added getCommandInfoCommand for gui

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index b4b467460693ef04b07a99392bf95735690a38e1..ebfd07565bcca4458d7ce51b4911d5cc659e711e 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -11,51 +11,55 @@
 #include "sequence.hpp"
 #include "listvector.hpp"
 
+
 //**********************************************************************************************************************
-vector<string> ListSeqsCommand::getValidParameters(){  
+vector<string> ListSeqsCommand::setParameters(){       
        try {
-               string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pfasta);
+               CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pname);
+               CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pgroup);
+               CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(plist);
+               CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
+               CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(palignreport);
+               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, "ListSeqsCommand", "getValidParameters");
-               exit(1);
-       }
-}
-//**********************************************************************************************************************
-ListSeqsCommand::ListSeqsCommand(){    
-       try {
-               abort = true;
-               //initialize outputTypes
-               vector<string> tempOutNames;
-               outputTypes["accnos"] = tempOutNames;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
+               m->errorOut(e, "ListSeqsCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-vector<string> ListSeqsCommand::getRequiredParameters(){       
+string ListSeqsCommand::getHelpString(){       
        try {
-               string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","or"};
-               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-               return myArray;
+               string helpString = "";
+               helpString += "The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n";
+               helpString += "The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport.  You must provide one of these parameters.\n";
+               helpString += "The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n";
+               helpString += "Example list.seqs(fasta=amazon.fasta).\n";
+               helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
+               return helpString;
        }
        catch(exception& e) {
-               m->errorOut(e, "ListSeqsCommand", "getRequiredParameters");
+               m->errorOut(e, "ListSeqsCommand", "getHelpString");
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
-vector<string> ListSeqsCommand::getRequiredFiles(){    
+ListSeqsCommand::ListSeqsCommand(){    
        try {
-               vector<string> myArray;
-               return myArray;
+               abort = true; calledHelp = true; 
+               setParameters();
+               vector<string> tempOutNames;
+               outputTypes["accnos"] = tempOutNames;
        }
        catch(exception& e) {
-               m->errorOut(e, "ListSeqsCommand", "getRequiredFiles");
+               m->errorOut(e, "ListSeqsCommand", "ListSeqsCommand");
                exit(1);
        }
 }
@@ -63,15 +67,13 @@ vector<string> ListSeqsCommand::getRequiredFiles(){
 
 ListSeqsCommand::ListSeqsCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
-                       //valid paramters for this command
-                       string Array[] =  {"fasta","name", "group", "alignreport","list","taxonomy","outputdir","inputdir"};
-                       vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+                       vector<string> myArray = setParameters();
                        
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
@@ -187,26 +189,10 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
 }
 //**********************************************************************************************************************
 
-void ListSeqsCommand::help(){
-       try {
-               m->mothurOut("The list.seqs command reads a fasta, name, group, list, taxonomy or alignreport file and outputs a .accnos file containing sequence names.\n");
-               m->mothurOut("The list.seqs command parameters are fasta, name, group, list, taxonomy and alignreport.  You must provide one of these parameters.\n");
-               m->mothurOut("The list.seqs command should be in the following format: list.seqs(fasta=yourFasta).\n");
-               m->mothurOut("Example list.seqs(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, "ListSeqsCommand", "help");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-
 int ListSeqsCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                //read functions fill names vector
                if (fastafile != "")            {       inputFileName = fastafile;      readFasta();    }
@@ -227,6 +213,7 @@ int ListSeqsCommand::execute(){
 
                ofstream out;
                m->openOutputFile(outputFileName, out);
+               outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
                
                //output to .accnos file
                for (int i = 0; i < names.size(); i++) {
@@ -238,12 +225,21 @@ int ListSeqsCommand::execute(){
                out.close();
                
                if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0; }
-
+               
+               m->setAccnosFile(outputFileName);
+               
                m->mothurOutEndLine();
                m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-               m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
+               m->mothurOut(outputFileName); m->mothurOutEndLine();    
                m->mothurOutEndLine();
                
+               //set accnos file as new current accnosfile
+               string current = "";
+               itTypes = outputTypes.find("accnos");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+               }
+               
                return 0;               
        }
 
@@ -260,7 +256,7 @@ int ListSeqsCommand::readFasta(){
                ifstream in;
                m->openInputFile(fastafile, in);
                string name;
-       
+               
                while(!in.eof()){
                        
                        if (m->control_pressed) { in.close(); return 0; }
@@ -367,7 +363,7 @@ int ListSeqsCommand::readGroup(){
                        
                        if (m->control_pressed) { in.close(); return 0; }
                        
-                       in >> name;                             //read from first column
+                       in >> name;     m->gobble(in);                  //read from first column
                        in >> group;                    //read from second column
                        
                        names.push_back(name);
@@ -445,6 +441,7 @@ int ListSeqsCommand::readTax(){
                        names.push_back(firstCol);
                        
                        m->gobble(in);
+                       
                }
                in.close();