X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setcurrentcommand.cpp;fp=setcurrentcommand.cpp;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=96735405c5e148159ab762a720a93f88ec2354ee;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/setcurrentcommand.cpp b/setcurrentcommand.cpp
deleted file mode 100644
index 9673540..0000000
--- a/setcurrentcommand.cpp
+++ /dev/null
@@ -1,488 +0,0 @@
-/*
- *  setcurrentcommand.cpp
- *  Mothur
- *
- *  Created by westcott on 3/16/11.
- *  Copyright 2011 Schloss Lab. All rights reserved.
- *
- */
-
-#include "setcurrentcommand.h"
-
-//**********************************************************************************************************************
-vector<string> SetCurrentCommand::setParameters(){	
-	try {
-		
-		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-		CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pflow);
-        CommandParameter pbiom("biom", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pbiom);
-		CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pphylip);
-		CommandParameter pcolumn("column", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pcolumn);
-		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
-		CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
-		CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
-		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(plist);
-		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptaxonomy);
-		CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
-		CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);		
-		CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prabund);
-		CommandParameter psabund("sabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psabund);
-		CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pdesign);
-		CommandParameter porder("order", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(porder);
-		CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptree);
-		CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pshared);
-		CommandParameter pordergroup("ordergroup", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pordergroup);
-		CommandParameter prelabund("relabund", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(prelabund);
-		CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
-		CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
-		CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
-		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, "SetCurrentCommand", "setParameters");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-string SetCurrentCommand::getHelpString(){	
-	try {
-		string helpString = "";
-		helpString += "The set.current command allows you to set the current files saved by mothur.\n";
-		helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom and taxonomy.\n";
-		helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
-		helpString += "The set.current command should be in the following format: \n";
-		helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
-		return helpString;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SetCurrentCommand", "getHelpString");
-		exit(1);
-	}
-}
-
-
-//**********************************************************************************************************************
-SetCurrentCommand::SetCurrentCommand(){	
-	try {
-		abort = true; calledHelp = true;
-		setParameters();
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-SetCurrentCommand::SetCurrentCommand(string option)  {
-	try {
-		abort = false; calledHelp = false;   
-		
-		//allow user to run help
-		if(option == "help") { help(); abort = true; calledHelp = true; }
-		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-		
-		else {
-			//valid paramters for this command
-			vector<string> myArray = setParameters();
-			
-			OptionParser parser(option);
-			map<string,string> parameters = parser.getParameters();
-			
-			ValidParameters validParameter;
-			map<string,string>::iterator it;
-			//check to make sure all parameters are valid for command
-			for (it = parameters.begin(); it != parameters.end(); it++) { 
-				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
-			}
-			
-			
-			//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 = "";		}
-			else {
-				string path;
-				it = parameters.find("phylip");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["phylip"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("column");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["column"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("fasta");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					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;		}
-				}
-				
-				it = parameters.find("list");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["list"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("rabund");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["rabund"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("sabund");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["sabund"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("name");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["name"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("group");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["group"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("design");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["design"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("order");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["order"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("tree");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["tree"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("shared");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["shared"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("ordergroup");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["ordergroup"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("relabund");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["relabund"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("fasta");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					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;		}
-				}
-				
-				it = parameters.find("qfile");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["qfile"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("sff");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["sff"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("oligos");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["oligos"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("accnos");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["accnos"] = inputDir + it->second;		}
-				}
-
-				it = parameters.find("taxonomy");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["taxonomy"] = inputDir + it->second;		}
-				}
-				
-				it = parameters.find("flow");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["flow"] = inputDir + it->second;		}
-				}
-                
-                it = parameters.find("biom");
-				//user has given a template file
-				if(it != parameters.end()){ 
-					path = m->hasPath(it->second);
-					//if the user has not given a path then, add inputdir. else leave path alone.
