X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getsharedotucommand.cpp;h=02d8413675bade0cf79f8781987cc45078b74db2;hb=2c97dd48b8e27ee0a6a86c7a082f4c504c3357c6;hp=99687701436dc5ffac7e71a444d97b42f4b6815a;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git

diff --git a/getsharedotucommand.cpp b/getsharedotucommand.cpp
index 9968770..02d8413 100644
--- a/getsharedotucommand.cpp
+++ b/getsharedotucommand.cpp
@@ -8,6 +8,7 @@
  */
 
 #include "getsharedotucommand.h"
+#include "sharedutilities.h"
 
 //**********************************************************************************************************************
 vector<string> GetSharedOTUCommand::setParameters(){	
@@ -45,8 +46,8 @@ string GetSharedOTUCommand::getHelpString(){
 		helpString += "The output parameter allows you to output the list of names without the group and bin number added. \n";
 		helpString += "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";
 		helpString += "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";
-		helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(label=yourLabels, groups=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
-		helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
+		helpString += "The get.sharedseqs command should be in the following format: get.sharedseqs(list=yourListFile, group=yourGroupFile, label=yourLabels, unique=yourGroups, fasta=yourFastafile, output=yourOutput).\n";
+		helpString += "Example get.sharedseqs(list=amazon.fn.list, label=unique-0.01, group= amazon.groups, unique=forest-pasture, fasta=amazon.fasta, output=accnos).\n";
 		helpString += "The output to the screen is the distance and the number of otus at that distance for the groups you specified.\n";
 		helpString += "The default value for label is all labels in your inputfile. The default for groups is all groups in your file.\n";
 		helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
@@ -148,7 +149,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
 					m->mothurOut("No valid current list file. You must provide a list file."); m->mothurOutEndLine(); 
 					abort = true;
 				}
-			}else {  format = "list"; 	}
+			}else {  format = "list"; 	m->setListFile(listfile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }	
@@ -159,7 +160,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
 					m->mothurOut("No valid current group file. You must provide a group file."); m->mothurOutEndLine(); 
 					abort = true;
 				}
-			}
+			}else { m->setGroupFile(groupfile); }
 						
 			if ((listfile == "") || (groupfile == "")) { m->mothurOut("The list and group parameters are required."); m->mothurOutEndLine(); abort = true; }
 			
@@ -181,7 +182,7 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
 			else { 
 				userGroups = "unique." + groups;
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 				
 			}
 			
@@ -190,14 +191,14 @@ GetSharedOTUCommand::GetSharedOTUCommand(string option)  {
 			else { 
 				userGroups = groups;
 				m->splitAtDash(groups, Groups);
-				m->Groups = Groups;
+				m->setGroups(Groups);
 				unique = false;
 			}
 			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { abort = true; }
 			else if (fastafile == "not found") {  fastafile = "";  }	
-				
+			else { m->setFastaFile(fastafile); }
 		}
 
 	}
@@ -220,12 +221,18 @@ int GetSharedOTUCommand::execute(){
 		if (m->control_pressed) { delete groupMap; return 0; }
 		
 		if (Groups.size() == 0) {
-			Groups = groupMap->namesOfGroups;
+			Groups = groupMap->getNamesOfGroups();
 			
 			//make string for outputfile name
 			userGroups = "unique.";
 			for(int i = 0; i < Groups.size(); i++) {  userGroups += Groups[i] + "-";  }
 			userGroups = userGroups.substr(0, userGroups.length()-1);
+		}else{
+			//sanity check for group names
+			SharedUtil util;
+			vector<string> namesOfGroups = groupMap->getNamesOfGroups(); 
+			util.setGroups(Groups, namesOfGroups);
+			groupMap->setNamesOfGroups(namesOfGroups);
 		}
 	
 		//put groups in map to find easier
@@ -261,7 +268,7 @@ 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()); }  outputTypes.clear();
+				for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]); }  outputTypes.clear();
 				delete groupMap; return 0;
 			}
 			
@@ -320,11 +327,11 @@ int GetSharedOTUCommand::execute(){
 		
 
 		//reset groups parameter
-		m->Groups.clear();  
+		m->clearGroups();  
 		
 		if (lastlist != NULL) {		delete lastlist;	}
 		
-		if (m->control_pressed) { outputTypes.clear(); 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++) {	m->mothurRemove(outputNames[i]); }  delete groupMap; return 0; } 
 		
 		//set fasta file as new current fastafile
 		string current = "";
@@ -376,7 +383,7 @@ int GetSharedOTUCommand::process(ListVector* shared) {
 				
 		//go through each bin, find out if shared
 		for (int i = 0; i < shared->getNumBins(); i++) {
-			if (m->control_pressed) { outNames.close(); remove(outputFileNames.c_str()); return 0; }
+			if (m->control_pressed) { outNames.close(); m->mothurRemove(outputFileNames); return 0; }
 			
 			bool uniqueOTU = true;
 			
@@ -454,7 +461,7 @@ int GetSharedOTUCommand::process(ListVector* shared) {
 		outNames.close();
 		
 		if (!wroteSomething) {
-			remove(outputFileNames.c_str());
+			m->mothurRemove(outputFileNames);
 			string outputString = "\t" + toString(num) + " - No otus shared by groups";
 			
 			string groupString = "";