added namefile to align.check and added seqs from namefile to optimizing piece of...

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index c9002cab4a458c1ef9fbb3a2acb85706e01513dc..2b474c14d22389778078d6012819fd1e9f0fc7e7 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -13,7 +13,7 @@
 //**********************************************************************************************************************
 vector<string> AlignCheckCommand::getValidParameters(){        
        try {
-               string Array[] =  {"fasta","map", "outputdir","inputdir"};
+               string Array[] =  {"fasta", "name","map", "outputdir","inputdir"};
                vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                return myArray;
        }
@@ -69,7 +69,7 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","map", "outputdir","inputdir"};
+                       string Array[] =  {"fasta","name","map", "outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -107,6 +107,14 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["map"] = inputDir + it->second;              }
                                }
+                               
+                               it = parameters.find("name");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = m->hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["name"] = inputDir + it->second;             }
+                               }
                        }
 
                        //check for required parameters
@@ -118,6 +126,10 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  m->mothurOut("You must provide an fasta file."); m->mothurOutEndLine(); abort = true;  } 
                        
+                       namefile = validParameter.validFile(parameters, "name", true);
+                       if (namefile == "not open") { namefile = ""; abort = true; }
+                       else if (namefile == "not found") { namefile = "";  }   
+                       
                        //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 = ""; 
@@ -159,6 +171,10 @@ int AlignCheckCommand::execute(){
                //get secondary structure info.
                readMap();
                
+               if (namefile != "") { nameMap = m->readNames(namefile); }
+               
+               if (m->control_pressed) { return 0; }
+               
                ifstream in;
                m->openInputFile(fastafile, in);
                
@@ -166,8 +182,9 @@ int AlignCheckCommand::execute(){
                string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "align.check";
                m->openOutputFile(outfile, out);
                
+                               
                out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
-               out << "loop" << '\t' << "tilde" << '\t' << "total" << endl;
+               out << "loop" << '\t' << "tilde" << '\t' << "total"  << '\t' << "numseqs" << endl;
 
                
                while(!in.eof()){
@@ -179,8 +196,17 @@ int AlignCheckCommand::execute(){
                                
                                if (haderror == 1) { break; }
                                
+                               int num = 1;
+                               if (namefile != "") {
+                                       //make sure this sequence is in the namefile, else error 
+                                       map<string, int>::iterator it = nameMap.find(seq.getName());
+                                       
+                                       if (it == nameMap.end()) { cout << "[ERROR]: " << seq.getName() << " is not in your namefile, please correct." << endl; m->control_pressed = true; }
+                                       else { num = it->second; }
+                               }
+                               
                                out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
-                               out << data.loop << '\t' << data.tilde << '\t' << data.total << endl;
+                               out << data.loop << '\t' << data.tilde << '\t' << data.total << '\t' << num << endl;
                        }
                }
 
@@ -305,6 +331,4 @@ statData AlignCheckCommand::getStats(string sequence){
                exit(1);
        }
 }
-
-
 //**********************************************************************************************************************