7 +381,7 @@ int AlignCommand::execute(){
                                        //align your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
                                        
-                                       if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); return 0; }
+                                       if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 
                                        MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD); 
                                }
@@ -357,7 +419,7 @@ int AlignCommand::execute(){
                        if(processors == 1){
                                numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
                                
-                               if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); return 0; }
+                               if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; }
                                
                                //delete accnos file if its blank else report to user
                                if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
@@ -408,12 +470,12 @@ int AlignCommand::execute(){
                                        m->mothurOutEndLine();
                                }else{ hasAccnos = false;  }
                                
-                               if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); return 0; }
+                               if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear(); return 0; }
                        }
        #else
                        numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
                        
-                       if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); return 0; }
+                       if (m->control_pressed) { remove(accnosFileName.c_str()); remove(alignFileName.c_str()); remove(reportFileName.c_str()); outputTypes.clear();  return 0; }
                        
                        //delete accnos file if its blank else report to user
                        if (m->isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
@@ -436,9 +498,9 @@ int AlignCommand::execute(){
                        if (pid == 0) { //only one process should output to screen
                #endif
 
-                       outputNames.push_back(alignFileName);
-                       outputNames.push_back(reportFileName);
-                       if (hasAccnos)  {       outputNames.push_back(accnosFileName);          }
+                       outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
+                       outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
+                       if (hasAccnos)  {       outputNames.push_back(accnosFileName);  outputTypes["accnos"].push_back(accnosFileName);  }
                        
                #ifdef USE_MPI
                        }