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

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index ac092083a53944207b926a6bb9d725a2249b571a..2591460a5ddd0bdcbe958bddc5ccf5ce9e644c7e 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -9,8 +9,53 @@
 
 #include "chimeracheckcommand.h"
 
+//**********************************************************************************************************************
+vector<string> ChimeraCheckCommand::getValidParameters(){      
+       try {
+               string AlignArray[] =  {"fasta","processors","increment","template","ksize","svg", "name","outputdir","inputdir" };
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraCheckCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraCheckCommand::getRequiredParameters(){   
+       try {
+               string AlignArray[] =  {"template","fasta"};
+               vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraCheckCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ChimeraCheckCommand::getRequiredFiles(){        
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraCheckCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+ChimeraCheckCommand::ChimeraCheckCommand(){    
+       try {
+               vector<string> tempOutNames;
+               outputTypes["chimera"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraCheckCommand", "ChimeraCheckCommand");
+               exit(1);
+       }
+}
 //***************************************************************************************************************
-
 ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
        try {
                abort = false;
@@ -34,6 +79,9 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       vector<string> tempOutNames;
+                       outputTypes["chimera"] = 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 = "";          }
@@ -75,6 +123,17 @@ ChimeraCheckCommand::ChimeraCheckCommand(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) { 
@@ -123,6 +182,17 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
                                                        nameFileNames[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(nameFileNames[i]);
+                                                       m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       nameFileNames[i] = tryPath;
+                                               }
+                                       }
+                                       
                                        in.close();
                                        
                                        if (ableToOpen == 1) { 
@@ -219,7 +289,7 @@ int ChimeraCheckCommand::execute(){
                        
                        if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it
                        string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
-                       outputNames.push_back(outputFileName);
+                       outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
                        
                #ifdef USE_MPI
                
@@ -246,7 +316,7 @@ int ChimeraCheckCommand::execute(){
                                MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
                                MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
                                
-                               if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); } delete chimera; return 0;  }
+                               if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0;  }
                                
                                if (pid == 0) { //you are the root process 
                                        MPIPos = m->setFilePosFasta(fastaFileNames[i], numSeqs); //fills MPIPos, returns numSeqs
@@ -266,7 +336,7 @@ int ChimeraCheckCommand::execute(){
                                        //align your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
                                        
-                                       if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); }   delete chimera; return 0;  }
+                                       if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  for (int j = 0; j < outputNames.size(); j++) {    remove(outputNames[j].c_str()); }   outputTypes.clear(); delete chimera; return 0;  }
                                        
                                        //wait on chidren
                                        for(int j = 1; j < processors; j++) { 
@@ -286,7 +356,7 @@ int ChimeraCheckCommand::execute(){
                                        //align your part
                                        driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
                                        
-                                       if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
+                                       if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  outputTypes.clear(); delete chimera; return 0;  }
                                        
                                        //tell parent you are done.
                                        char buf[5];
@@ -311,7 +381,7 @@ int ChimeraCheckCommand::execute(){
                                if(processors == 1){
                                        numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
                                        
-                                       if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); } for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear(); delete chimera; return 0; }
+                                       if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); } for (int j = 0; j < lines.size(); j++) {  delete lines[j];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
                                                                        
                                }else{
                                        processIDS.resize(0);
@@ -327,7 +397,7 @@ int ChimeraCheckCommand::execute(){
                                        }
                                        
                                        if (m->control_pressed) { 
-                                               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 j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear();
                                                delete chimera;
                                                return 0;
@@ -337,7 +407,7 @@ int ChimeraCheckCommand::execute(){
                        #else
                                numSeqs = driver(lines[0], outputFileName, fastaFileNames[i]);
                                
-                               if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear(); for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } delete chimera; return 0; }
+                               if (m->control_pressed) { for (int j = 0; j < lines.size(); j++) {  delete lines[j];  }  lines.clear(); for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } outputTypes.clear(); delete chimera; return 0; }
                        #endif
                #endif          
                        delete chimera;