X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=listseqscommand.cpp;h=afbacc00aaaec2b92c5d81278d16b463c0f43ffe;hb=d205e70ae86dbee2efc2df02f2717975854de6ba;hp=b977304c9ce54493e5f34dc20705ea1855b21bc4;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index b977304..afbacc0 100644
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -41,7 +41,7 @@ string ListSeqsCommand::getHelpString(){
 		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\n";
+		helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
 		return helpString;
 	}
 	catch(exception& e) {
@@ -71,7 +71,7 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
-		
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		else {
 			vector<string> myArray = setParameters();
 			
@@ -150,15 +150,18 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
 			//check for required parameters
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { abort = true; }
-			else if (fastafile == "not found") {  fastafile = "";  }	
+			else if (fastafile == "not found") {  fastafile = "";  }
+			else { m->setFastaFile(fastafile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }
 			else if (namefile == "not found") {  namefile = "";  }	
+			else { m->setNameFile(namefile); }
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }
 			else if (groupfile == "not found") {  groupfile = "";  }	
+			else { m->setGroupFile(groupfile); }
 			
 			alignfile = validParameter.validFile(parameters, "alignreport", true);
 			if (alignfile == "not open") { abort = true; }
@@ -167,10 +170,12 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not open") { abort = true; }
 			else if (listfile == "not found") {  listfile = "";  }
-
+			else { m->setListFile(listfile); }
+			
 			taxfile = validParameter.validFile(parameters, "taxonomy", true);
 			if (taxfile == "not open") { abort = true; }
 			else if (taxfile == "not found") {  taxfile = "";  }
+			else { m->setTaxonomyFile(taxfile); }
 			
 			if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }
 			
@@ -218,13 +223,13 @@ int ListSeqsCommand::execute(){
 		//output to .accnos file
 		for (int i = 0; i < names.size(); i++) {
 			
-			if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+			if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
 			
 			out << names[i] << endl;
 		}
 		out.close();
 		
-		if (m->control_pressed) { outputTypes.clear();  remove(outputFileName.c_str()); return 0; }
+		if (m->control_pressed) { outputTypes.clear();  m->mothurRemove(outputFileName); return 0; }
 		
 		m->setAccnosFile(outputFileName);
 		
@@ -257,18 +262,32 @@ int ListSeqsCommand::readFasta(){
 		m->openInputFile(fastafile, in);
 		string name;
 		
+		//ofstream out;
+		//string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
+		//m->openOutputFile(newFastaName, out);
+		//int count = 1;
+		//string lastName = "";
+		
 		while(!in.eof()){
 			
 			if (m->control_pressed) { in.close(); return 0; }
 			
 			Sequence currSeq(in);
 			name = currSeq.getName();
+			//if (lastName == "") { lastName = name; }
+			//if (name != lastName) { count = 1; }
+		//	lastName = name;
+			
+			//Sequence newSeq(name+"_"+toString(count), currSeq.getAligned());
+			//newSeq.printSequence(out);
 			
 			if (name != "") {  names.push_back(name);  }
 			
 			m->gobble(in);
+			//count++;
 		}
 		in.close();	
+		//out.close();
 		
 		return 0;
 
@@ -294,13 +313,7 @@ int ListSeqsCommand::readList(){
 				
 				if (m->control_pressed) { in.close(); return 0; }
 				
-				while (binnames.find_first_of(',') != -1) { 
-					string name = binnames.substr(0,binnames.find_first_of(','));
-					binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
-					names.push_back(name);
-				}
-			
-				names.push_back(binnames);
+				m->splitAtComma(binnames, names);
 			}
 		}
 		in.close();	
@@ -330,14 +343,7 @@ int ListSeqsCommand::readName(){
 			in >> secondCol;			
 			
 			//parse second column saving each name
-			while (secondCol.find_first_of(',') != -1) { 
-				name = secondCol.substr(0,secondCol.find_first_of(','));
-				secondCol = secondCol.substr(secondCol.find_first_of(',')+1, secondCol.length());
-				names.push_back(name);
-			}
-			
-			//get name after last ,
-			names.push_back(secondCol);
+			m->splitAtComma(secondCol, names);
 			
 			m->gobble(in);
 		}
@@ -394,14 +400,14 @@ int ListSeqsCommand::readAlign(){
 			if (!in.eof())	{	in >> junk;		}
 			else			{	break;			}
 		}
-		
+		//m->getline(in);
 		
 		while(!in.eof()){
 		
 			if (m->control_pressed) { in.close(); return 0; }
 
 			in >> name;				//read from first column
-			
+			//m->getline(in);
 			//read rest
 			for (int i = 0; i < 15; i++) {  
 				if (!in.eof())	{	in >> junk;		}