X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylosummary.cpp;h=2f565150aabeec35cc8a3c03a459d8b85090550b;hb=791f42d21a85f794529fd4c912dcc27d873c25e8;hp=b645bac794777a1050de116407fa834370e7940e;hpb=4f2c7f477a1ef2d60a1c0c84ab1ba8243af67f87;p=mothur.git

diff --git a/phylosummary.cpp b/phylosummary.cpp
index b645bac..2f56515 100644
--- a/phylosummary.cpp
+++ b/phylosummary.cpp
@@ -25,7 +25,7 @@ PhyloSummary::PhyloSummary(string refTfile, string groupFile){
 		}
 				
 		//check for necessary files
-		string taxFileNameTest = refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum";
+		string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
 		ifstream FileTest(taxFileNameTest.c_str());
 		
 		if (!FileTest) { 
@@ -121,6 +121,7 @@ string PhyloSummary::getNextTaxon(string& heirarchy){
 
 int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 	try {
+				
 		numSeqs++;
 		
 		map<string, int>::iterator childPointer;
@@ -131,7 +132,7 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 		int level = 0;
 		
 		//are there confidence scores, if so remove them
-		if (seqTaxonomy.find_first_of('(') != -1) {  removeConfidences(seqTaxonomy);	}
+		if (seqTaxonomy.find_first_of('(') != -1) {  m->removeConfidences(seqTaxonomy);	}
 		
 		while (seqTaxonomy != "") {
 			
@@ -229,7 +230,7 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, vector<string> names){
 		int level = 0;
 		
 		//are there confidence scores, if so remove them
-		if (seqTaxonomy.find_first_of('(') != -1) {  removeConfidences(seqTaxonomy);	}
+		if (seqTaxonomy.find_first_of('(') != -1) {  m->removeConfidences(seqTaxonomy);	}
 		
 		while (seqTaxonomy != "") {
 			
@@ -496,35 +497,6 @@ void PhyloSummary::readTreeStruct(ifstream& in){
 	}
 }
 /**************************************************************************************************/
-void PhyloSummary::removeConfidences(string& tax) {
-	try {
-		
-		string taxon;
-		string newTax = "";
-		
-		while (tax.find_first_of(';') != -1) {
-			//get taxon
-			taxon = tax.substr(0,tax.find_first_of(';'));
-			
-			int pos = taxon.find_first_of('(');
-			if (pos != -1) {
-				taxon = taxon.substr(0, pos); //rip off confidence 
-			}
-			
-			taxon += ";";
-			
-			tax = tax.substr(tax.find_first_of(';')+1, tax.length());
-			newTax += taxon;
-		}
-		
-		tax = newTax;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "PhyloSummary", "removeConfidences");
-		exit(1);
-	}
-}
-/**************************************************************************************************/