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

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index e23a0ac6a431ad14cdab21fb0bfa4276f4afd8c6..36e0f609ca67bd3cd37e7c0d33a98e88cee65e6f 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -10,6 +10,53 @@
 #include "secondarystructurecommand.h"
 #include "sequence.hpp"
 
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getValidParameters(){        
+       try {
+               string Array[] =  {"fasta","map", "outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCheckCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+AlignCheckCommand::AlignCheckCommand(){        
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["aligncheck"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredParameters(){     
+       try {
+               string Array[] =  {"fasta","map"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCheckCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> AlignCheckCommand::getRequiredFiles(){  
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AlignCheckCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 
 AlignCheckCommand::AlignCheckCommand(string option)  {
@@ -36,6 +83,10 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["aligncheck"] = 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 = "";          }
@@ -44,7 +95,7 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                                it = parameters.find("fasta");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->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;            }
                                }
@@ -52,7 +103,7 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                                it = parameters.find("map");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->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;              }
                                }
@@ -70,7 +121,7 @@ AlignCheckCommand::AlignCheckCommand(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 += hasPath(fastafile); //if user entered a file with a path then preserve it  
+                               outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it       
                        }
 
                }
@@ -109,19 +160,20 @@ int AlignCheckCommand::execute(){
                readMap();
                
                ifstream in;
-               openInputFile(fastafile, in);
+               m->openInputFile(fastafile, in);
                
                ofstream out;
-               string outfile = outputDir + getRootName(getSimpleName(fastafile)) + "align.check";
-               openOutputFile(outfile, out);
+               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;
 
                
                while(!in.eof()){
+                       if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
                        
-                       Sequence seq(in);  gobble(in);
+                       Sequence seq(in);  m->gobble(in);
                        if (seq.getName() != "") {
                                statData data = getStats(seq.getAligned());
                                
@@ -135,9 +187,11 @@ int AlignCheckCommand::execute(){
                in.close();
                out.close();
                
+               if (m->control_pressed) {  remove(outfile.c_str()); return 0; }
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-               m->mothurOut(outfile); m->mothurOutEndLine();   
+               m->mothurOut(outfile); m->mothurOutEndLine();   outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
                m->mothurOutEndLine();
                
                return 0;               
@@ -155,13 +209,13 @@ void AlignCheckCommand::readMap(){
                structMap.resize(1, 0);
                ifstream in;
                
-               openInputFile(mapfile, in);
+               m->openInputFile(mapfile, in);
                
                while(!in.eof()){
                        int position;
                        in >> position;
                        structMap.push_back(position);  
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();