X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylosummary.cpp;h=5f7bbc3c73a2161417a1841f567719a4bd1f8c4a;hb=f06b339c5fc4b6d1b9d2a08fe16bf7670bf7aeb4;hp=b645bac794777a1050de116407fa834370e7940e;hpb=4f2c7f477a1ef2d60a1c0c84ab1ba8243af67f87;p=mothur.git

diff --git a/phylosummary.cpp b/phylosummary.cpp
index b645bac..5f7bbc3 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) { 
@@ -73,24 +73,16 @@ PhyloSummary::PhyloSummary(string groupFile){
 
 int PhyloSummary::summarize(string userTfile){
 	try {
-		
-		ifstream in;
-		m->openInputFile(userTfile, in);
-		
-		//read in users taxonomy file and add sequences to tree
-		string name, tax;
-		int numSeqs = 0;
-		while(!in.eof()){
-			in >> name >> tax; m->gobble(in);
-			
-			addSeqToTree(name, tax);
+		map<string, string> temp;
+        m->readTax(userTfile, temp);
+        
+        for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end();) {
+            addSeqToTree(itTemp->first, itTemp->second);
 			numSeqs++;
-			
-			if (m->control_pressed) { break;  }
-		}
-		in.close();
-		
-		return numSeqs;
+            temp.erase(itTemp++);
+        }
+        
+        return numSeqs;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "PhyloSummary", "summarize");
@@ -121,6 +113,7 @@ string PhyloSummary::getNextTaxon(string& heirarchy){
 
 int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 	try {
+				
 		numSeqs++;
 		
 		map<string, int>::iterator childPointer;
@@ -131,7 +124,7 @@ 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 +222,7 @@ 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 +489,6 @@ 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);
-	}
-}
-/**************************************************************************************************/