fixed clearcut version bug, added group count output to get.groups and remove.groups

[mothur.git] / getsharedotucommand.cpp

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 492195d702286af6cc82d919311aae7a59260596..4fe711e568728f0fa1af026bec4c21af822732cd 100644 (file)
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -9,19 +9,68 @@
 
 #include "getsharedotucommand.h"
 
-//**********************************************************************************************************************
 
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getValidParameters(){      
+       try {
+               string Array[] =  {"label","unique","shared","fasta","list","group","output","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSharedOTUCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+GetSharedOTUCommand::GetSharedOTUCommand(){    
+       try {
+               abort = true; calledHelp = true; 
+               vector<string> tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+               outputTypes["accnos"] = tempOutNames;
+               outputTypes["sharedseqs"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getRequiredParameters(){   
+       try {
+               string Array[] =  {"list","group"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSharedOTUCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getRequiredFiles(){        
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetSharedOTUCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
        try {
        
                globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                unique = true;
                allLines = 1;
                labels.clear();
                
                //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
@@ -39,6 +88,12 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["fasta"] = tempOutNames;
+                       outputTypes["accnos"] = tempOutNames;
+                       outputTypes["sharedseqs"] = tempOutNames;
+                       
                        //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 = "";         }
                        
@@ -141,7 +196,7 @@ void GetSharedOTUCommand::help(){
                m->mothurOut("The output parameter allows you to output the list of names without the group and bin number added. \n");
                m->mothurOut("With this option you can use the names file as an input in get.seqs and remove.seqs commands. To do this enter output=accnos. \n");
                m->mothurOut("The get.sharedseqs command outputs a .names file for each distance level containing a list of sequences in the OTUs shared by the groups specified.\n");
-               m->mothurOut("The get.sharedseqs command should be in the following format: get.sabund(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n");
+               m->mothurOut("The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n");
                m->mothurOut("Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n");
                m->mothurOut("The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n");
                m->mothurOut("The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n");
@@ -162,7 +217,7 @@ GetSharedOTUCommand::~GetSharedOTUCommand(){}
 int GetSharedOTUCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                groupMap = new GroupMap(groupfile);
                int error = groupMap->readMap();
@@ -191,7 +246,7 @@ int GetSharedOTUCommand::execute(){
                        m->openInputFile(fastafile, inFasta);
                        
                        while(!inFasta.eof()) {
-                               if (m->control_pressed) { inFasta.close(); delete groupMap; return 0; }
+                               if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; }
                                
                                Sequence seq(inFasta); m->gobble(inFasta);
                                if (seq.getName() != "") {  seqs.push_back(seq);   }
@@ -214,7 +269,7 @@ int GetSharedOTUCommand::execute(){
                        
                        if (m->control_pressed) { 
                                if (lastlist != NULL) {         delete lastlist;        }
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }  
+                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }  outputTypes.clear();
                                delete groupMap; return 0;
                        }
                        
@@ -277,7 +332,21 @@ int GetSharedOTUCommand::execute(){
                
                if (lastlist != NULL) {         delete lastlist;        }
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); }  delete groupMap; return 0; } 
+               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); }  delete groupMap; return 0; } 
+               
+               //set fasta file as new current fastafile
+               string current = "";
+               itTypes = outputTypes.find("fasta");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+               }
+               
+               if (output == "accnos") {
+                       itTypes = outputTypes.find("accnos");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+                       }
+               }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -406,6 +475,8 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                }else { 
                        m->mothurOut("\t" + toString(num)); m->mothurOutEndLine(); 
                        outputNames.push_back(outputFileNames);
+                       if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
+                       else { outputTypes["accnos"].push_back(outputFileNames); }
                }
                
                //if fasta file provided output new fasta file
@@ -414,7 +485,7 @@ int GetSharedOTUCommand::process(ListVector* shared) {
                        string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
                        ofstream outFasta;
                        m->openOutputFile(outputFileFasta, outFasta);
-                       outputNames.push_back(outputFileFasta);
+                       outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
                        
                        for (int k = 0; k < seqs.size(); k++) {
                                if (m->control_pressed) { outFasta.close(); return 0; }