fixes while testing 1.33.0

[mothur.git] / removelineagecommand.cpp

diff --git a/removelineagecommand.cpp b/removelineagecommand.cpp
index 01f45ca97329fbbe383c2157f12880ca05671a10..7349203007d90b4228502680b95b93b7ab9c3240 100644 (file)
--- a/removelineagecommand.cpp
+++ b/removelineagecommand.cpp
@@ -75,7 +75,7 @@ string RemoveLineageCommand::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]-[filename],[distance],pick,[extension]";    }
+        else if (type == "list")            {   pattern = "[filename],[distance],pick,[extension]";    }
         else if (type == "shared")          {   pattern = "[filename],[distance],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;  }
@@ -481,9 +481,6 @@ int RemoveLineageCommand::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);
@@ -491,12 +488,25 @@ int RemoveLineageCommand::readList(){
                bool wroteSomething = false;
                
                while(!in.eof()){
+            
                        //read in list vector
                        ListVector list(in);
                        
                        //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);
+            
+            if (m->control_pressed) { in.close(); out.close(); return 0; }
+            
+            vector<string> binLabels = list.getLabels();
+            vector<string> newBinLabels;
                        
                        //for each bin
                        for (int i = 0; i < list.getNumBins(); i++) {
@@ -517,23 +527,26 @@ int RemoveLineageCommand::readList(){
                                //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 list file contains only sequences from " + taxons + "."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName); 
                                
                return 0;
 
@@ -692,6 +705,8 @@ int RemoveLineageCommand::readConsList(){
         bool wroteSomething = false;
         string snumBins = toString(list->getNumBins());
         
+        vector<string> binLabels = list->getLabels();
+        vector<string> newBinLabels;
         for (int i = 0; i < list->getNumBins(); i++) {
             
             if (m->control_pressed) { delete list; return 0;}
@@ -707,6 +722,7 @@ int RemoveLineageCommand::readConsList(){
             
             if (names.count(m->getSimpleLabel(otuLabel)) == 0) {
                 newList.push_back(list->get(i));
+                newBinLabels.push_back(binLabels[i]);
             }else { removedCount++; }
         }
         
@@ -724,6 +740,8 @@ int RemoveLineageCommand::readConsList(){
         //print new listvector
         if (newList.getNumBins() != 0) {
             wroteSomething = true;
+            newList.setLabels(newBinLabels);
+            newList.printHeaders(out);
             newList.print(out);
         }
                out.close();
@@ -843,9 +861,9 @@ int RemoveLineageCommand::readShared(){
             if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; } return 0; }
             
             //is this otu on the list
-            if (names.count(m->getSimpleLabel(m->currentBinLabels[i])) == 0) {
+            if (names.count(m->getSimpleLabel(m->currentSharedBinLabels[i])) == 0) {
                 wroteSomething = true;
-                newLabels.push_back(m->currentBinLabels[i]);
+                newLabels.push_back(m->currentSharedBinLabels[i]);
                 for (int j = 0; j < newLookup.size(); j++) { //add this OTU to the new lookup
                     newLookup[j]->push_back(lookup[j]->getAbundance(i), lookup[j]->getGroup());
                 }
@@ -865,7 +883,7 @@ int RemoveLineageCommand::readShared(){
         
                for (int j = 0; j < lookup.size(); j++) { delete lookup[j]; }
         
-        m->currentBinLabels = newLabels;
+        m->currentSharedBinLabels = newLabels;
         
                newLookup[0]->printHeaders(out);