added save parameter to align.seqs, chimera commands, classify.seqs, and seq.error...

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 482bf7b5c2a67e57aaefc4cf4fc93c76a2b78611..66fe65d2318642610d77e1325c96c1fb2135ac1f 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -10,6 +10,7 @@
 #include "chimerapintailcommand.h"
 #include "pintail.h"
 
+
 //**********************************************************************************************************************
 vector<string> ChimeraPintailCommand::setParameters(){ 
        try {
@@ -24,7 +25,8 @@ vector<string> ChimeraPintailCommand::setParameters(){
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-               
+               CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
                return myArray;
@@ -50,6 +52,7 @@ string ChimeraPintailCommand::getHelpString(){
 #ifdef USE_MPI
                helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
 #endif
+               helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
                helpString += "The window parameter allows you to specify the window size for searching for chimeras, default=300. \n";
                helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=25.\n";
                helpString += "The conservation parameter allows you to enter a frequency file containing the highest bases frequency at each place in the alignment.\n";
@@ -83,6 +86,7 @@ ChimeraPintailCommand::ChimeraPintailCommand(){
 ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
        try {
                abort = false; calledHelp = false;   
+               rdb = ReferenceDB::getInstance();
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
@@ -229,6 +233,28 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
                        temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "25"; }
                        convert(temp, increment);
                        
+                       temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
+                       save = m->isTrue(temp); 
+                       rdb->save = save; 
+                       if (save) { //clear out old references
+                               rdb->clearMemory();     
+                       }
+                       
+                       //this has to go after save so that if the user sets save=t and provides no reference we abort
+                       templatefile = validParameter.validFile(parameters, "reference", true);
+                       if (templatefile == "not found") { 
+                               //check for saved reference sequences
+                               if (rdb->referenceSeqs.size() != 0) {
+                                       templatefile = "saved";
+                               }else {
+                                       m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required."); 
+                                       m->mothurOutEndLine();
+                                       abort = true; 
+                               }
+                       }else if (templatefile == "not open") { abort = true; } 
+                       else {  if (save) {     rdb->setSavedReference(templatefile);   }       }
+                       
+                       
                        maskfile = validParameter.validFile(parameters, "mask", false);
                        if (maskfile == "not found") { maskfile = "";  }        
                        else if (maskfile != "default")  { 
@@ -274,10 +300,6 @@ ChimeraPintailCommand::ChimeraPintailCommand(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 = ""; }
                
-                       templatefile = validParameter.validFile(parameters, "reference", true);
-                       if (templatefile == "not open") { abort = true; }
-                       else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.pintail command."); m->mothurOutEndLine(); abort = true;  }
-                       
                        consfile = validParameter.validFile(parameters, "conservation", true);
                        if (consfile == "not open") { abort = true; }
                        else if (consfile == "not found") { 
@@ -329,15 +351,18 @@ int ChimeraPintailCommand::execute(){
                        if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine();  }
                        
                        //check for quantile to save the time
+                       string baseName = templatefile;
+                       if (templatefile == "saved") { baseName = rdb->getSavedReference(); }
+                       
                        string tempQuan = "";
                        if ((!filter) && (maskfile == "")) {
-                               tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.quan";
+                               tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.quan";
                        }else if ((!filter) && (maskfile != "")) { 
-                               tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.masked.quan";
+                               tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.masked.quan";
                        }else if ((filter) && (maskfile != "")) { 
-                               tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
+                               tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
                        }else if ((filter) && (maskfile == "")) { 
-                               tempQuan = inputDir + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
+                               tempQuan = inputDir + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
                        }
                        
                        ifstream FileTest(tempQuan.c_str());
@@ -350,13 +375,13 @@ int ChimeraPintailCommand::execute(){
                                string tryPath = m->getDefaultPath();
                                string tempQuan = "";
                                if ((!filter) && (maskfile == "")) {
-                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.quan";
+                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.quan";
                                }else if ((!filter) && (maskfile != "")) { 
-                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.masked.quan";
+                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.masked.quan";
                                }else if ((filter) && (maskfile != "")) { 
-                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
+                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "masked.quan";
                                }else if ((filter) && (maskfile == "")) { 
-                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(templatefile)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
+                                       tempQuan = tryPath + m->getRootName(m->getSimpleName(baseName)) + "pintail.filtered." + m->getSimpleName(m->getRootName(fastaFileNames[s])) + "quan";
                                }
                                
                                ifstream FileTest2(tempQuan.c_str());