removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index ece2de0fee12364effae1b23065ef30903c22485..fec93e6e9f5f94414a392a1220b86153999b1f9d 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -11,49 +11,49 @@
 #include "sequence.hpp"
 
 //**********************************************************************************************************************
-vector<string> AlignCheckCommand::getValidParameters(){        
+vector<string> AlignCheckCommand::setParameters(){     
        try {
-               string Array[] =  {"fasta", "name","map", "outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
+               CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pmap);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               
+               vector<string> myArray;
+               for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
                return myArray;
        }
        catch(exception& e) {
-               m->errorOut(e, "AlignCheckCommand", "getValidParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-AlignCheckCommand::AlignCheckCommand(){        
-       try {
-               abort = true; calledHelp = true; 
-               vector<string> tempOutNames;
-               outputTypes["aligncheck"] = tempOutNames;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
+               m->errorOut(e, "AlignCheckCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> AlignCheckCommand::getRequiredParameters(){     
+string AlignCheckCommand::getHelpString(){     
        try {
-               string Array[] =  {"fasta","map"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
+               string helpString = "";
+               helpString += "The align.check command reads a fasta file and map file.\n";
+               helpString += "It outputs a file containing the secondary structure matches in the .align.check file.\n";
+               helpString += "The align.check command parameters are fasta and map, both are required.\n";
+               helpString += "The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n";
+               helpString += "Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "AlignCheckCommand", "getRequiredParameters");
+               m->errorOut(e, "AlignCheckCommand", "getHelpString");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> AlignCheckCommand::getRequiredFiles(){  
+AlignCheckCommand::AlignCheckCommand(){        
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["aligncheck"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "AlignCheckCommand", "getRequiredFiles");
+               m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
                exit(1);
        }
 }
@@ -68,9 +68,7 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"fasta","name","map", "outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -124,7 +122,11 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  m->mothurOut("You must provide an fasta file."); m->mothurOutEndLine(); abort = true;  } 
+                       else if (fastafile == "not found") {                            
+                               fastafile = m->getFastaFile(); 
+                               if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+                               else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
+                       }       
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { namefile = ""; abort = true; }
@@ -140,27 +142,10 @@ AlignCheckCommand::AlignCheckCommand(string option)  {
 
        }
        catch(exception& e) {
-               m->errorOut(e, "AlignCheckCommand", "RemoveSeqsCommand");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-
-void AlignCheckCommand::help(){
-       try {
-               m->mothurOut("The align.check command reads a fasta file and map file.\n");
-               m->mothurOut("It outputs a file containing the secondary structure matches in the .align.check file.\n");
-               m->mothurOut("The align.check command parameters are fasta and map, both are required.\n");
-               m->mothurOut("The align.check command should be in the following format: align.check(fasta=yourFasta, map=yourMap).\n");
-               m->mothurOut("Example align.check(map=silva.ss.map, fasta=amazon.fasta).\n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
-       }
-       catch(exception& e) {
-               m->errorOut(e, "AlignCheckCommand", "help");
+               m->errorOut(e, "AlignCheckCommand", "AlignCheckCommand");
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
 
 int AlignCheckCommand::execute(){
@@ -209,7 +194,7 @@ int AlignCheckCommand::execute(){
                                        //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; }
+                                       if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + seq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
                                        else { num = it->second; }
                                }