added count file to get.oturep, pre.cluster, screen.seqs, tree.shared. made remove...

[mothur.git] / getseqscommand.cpp

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index e0faef4cc07bd3fc6626fe186ec67fe05c512023..6b16111fdcda83099c0e36396543d40ee345c865 100644 (file)
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -10,6 +10,7 @@
 #include "getseqscommand.h"
 #include "sequence.hpp"
 #include "listvector.hpp"
+#include "counttable.h"
 
 //**********************************************************************************************************************
 vector<string> GetSeqsCommand::setParameters(){        
@@ -90,7 +91,7 @@ string GetSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
             if (type == "fasta")            {   outputFileName =  "pick" + m->getExtension(inputName);   }
             else if (type == "taxonomy")    {   outputFileName =  "pick" + m->getExtension(inputName);   }
             else if (type == "name")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
-            else if (type == "count")       {   outputFileName =  "pick.count.table";   }
+            else if (type == "count")       {   outputFileName =  "pick.count_table";   }
             else if (type == "group")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
             else if (type == "list")        {   outputFileName =  "pick" + m->getExtension(inputName);   }
             else if (type == "qfile")       {   outputFileName =  "pick" + m->getExtension(inputName);   }
@@ -568,6 +569,13 @@ int GetSeqsCommand::readCount(){
         }
         in.close();
                out.close();
+        
+        //check for groups that have been eliminated
+        CountTable ct;
+        if (ct.testGroups(outputFileName)) {
+            ct.readTable(outputFileName);
+            ct.printTable(outputFileName);
+        }
                
                if (wroteSomething == false) {  m->mothurOut("Your file does not contain any sequence from the .accnos file."); m->mothurOutEndLine();  }
                outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
@@ -617,19 +625,16 @@ int GetSeqsCommand::readList(){
                        
                                //parse out names that are in accnos file
                                string binnames = list.get(i);
+                vector<string> bnames;
+                m->splitAtComma(binnames, 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());
-                                       
+                for (int i = 0; i < bnames.size(); i++) {
+                                       string name = bnames[i];
                                        //if that name is in the .accnos file, add it
                                        if (names.count(name) != 0) {  newNames += name + ",";  selectedCount++; if (m->debug) { sanity["list"].insert(name); } }
                                }
                        
-                               //get last name
-                               if (names.count(binnames) != 0) {  newNames += binnames + ",";  selectedCount++;  if (m->debug) { sanity["list"].insert(binnames); } }
-
                                //if there are names in this bin add to new list
                                if (newNames != "") { 
                                        newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma