Merge remote-tracking branch 'origin/master'

[mothur.git] / getlineagecommand.cpp

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 1cd139b5213733e759a7a32a1fbdf8221d09dfb6..99359bd882e1e2b668cd6bef2b2ec7cfc32fc0bf 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);
                                                }
                                        
@@ -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];
+                
                        }
                }