working on chimera.perseus. made removeConfidences function smarter. Fixed bug in...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index df1a1c0615be21cd53ab51b0a82cfaab3871e847..32f3b85819bb05206cb789d4e41e70d02fcd2e65 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -434,7 +434,7 @@ void MothurOut::gobble(istream& f){
                
                char d;
                while(isspace(d=f.get()))               { ;}
-               f.putback(d);
+               if(!f.eof()) { f.putback(d); }
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "gobble");
@@ -446,7 +446,7 @@ void MothurOut::gobble(istringstream& f){
        try {
                char d;
                while(isspace(d=f.get()))               {;}
-               f.putback(d);
+               if(!f.eof()) { f.putback(d); }
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "gobble");
@@ -891,10 +891,10 @@ int MothurOut::renameFile(string oldName, string newName){
        try {
                ifstream inTest;
                int exist = openInputFile(newName, inTest, "");
+               inTest.close();
                
        #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)           
                if (exist == 0) { //you could open it so you want to delete it
-                       inTest.close();
                        string command = "rm " + newName;
                        system(command.c_str());
                }
@@ -2020,6 +2020,46 @@ bool MothurOut::isContainingOnlyDigits(string input) {
        }
 }
 /**************************************************************************************************/
+int MothurOut::removeConfidences(string& tax) {
+       try {
+               
+               string taxon;
+               string newTax = "";
+               
+               while (tax.find_first_of(';') != -1) {
+                       
+                       if (control_pressed) { return 0; }
+                       
+                       //get taxon
+                       taxon = tax.substr(0,tax.find_first_of(';'));
+       
+                       int pos = taxon.find_last_of('(');
+                       if (pos != -1) {
+                               //is it a number?
+                               int pos2 = taxon.find_last_of(')');
+                               if (pos2 != -1) {
+                                       string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
+                                       if (isContainingOnlyDigits(confidenceScore)) {
+                                               taxon = taxon.substr(0, pos); //rip off confidence 
+                                       }
+                               }
+                       }
+                       taxon += ";";
+                       
+                       tax = tax.substr(tax.find_first_of(';')+1, tax.length());
+                       newTax += taxon;
+               }
+               
+               tax = newTax;
+               
+               return 0;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "removeConfidences");
+               exit(1);
+       }
+}
+/**************************************************************************************************/