fixed subsample name file name issue. added count parameter to cluster command....

[mothur.git] / phylosummary.cpp

diff --git a/phylosummary.cpp b/phylosummary.cpp
index 7d9fcac2558da8f50653a11ddafd997b58c1c286..5f7bbc3c73a2161417a1841f567719a4bd1f8c4a 100644 (file)
--- 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");