working on pam

[mothur.git] / reportfile.cpp

diff --git a/reportfile.cpp b/reportfile.cpp
index f392ed974c5cd5e535e7593e4e3246b1ff70e524..8e3b746159a02da7082749bea103222540e0c4a6 100644 (file)
--- a/reportfile.cpp
+++ b/reportfile.cpp
@@ -7,6 +7,8 @@
  *
  */
 
+#include "mothur.h"
+#include "mothurout.h"
 #include "reportfile.h"
 
 /**************************************************************************************************/
@@ -49,7 +51,7 @@ ReportFile::ReportFile(ifstream& repFile){
                repFile >> templateName;
                repFile >> templateLength;
                repFile >> searchMethod;
-               repFile >> searchScore;
+               repFile >> dummySearchScore;
                repFile >> alignmentMethod;
                repFile >> queryStart;
                repFile >> queryEnd;
@@ -61,6 +63,14 @@ ReportFile::ReportFile(ifstream& repFile){
                repFile >> longestInsert;
                repFile >> simBtwnQueryAndTemplate;
 
+               if(dummySearchScore != "nan"){
+                       istringstream stream(dummySearchScore);
+                       stream >> searchScore;
+               }
+               else{
+                       searchScore = 0;
+               }
+               
                m->gobble(repFile);             
        }
        catch(exception& e) {