-					if (path == "") {	parameters["biom"] = inputDir + it->second;		}
-				}
-			}
-			
-			//check for parameters
-			phylipfile = validParameter.validFile(parameters, "phylip", true);
-			if (phylipfile == "not open") { m->mothurOut("Ignoring: " + parameters["phylip"]); m->mothurOutEndLine(); phylipfile = ""; }
-			else if (phylipfile == "not found") {  phylipfile = "";  }	
-			if (phylipfile != "") { m->setPhylipFile(phylipfile); }
-			
-			columnfile = validParameter.validFile(parameters, "column", true);
-			if (columnfile == "not open") { m->mothurOut("Ignoring: " + parameters["column"]); m->mothurOutEndLine(); columnfile = ""; }
-			else if (columnfile == "not found") {  columnfile = "";  }	
-			if (columnfile != "") { m->setColumnFile(columnfile); }
-			
-			listfile = validParameter.validFile(parameters, "list", true);
-			if (listfile == "not open") { m->mothurOut("Ignoring: " + parameters["list"]); m->mothurOutEndLine(); listfile = ""; }
-			else if (listfile == "not found") {  listfile = "";  }	
-			if (listfile != "") { m->setListFile(listfile); }
-			
-			rabundfile = validParameter.validFile(parameters, "rabund", true);
-			if (rabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["rabund"]); m->mothurOutEndLine(); rabundfile = ""; }
-			else if (rabundfile == "not found") {  rabundfile = "";  }	
-			if (rabundfile != "") { m->setRabundFile(rabundfile); }
-			
-			sabundfile = validParameter.validFile(parameters, "sabund", true);
-			if (sabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["sabund"]); m->mothurOutEndLine(); sabundfile = ""; }
-			else if (sabundfile == "not found") {  sabundfile = "";  }	
-			if (sabundfile != "") { m->setSabundFile(sabundfile); }
-			
-			namefile = validParameter.validFile(parameters, "name", true);
-			if (namefile == "not open") { m->mothurOut("Ignoring: " + parameters["name"]); m->mothurOutEndLine(); namefile = ""; }
-			else if (namefile == "not found") {  namefile = "";  }	
-			if (namefile != "") { m->setNameFile(namefile); }
-			
-			groupfile = validParameter.validFile(parameters, "group", true);
-			if (groupfile == "not open") { m->mothurOut("Ignoring: " + parameters["group"]); m->mothurOutEndLine(); groupfile = ""; }
-			else if (groupfile == "not found") {  groupfile = "";  }
-			if (groupfile != "") { m->setGroupFile(groupfile); }
-			
-			designfile = validParameter.validFile(parameters, "design", true);
-			if (designfile == "not open") { m->mothurOut("Ignoring: " + parameters["design"]); m->mothurOutEndLine(); designfile = ""; }
-			else if (designfile == "not found") {  designfile = "";  }	
-			if (designfile != "") { m->setDesignFile(designfile); }
-			
-			orderfile = validParameter.validFile(parameters, "order", true);
-			if (orderfile == "not open") { m->mothurOut("Ignoring: " + parameters["order"]); m->mothurOutEndLine(); orderfile = ""; }
-			else if (orderfile == "not found") {  orderfile = "";  }
-			if (orderfile != "") { m->setOrderFile(orderfile); }
-			
-			treefile = validParameter.validFile(parameters, "tree", true);
-			if (treefile == "not open") { m->mothurOut("Ignoring: " + parameters["tree"]); m->mothurOutEndLine(); treefile = ""; }
-			else if (treefile == "not found") {  treefile = "";  }	
-			if (treefile != "") { m->setTreeFile(treefile); }
-			
-			sharedfile = validParameter.validFile(parameters, "shared", true);
-			if (sharedfile == "not open") { m->mothurOut("Ignoring: " + parameters["shared"]); m->mothurOutEndLine(); sharedfile = ""; }
-			else if (sharedfile == "not found") {  sharedfile = "";  }	
-			if (sharedfile != "") { m->setSharedFile(sharedfile); }
-			
-			ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
-			if (ordergroupfile == "not open") { m->mothurOut("Ignoring: " + parameters["ordergroup"]); m->mothurOutEndLine(); ordergroupfile = ""; }
-			else if (ordergroupfile == "not found") {  ordergroupfile = "";  }	
-			if (ordergroupfile != "") { m->setOrderGroupFile(ordergroupfile); }
-			
-			relabundfile = validParameter.validFile(parameters, "relabund", true);
-			if (relabundfile == "not open") { m->mothurOut("Ignoring: " + parameters["relabund"]); m->mothurOutEndLine(); relabundfile = ""; }
-			else if (relabundfile == "not found") {  relabundfile = "";  }	
-			if (relabundfile != "") { m->setRelAbundFile(relabundfile); }
-			
-			fastafile = validParameter.validFile(parameters, "fasta", true);
-			if (fastafile == "not open") { m->mothurOut("Ignoring: " + parameters["fasta"]); m->mothurOutEndLine(); fastafile = ""; }
-			else if (fastafile == "not found") {  fastafile = "";  }
-			if (fastafile != "") { m->setFastaFile(fastafile); }
-			
-			qualfile = validParameter.validFile(parameters, "qfile", true);
-			if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLine(); qualfile = ""; }
