changes while testing

[mothur.git] / alignmentdb.cpp

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index f59c5db7d6e6ef2d039ccdda8b48a6ea3fb6428a..9fec737778e01704e98f5c813e3c0554e7ab0981 100644 (file)
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -42,12 +42,14 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                        
                        numSeqs = templateSequences.size();
                        if (!silent) { m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();  }
-
+            
                }else {
                        int start = time(NULL);
                        m->mothurOutEndLine();
                        m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t");   cout.flush();
-                       
+                       //bool aligned = false;
+            int tempLength = 0;
+            
                        #ifdef USE_MPI  
                                int pid, processors;
                                vector<unsigned long long> positions;
@@ -102,6 +104,9 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                                                
                                                //save longest base
                                                if (temp.getUnaligned().length() >= longest)  { longest = temp.getUnaligned().length()+1; }
+                        if (tempLength != 0) {
+                            if (tempLength != temp.getAligned().length()) { m->mothurOut("[ERROR]: template is not aligned, aborting.\n"); m->control_pressed=true; }
+                        }else { tempLength = temp.getAligned().length(); }
                                        }
                                }
                                
@@ -125,6 +130,10 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                                        
                                        //save longest base
                                        if (temp.getUnaligned().length() >= longest)  { longest = (temp.getUnaligned().length()+1); }
+                    
+                    if (tempLength != 0) {
+                        if (tempLength != temp.getAligned().length()) { m->mothurOut("[ERROR]: template is not aligned, aborting.\n"); m->control_pressed=true; }
+                    }else { tempLength = temp.getAligned().length(); }
                                }
                        }
                        fastaFile.close();