X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=alignmentdb.cpp;h=9fec737778e01704e98f5c813e3c0554e7ab0981;hp=df4eaec783dbb81e33c09c3d97473c02425ba1ce;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index df4eaec..9fec737 100644
--- 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?
@@ -69,12 +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;
@@ -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();