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

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index 17809631f9e9cc590e510a33ec5528e493a14d3c..607009129b3c13ec8b7adfafd66e4d3fb006c486 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -9,6 +9,57 @@
 
 #include "splitabundcommand.h"
 
+//**********************************************************************************************************************
+vector<string> SplitAbundCommand::getValidParameters(){        
+       try {
+               string Array[] =  {"name","group","list","label","accnos","groups","fasta","cutoff","outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SplitAbundCommand", "getValidParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+SplitAbundCommand::SplitAbundCommand(){        
+       try {
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["list"] = tempOutNames;
+               outputTypes["name"] = tempOutNames;
+               outputTypes["accnos"] = tempOutNames;
+               outputTypes["group"] = tempOutNames;
+               outputTypes["fasta"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SplitAbundCommand", "SplitAbundCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SplitAbundCommand::getRequiredParameters(){     
+       try {
+               string Array[] =  {"fasta","list","name","or"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SplitAbundCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> SplitAbundCommand::getRequiredFiles(){  
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "SplitAbundCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 SplitAbundCommand::SplitAbundCommand(string option)  {
        try {
@@ -33,7 +84,15 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
-                                               
+                       
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["list"] = tempOutNames;
+                       outputTypes["name"] = tempOutNames;
+                       outputTypes["accnos"] = tempOutNames;
+                       outputTypes["group"] = tempOutNames;
+                       outputTypes["fasta"] = 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 = "";          }
@@ -186,6 +245,8 @@ int SplitAbundCommand::execute(){
                                
                                outputNames.push_back((fileroot + "rare.list"));
                                outputNames.push_back((fileroot + "abund.list"));
+                               outputTypes["list"].push_back((fileroot + "rare.list"));
+                               outputTypes["list"].push_back((fileroot + "abund.list"));
                        }else{
                                for (int i=0; i<Groups.size(); i++) {
                                        remove((fileroot + Groups[i] + ".rare.list").c_str());
@@ -193,6 +254,8 @@ int SplitAbundCommand::execute(){
                                        
                                        outputNames.push_back((fileroot + Groups[i] + ".rare.list"));
                                        outputNames.push_back((fileroot + Groups[i] + ".abund.list"));
+                                       outputTypes["list"].push_back((fileroot + Groups[i] + ".rare.list"));
+                                       outputTypes["list"].push_back((fileroot + Groups[i] + ".abund.list"));
                                }
                        }
                        
@@ -572,11 +635,11 @@ int SplitAbundCommand::writeNames() { //namefile
                        
                        string rare = outputDir + m->getRootName(m->getSimpleName(namefile))  + "rare.names";
                        m->openOutputFile(rare, rout);
-                       outputNames.push_back(rare);
+                       outputNames.push_back(rare); outputTypes["name"].push_back(rare);
                        
                        string abund = outputDir + m->getRootName(m->getSimpleName(namefile))  + "abund.names";
                        m->openOutputFile(abund, aout);
-                       outputNames.push_back(abund);
+                       outputNames.push_back(abund); outputTypes["name"].push_back(abund);
                        
                        if (rareNames.size() != 0) {
                                for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
@@ -642,7 +705,7 @@ int SplitAbundCommand::writeNames() { //namefile
                        
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + it3->first + ".names");  
+                               outputNames.push_back(fileroot + it3->first + ".names");  outputTypes["name"].push_back(fileroot + it3->first + ".names");
                                delete it3->second;
                        }
                }
@@ -669,7 +732,7 @@ int SplitAbundCommand::writeAccnos(string tag) {
                        
                        string rare = outputDir + m->getRootName(m->getSimpleName(inputFile))  + tag + "rare.accnos";
                        m->openOutputFile(rare, rout);
-                       outputNames.push_back(rare);
+                       outputNames.push_back(rare); outputTypes["accnos"].push_back(rare); 
                        
                        for (set<string>::iterator itRare = rareNames.begin(); itRare != rareNames.end(); itRare++) {
                                rout << (*itRare) << endl;
@@ -678,7 +741,7 @@ int SplitAbundCommand::writeAccnos(string tag) {
                
                        string abund = outputDir + m->getRootName(m->getSimpleName(inputFile)) + tag  + "abund.accnos";
                        m->openOutputFile(abund, aout);
-                       outputNames.push_back(abund);
+                       outputNames.push_back(abund); outputTypes["accnos"].push_back(abund);
                        
                        for (set<string>::iterator itAbund = abundNames.begin(); itAbund != abundNames.end(); itAbund++) {
                                aout << (*itAbund) << endl;
@@ -723,7 +786,7 @@ int SplitAbundCommand::writeAccnos(string tag) {
                        //close files
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + tag + it3->first + ".accnos");  
+                               outputNames.push_back(fileroot + tag + it3->first + ".accnos");  outputTypes["accnos"].push_back(fileroot + tag + it3->first + ".accnos");
                                delete it3->second;
                        }
                }
@@ -748,11 +811,11 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile
                        
                        string rare = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "rare.groups";
                        m->openOutputFile(rare, rout);
-                       outputNames.push_back(rare);
+                       outputNames.push_back(rare); outputTypes["group"].push_back(rare);
                
                        string abund = outputDir + m->getRootName(m->getSimpleName(groupfile))  + tag + "abund.groups";
                        m->openOutputFile(abund, aout);
-                       outputNames.push_back(abund);
+                       outputNames.push_back(abund); outputTypes["group"].push_back(abund);
                        
                        for (map<string, string>::iterator itName = nameMap.begin(); itName != nameMap.end(); itName++) {                               
                                vector<string> names;
@@ -817,7 +880,7 @@ int SplitAbundCommand::parseGroup(string tag) { //namefile
                        
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + tag + it3->first + ".groups");  
+                               outputNames.push_back(fileroot + tag + it3->first + ".groups");  outputTypes["group"].push_back(fileroot + tag + it3->first + ".groups");
                                delete it3->second;
                        }
                }
@@ -842,11 +905,11 @@ int SplitAbundCommand::parseFasta(string tag) { //namefile
                        
                        string rare = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "rare.fasta";
                        m->openOutputFile(rare, rout);
-                       outputNames.push_back(rare);
+                       outputNames.push_back(rare); outputTypes["fasta"].push_back(rare);
                
                        string abund = outputDir + m->getRootName(m->getSimpleName(fastafile))  + tag + "abund.fasta";
                        m->openOutputFile(abund, aout);
-                       outputNames.push_back(abund);
+                       outputNames.push_back(abund); outputTypes["fasta"].push_back(abund);
                
                        //open input file
                        ifstream in;
@@ -937,7 +1000,7 @@ int SplitAbundCommand::parseFasta(string tag) { //namefile
                        
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) { 
                                (*(filehandles[it3->first])).close();
-                               outputNames.push_back(fileroot + tag + it3->first + ".fasta");  
+                               outputNames.push_back(fileroot + tag + it3->first + ".fasta");  outputTypes["fasta"].push_back(fileroot + tag + it3->first + ".fasta");
                                delete it3->second;
                        }
                }