added zscore method to normalize.shared

[mothur.git] / chimerabellerophoncommand.cpp

diff --git a/chimerabellerophoncommand.cpp b/chimerabellerophoncommand.cpp
index a504d0b496dec5b23795b546c70b573bc6c0c2ca..5d7d6d452b2c741ad764623557f0a0d31895ba0e 100644 (file)
--- a/chimerabellerophoncommand.cpp
+++ b/chimerabellerophoncommand.cpp
@@ -10,8 +10,57 @@
 #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 {
+               abort = true;
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["chimera"] = tempOutNames;
+               outputTypes["accnos"] = tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ChimeraBellerophonCommand", "ChimeraBellerophonCommand");
+               exit(1);
+       }
+}
 //***************************************************************************************************************
-
 ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
        try {
                abort = false;
@@ -35,6 +84,12 @@ 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;
+                       outputTypes["fasta"] = 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 = "";          }
@@ -62,10 +117,25 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                                                if (m->getDefaultPath() != "") { //default path is set
                                                        string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
                                                        m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-                                                       ableToOpen = m->openInputFile(tryPath, in, "noerror");
+                                                       ifstream in2;
+                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                       in2.close();
                                                        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();
+                                                       ifstream in2;
+                                                       ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+                                                       in2.close();
+                                                       fastaFileNames[i] = tryPath;
+                                               }
+                                       }
+                                       
                                        in.close();
 
                                        if (ableToOpen == 1) { 
@@ -82,10 +152,7 @@ ChimeraBellerophonCommand::ChimeraBellerophonCommand(string option)  {
                        }
                        
                        //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 = ""; 
-                               outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it       
-                       }
+                       outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 
                        string temp;
                        temp = validParameter.validFile(parameters, "filter", false);                   if (temp == "not found") { temp = "F"; }
@@ -152,13 +219,14 @@ int ChimeraBellerophonCommand::execute(){
                        int start = time(NULL); 
                        
                        chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);     
-                                       
+                       
+                       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])) +  "bellerophon.chimeras";
                        string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "bellerophon.accnos";
                        
                        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;
@@ -175,7 +243,7 @@ int ChimeraBellerophonCommand::execute(){
                        MPI_File_open(MPI_COMM_WORLD, FileName, outMode, MPI_INFO_NULL, &outMPI);  //comm, filename, mode, info, filepointer
                        MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
        
-                       numSeqs = chimera->print(outMPI, outMPIAccnos);
+                       numSeqs = chimera->print(outMPI, outMPIAccnos, "");
                        
                        MPI_File_close(&outMPI);
                        MPI_File_close(&outMPIAccnos);
@@ -188,18 +256,18 @@ int ChimeraBellerophonCommand::execute(){
                        ofstream out2;
                        m->openOutputFile(accnosFileName, out2);
                        
-                       numSeqs = chimera->print(out, out2);
+                       numSeqs = chimera->print(out, out2, "");
                        out.close();
                        out2.close(); 
                        
                #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;
                }