-			else if (qualfile == "not found") {  qualfile = "";  }	
-			if (qualfile != "") { m->setQualFile(qualfile); }
-			
-			sfffile = validParameter.validFile(parameters, "sff", true);
-			if (sfffile == "not open") { m->mothurOut("Ignoring: " + parameters["sff"]); m->mothurOutEndLine(); sfffile = ""; }
-			else if (sfffile == "not found") {  sfffile = "";  }	
-			if (sfffile != "") { m->setSFFFile(sfffile); }
-			
-			oligosfile = validParameter.validFile(parameters, "oligos", true);
-			if (oligosfile == "not open") { m->mothurOut("Ignoring: " + parameters["oligos"]); m->mothurOutEndLine(); oligosfile = ""; }
-			else if (oligosfile == "not found") {  oligosfile = "";  }	
-			if (oligosfile != "") { m->setOligosFile(oligosfile); }
-			
-			accnosfile = validParameter.validFile(parameters, "accnos", true);
-			if (accnosfile == "not open") { m->mothurOut("Ignoring: " + parameters["accnos"]); m->mothurOutEndLine(); accnosfile = ""; }
-			else if (accnosfile == "not found") {  accnosfile = "";  }	
-			if (accnosfile != "") { m->setAccnosFile(accnosfile); }
-			
-			taxonomyfile = validParameter.validFile(parameters, "taxonomy", true);
-			if (taxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["taxonomy"]); m->mothurOutEndLine(); taxonomyfile = ""; }
-			else if (taxonomyfile == "not found") {  taxonomyfile = "";  }	
-			if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
-			
-			flowfile = validParameter.validFile(parameters, "flow", true);
-			if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; }
-			else if (flowfile == "not found") {  flowfile = "";  }	
-			if (flowfile != "") { m->setFlowFile(flowfile); }
-            
-            biomfile = validParameter.validFile(parameters, "biom", true);
-			if (biomfile == "not open") { m->mothurOut("Ignoring: " + parameters["biom"]); m->mothurOutEndLine(); biomfile = ""; }
-			else if (biomfile == "not found") {  biomfile = "";  }	
-			if (biomfile != "") { m->setBiomFile(biomfile); }
-			
-			processors = validParameter.validFile(parameters, "processors", false);
-			if (processors == "not found") {  processors = "1";  }	
-			if (processors != "") { m->setProcessors(processors); }
-			
-			clearTypes = validParameter.validFile(parameters, "clear", false);			
-			if (clearTypes == "not found") { clearTypes = ""; }
-			else { m->splitAtDash(clearTypes, types);	}
-		}
-		
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SetCurrentCommand", "SetCurrentCommand");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-
-int SetCurrentCommand::execute(){
-	try {
-		
-		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
-		
-		//user wants to clear a type
-		if (types.size() != 0) {
-			for (int i = 0; i < types.size(); i++) {
-				
-				if (m->control_pressed) { break; }
-				
-				//look for file types
-				if (types[i] == "fasta") {
-					m->setFastaFile("");
-				}else if (types[i] == "qfile") {
-					m->setQualFile("");
-				}else if (types[i] == "phylip") {
-					m->setPhylipFile("");
-				}else if (types[i] == "column") {
-					m->setColumnFile("");
-				}else if (types[i] == "list") {
-					m->setListFile("");
-				}else if (types[i] == "rabund") {
-					m->setRabundFile("");
-				}else if (types[i] == "sabund") {
-					m->setSabundFile("");
-				}else if (types[i] == "name") {
-					m->setNameFile("");
-				}else if (types[i] == "group") {
-					m->setGroupFile("");
-				}else if (types[i] == "order") {
-					m->setOrderFile("");
-				}else if (types[i] == "ordergroup") {
-					m->setOrderGroupFile("");
-				}else if (types[i] == "tree") {
-					m->setTreeFile("");
-				}else if (types[i] == "shared") {
-					m->setSharedFile("");
-				}else if (types[i] == "relabund") {
-					m->setRelAbundFile("");
-				}else if (types[i] == "design") {
-					m->setDesignFile("");
-				}else if (types[i] == "sff") {
-					m->setSFFFile("");
-				}else if (types[i] == "oligos") {
-					m->setOligosFile("");
-				}else if (types[i] == "accnos") {
-					m->setAccnosFile("");
-				}else if (types[i] == "taxonomy") {
-					m->setTaxonomyFile("");
-				}else if (types[i] == "flow") {
-					m->setFlowFile("");
-                }else if (types[i] == "biom") {
-					m->setBiomFile("");
-				}else if (types[i] == "processors") {
-					m->setProcessors("1");
-				}else if (types[i] == "all") {
-					m->clearCurrentFiles();
-				}else {
-					m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
-				}
-			}
-		}
-		
-		m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
-		m->printCurrentFiles();
-		
-		return 0;	
-	}
-	
-	catch(exception& e) {
-		m->errorOut(e, "SetCurrentCommand", "execute");
-		exit(1);
-	}
-}
-
-//**********************************************************************************************************************
-
-
-