changes while testing

[mothur.git] / alignmentdb.cpp

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 57975d6d774a97b1d171b468c7a238158a7b0ebe..9fec737778e01704e98f5c813e3c0554e7ab0981 100644 (file)
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -13,33 +13,6 @@
 #include "blastdb.hpp"
 #include "referencedb.h"
 
-/**************************************************************************************************/
-//deep copy
-AlignmentDB::AlignmentDB(const AlignmentDB& adb) : numSeqs(adb.numSeqs), longest(adb.longest), method(adb.method), emptySequence(adb.emptySequence), threadID(adb.threadID) {
-       try {
-               
-               m = MothurOut::getInstance();
-               if (adb.method == "blast") {
-                       search = new BlastDB(*((BlastDB*)adb.search));
-               }else if(adb.method == "kmer") {
-                       search = new KmerDB(*((KmerDB*)adb.search));
-               }else if(adb.method == "suffix") {
-                       search = new SuffixDB(*((SuffixDB*)adb.search));
-               }else {
-                       m->mothurOut("[ERROR]: cannot create copy of alignment database, unrecognized method - " + adb.method); m->mothurOutEndLine();
-               }
-               
-               for (int i = 0; i < adb.templateSequences.size(); i++) {
-                       Sequence temp(adb.templateSequences[i]);
-                       templateSequences.push_back(temp);
-               }
-       }
-       catch(exception& e) {
-               m->errorOut(e, "AlignmentDB", "AlignmentDB");
-               exit(1);
-       }
-       
-}
 /**************************************************************************************************/
 AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid){          //      This assumes that the template database is in fasta format, may 
        try {                                                                                   //      need to alter this in the future?
@@ -69,15 +42,17 @@ 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 int> positions;
+                               vector<unsigned long long> positions;
                        
                                MPI_Status status; 
                                MPI_File inMPI;
@@ -129,6 +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(); }
                                        }
                                }
                                
@@ -152,6 +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();