X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removeseqscommand.cpp;h=25d45a7c578c47167fac24164cac3322f3462772;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=019a659f44f446be2d3c87e5c195ab93663f1773;hpb=2ff2d03fbe46ce8cf2738bff4403a52be4f31e2f;p=mothur.git

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 019a659..25d45a7 100644
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -67,7 +67,7 @@ string RemoveSeqsCommand::getOutputPattern(string type) {
         else if (type == "name")        {   pattern = "[filename],pick,[extension]";    }
         else if (type == "group")       {   pattern = "[filename],pick,[extension]";    }
         else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
-        else if (type == "list")        {   pattern = "[filename],pick,[extension]";    }
+        else if (type == "list")        {   pattern = "[filename],[distance],pick,[extension]";    }
         else if (type == "qfile")       {   pattern = "[filename],pick,[extension]";    }
         else if (type == "alignreport")      {   pattern = "[filename],pick.align.report";    }
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
@@ -664,10 +664,7 @@ int RemoveSeqsCommand::readList(){
 		map<string, string> variables; 
 		variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
         variables["[extension]"] = m->getExtension(listfile);
-		string outputFileName = getOutputFileName("list", variables);	
-		ofstream out;
-		m->openOutputFile(outputFileName, out);
-		
+				
 		ifstream in;
 		m->openInputFile(listfile, in);
 		
@@ -684,48 +681,60 @@ int RemoveSeqsCommand::readList(){
 			//make a new list vector
 			ListVector newList;
 			newList.setLabel(list.getLabel());
+            
+			variables["[distance]"] = list.getLabel();
+            string outputFileName = getOutputFileName("list", variables);
 			
+			ofstream out;
+			m->openOutputFile(outputFileName, out);
+			outputTypes["list"].push_back(outputFileName);  outputNames.push_back(outputFileName);
+            
+            vector<string> binLabels = list.getLabels();
+            vector<string> newBinLabels;
+            
+            if (m->control_pressed) { in.close(); out.close();  return 0; }
+
 			//for each bin
 			for (int i = 0; i < list.getNumBins(); i++) {
 				if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
 			
 				//parse out names that are in accnos file
-				string binnames = list.get(i);
+				string bin = list.get(i);
+                vector<string> bnames;
+                m->splitAtComma(bin, bnames);
 				
 				string newNames = "";
-				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());
-					
-					//if that name is in the .accnos file, add it
+                for (int j = 0; j < bnames.size(); j++) {
+					string name = bnames[j];
+                    //if that name is in the .accnos file, add it
 					if (names.count(name) == 0) {  newNames += name + ",";  }
 					else {  removedCount++;  }
-				}
-			
-				//get last name
-				if (names.count(binnames) == 0) {  newNames += binnames + ",";  }
-				else {  removedCount++;  }
+                }
 
 				//if there are names in this bin add to new list
 				if (newNames != "") {  
 					newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
-					newList.push_back(newNames);	
+					newList.push_back(newNames);
+                    newBinLabels.push_back(binLabels[i]);
 				}
 			}
 				
 			//print new listvector
 			if (newList.getNumBins() != 0) {
 				wroteSomething = true;
+				newList.setLabels(newBinLabels);
+                newList.printHeaders(out);
 				newList.print(out);
+
 			}
 			
 			m->gobble(in);
+            out.close();
 		}
 		in.close();	
-		out.close();
+		
 		
 		if (wroteSomething == false) {  m->mothurOut("Your file contains only sequences from the .accnos file."); m->mothurOutEndLine();  }
-		outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
 		
 		m->mothurOut("Removed " + toString(removedCount) + " sequences from your list file."); m->mothurOutEndLine();