X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylosummary.cpp;h=5f7bbc3c73a2161417a1841f567719a4bd1f8c4a;hb=5a4ac4f954c4b4445bcee272f1f8220ddcc9c1e4;hp=7d9fcac2558da8f50653a11ddafd997b58c1c286;hpb=16abd6271c455bd01b34ff89a2e3641bef0fa128;p=mothur.git

diff --git a/phylosummary.cpp b/phylosummary.cpp
index 7d9fcac..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");