pat's differences before v.1.8

[mothur.git] / chimera.cpp

diff --git a/chimera.cpp b/chimera.cpp
index 8851b755a09a0b030418e7881d09caedb4753584..4ae4991c8d78ebe7a90920972175554dd83b6d36 100644 (file)
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -90,13 +90,21 @@ vector<Sequence*> Chimera::readSeqs(string file) {
                ifstream in;
                openInputFile(file, in);
                vector<Sequence*> container;
+               int count = 0;
+               int length = 0;
+               unaligned = false;
                
                //read in seqs and store in vector
                while(!in.eof()){
                        
-                       Sequence* current = new Sequence(in);
-                       container.push_back(current);
-                       gobble(in);
+                       Sequence* current = new Sequence(in);  gobble(in);
+                       
+                       if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
+                       else if (length != current->getAligned().length()) { //seqs are unaligned
+                               unaligned = true;
+                       }
+                       
+                       if (current->getName() != "") {  container.push_back(current);  }
                }
                
                in.close();