pat's differences before v.1.8

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 7156082f8b1b43228a62c6cf93abec9f2d900109..8acd696406c288303128a3c36aef3e6d816f2fbe 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -15,25 +15,49 @@
 AlignCheckCommand::AlignCheckCommand(string option){
        try {
                abort = false;
+               haderror = 0;
                
                //allow user to run help
                if(option == "help") { help(); abort = true; }
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta","map"};
+                       string Array[] =  {"fasta","map", "outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
                        
                        ValidParameters validParameter;
+                       map<string,string>::iterator it;
                        
                        //check to make sure all parameters are valid for command
-                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                       for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //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 = "";          }
+                       else {
+                               string path;
+                               it = parameters.find("fasta");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
+                               }
+                               
+                               it = parameters.find("map");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["map"] = inputDir + it->second;              }
+                               }
+                       }
+
                        //check for required parameters
                        mapfile = validParameter.validFile(parameters, "map", true);
                        if (mapfile == "not open") { abort = true; }
@@ -43,6 +67,12 @@ AlignCheckCommand::AlignCheckCommand(string option){
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") {  fastafile = "";  mothurOut("You must provide an fasta file."); mothurOutEndLine(); abort = true;  }       
                        
+                       //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 += hasPath(fastafile); //if user entered a file with a path then preserve it  
+                       }
+
                }
 
        }
@@ -82,7 +112,7 @@ int AlignCheckCommand::execute(){
                openInputFile(fastafile, in);
                
                ofstream out;
-               string outfile = getRootName(fastafile) + "align.check";
+               string outfile = outputDir + getRootName(getSimpleName(fastafile)) + "align.check";
                openOutputFile(outfile, out);
                
                out << "name" << '\t' << "pound" << '\t' << "dash" << '\t' << "plus" << '\t' << "equal" << '\t';
@@ -91,11 +121,15 @@ int AlignCheckCommand::execute(){
                
                while(!in.eof()){
                        
-                       Sequence seq(in);
-                       statData data = getStats(seq.getAligned());
-                       
-                       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;
+                       Sequence seq(in);  gobble(in);
+                       if (seq.getName() != "") {
+                               statData data = getStats(seq.getAligned());
+                               
+                               if (haderror == 1) { break; }
+                               
+                               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;
+                       }
                }
 
                in.close();
@@ -153,8 +187,11 @@ statData AlignCheckCommand::getStats(string sequence){
                statData data;
                sequence = "*" + sequence; // need to pad the sequence so we can index it by 1
                
-               int seqLength = sequence.length();
-               for(int i=1;i<seqLength;i++){
+               int length = sequence.length();
+               
+               if (length != seqLength) { mothurOut("your sequences are " + toString(length) + " long, but your map file only contains " + toString(seqLength) + " entries. please correct."); mothurOutEndLine(); haderror = 1; return data;  }
+               
+               for(int i=1;i<length;i++){
                        if(structMap[i] != 0){
                                if(sequence[i] == 'A'){
                                        if(sequence[structMap[i]] == 'T')               {       data.tilde++;   }