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

[mothur.git] / getlineagecommand.cpp

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 1cd139b5213733e759a7a32a1fbdf8221d09dfb6..645655d03f72bbebac45cfa108c499cc1daf8e3b 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -10,6 +10,7 @@
 #include "getlineagecommand.h"
 #include "sequence.hpp"
 #include "listvector.hpp"
+#include "counttable.h"
 
 //**********************************************************************************************************************
 vector<string> GetLineageCommand::setParameters(){     
@@ -71,7 +72,7 @@ string GetLineageCommand::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 == "alignreport") {   outputFileName =  "pick.align.report";   }
@@ -438,6 +439,14 @@ int GetLineageCommand::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 contains does not contain any sequences from " + taxons + "."); m->mothurOutEndLine();  }
                outputTypes["count"].push_back(outputFileName); outputNames.push_back(outputFileName);
@@ -691,15 +700,17 @@ int GetLineageCommand::readTax(){
                        in >> name;                             //read from first column
                        in >> tax;                      //read from second column
                        
+            string noQuotesTax = m->removeQuotes(tax);
+            
                        for (int j = 0; j < listOfTaxons.size(); j++) {
                                                        
-                               string newtax = tax;
+                               string newtax = noQuotesTax;
                        
                                //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
                                if (!taxonsHasConfidence[j]) {
-                                       int hasConfidences = tax.find_first_of('(');
+                                       int hasConfidences = noQuotesTax.find_first_of('(');
                                        if (hasConfidences != string::npos) { 
-                                               newtax = tax;
+                                               newtax = noQuotesTax;
                                                m->removeConfidences(newtax);
                                        }
                                
@@ -712,7 +723,7 @@ int GetLineageCommand::readTax(){
                                                break;
                                        }
                                }else{//if listOfTaxons[i] has them and you don't them remove taxons
-                                       int hasConfidences = tax.find_first_of('(');
+                                       int hasConfidences = noQuotesTax.find_first_of('(');
                                        if (hasConfidences == string::npos) { 
                                        
                                                int pos = newtax.find(noConfidenceTaxons[j]);
@@ -726,10 +737,10 @@ int GetLineageCommand::readTax(){
                                        }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
                                                //first remove confidences from both and see if the taxonomy exists
                                        
-                                               string noNewTax = tax;
-                                               int hasConfidences = tax.find_first_of('(');
+                                               string noNewTax = noQuotesTax;
+                                               int hasConfidences = noQuotesTax.find_first_of('(');
                                                if (hasConfidences != string::npos) { 
-                                                       noNewTax = tax;
+                                                       noNewTax = noQuotesTax;
                                                        m->removeConfidences(noNewTax);
                                                }