X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getlineagecommand.cpp;h=99359bd882e1e2b668cd6bef2b2ec7cfc32fc0bf;hb=006601d68abe8d0061f77e8d28323b160750e343;hp=1cd139b5213733e759a7a32a1fbdf8221d09dfb6;hpb=ea4f373c28543cd1002b0dd7dc6e55c526647d59;p=mothur.git

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 1cd139b..99359bd 100644
--- 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);
 						}
 					
@@ -803,20 +814,27 @@ int GetLineageCommand::readTax(){
 /**************************************************************************************************/
 vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
 	try {
-		
+        
 		vector< map<string, float> > t;
 		string taxon = "";
 		int taxLength = tax.length();
+        
 		for(int i=0;i<taxLength;i++){
 			if(tax[i] == ';'){
-		
-				int openParen = taxon.find_first_of('(');
+                
+				int openParen = taxon.find_last_of('(');
 				int closeParen = taxon.find_last_of(')');
 				
 				string newtaxon, confidence;
 				if ((openParen != string::npos) && (closeParen != string::npos)) {
-					newtaxon = taxon.substr(0, openParen); //rip off confidence
-					confidence = taxon.substr((openParen+1), (closeParen-openParen-1));  
+                    string confidenceScore = taxon.substr(openParen+1, (closeParen-(openParen+1)));
+                    if (m->isNumeric1(confidenceScore)) {  //its a confidence
+                        newtaxon = taxon.substr(0, openParen); //rip off confidence
+                        confidence = taxon.substr((openParen+1), (closeParen-openParen-1));  
+                    }else { //its part of the taxon
+                        newtaxon = taxon;
+                        confidence = "0";
+                    }
 				}else{
 					newtaxon = taxon;
 					confidence = "0";
@@ -826,12 +844,13 @@ vector< map<string, float> > GetLineageCommand::getTaxons(string tax) {
 				
 				map<string, float> temp;
 				temp[newtaxon] = con;
+                
 				t.push_back(temp);
-				
 				taxon = "";
 			}
 			else{
 				taxon += tax[i];
+                
 			}
 		}