modifications to commands to add headers to list file.

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 019a659f44f446be2d3c87e5c195ab93663f1773..25d45a7c578c47167fac24164cac3322f3462772 100644 (file)
--- 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();