adding labels to list file.

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index 82f9710e6e40cb84b8fee9f285fca71b3fe0099c..7f0f3ddb51da8496c292367b5dfc728b3915d53f 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -88,7 +88,7 @@ string GetSeqsCommand::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 == "accnosreport")      {   pattern = "[filename],pick.accnos.report";    }
         else if (type == "alignreport")      {   pattern = "[filename],pick.align.report";    }
@@ -614,9 +614,6 @@ int GetSeqsCommand::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);
@@ -629,8 +626,6 @@ int GetSeqsCommand::readList(){
                while(!in.eof()){
                        
                        selectedCount = 0;
-                       
-                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName);  return 0; }
 
                        //read in list vector
                        ListVector list(in);
@@ -638,6 +633,18 @@ int GetSeqsCommand::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++) {
@@ -657,23 +664,26 @@ int GetSeqsCommand::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 file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
-               outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
                
                m->mothurOut("Selected " + toString(selectedCount) + " sequences from your list file."); m->mothurOutEndLine();