addition of summary.seq command [pds]

[mothur.git] / fastamap.cpp

diff --git a/fastamap.cpp b/fastamap.cpp
index a1beda31ac5ee82c532676163179197a004f91eb..ebfecedb860bafb6385ca2f75a3752702354498b 100644 (file)
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -19,7 +19,7 @@ void FastaMap::readFastaFile(ifstream& in) {
                name = line.substr(1, line.length());  //rips off '>'
        
                //read through file
-               while (in.eof() != true) {
+               while (!in.eof()) {
                        in >> line;
                        if (line != "") {
                                if (isalnum(line.at(0))) {  //if it's a sequence line
@@ -41,19 +41,9 @@ void FastaMap::readFastaFile(ifstream& in) {
                                        sequence = "";
                                }
                        }
+                       gobble(in);
                }
        
-               //store last sequence and name info.
-               seqmap[name] = sequence;
-               it = data.find(sequence);
-               if (it == data.end()) {         //it's unique.
-                       data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
-                       data[sequence].groupnumber = 1;
-                       data[sequence].names = name;
-               }else { // its a duplicate.
-                       data[sequence].names += "," + name;
-                       data[sequence].groupnumber++;
-               }
                        
        }
        catch(exception& e) {