X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=alignmentdb.cpp;h=9fec737778e01704e98f5c813e3c0554e7ab0981;hp=7c2916c54970c72f73942db5726fe3a0d8c85655;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=4e4d3cb3315fe25b40383c6f65cd6be23f58903d

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 7c2916c..9fec737 100644
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -13,19 +13,25 @@
 #include "blastdb.hpp"
 #include "referencedb.h"
 
-
 /**************************************************************************************************/
-AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){		//	This assumes that the template database is in fasta format, may 
+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?
 		m = MothurOut::getInstance();
 		longest = 0;
 		method = s;
 		bool needToGenerate = true;
 		ReferenceDB* rdb = ReferenceDB::getInstance();
+		bool silent = false;
+		threadID = tid;
+		
+		if (fastaFileName == "saved-silent") {
+			fastaFileName = "saved"; silent = true;
+		}
 		
 		if (fastaFileName == "saved") {
 			int start = time(NULL);
-			m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");	m->mothurOutEndLine();
+			
+			if (!silent) { m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");	m->mothurOutEndLine(); }
 
 			for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
 				templateSequences.push_back(rdb->referenceSeqs[i]);
@@ -35,16 +41,18 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 			fastaFileName = rdb->getSavedReference();
 			
 			numSeqs = templateSequences.size();
-			m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();  
-
+			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;
@@ -96,6 +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(); }
 					}
 				}
 				
@@ -119,6 +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();
@@ -129,7 +144,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 			
 			m->mothurOut("DONE.");
 			m->mothurOutEndLine();	cout.flush();
-			m->mothurOut("It took " + toString(time(NULL) - start) + " to read  " + toString(rdb->referenceSeqs.size()) + " sequences."); m->mothurOutEndLine();  
+			m->mothurOut("It took " + toString(time(NULL) - start) + " to read  " + toString(templateSequences.size()) + " sequences."); m->mothurOutEndLine();  
 
 		}
 		
@@ -157,8 +172,9 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
 			#endif
 		}
 		else if(method == "suffix")		{	search = new SuffixDB(numSeqs);								}
-		else if(method == "blast")		{	search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "");	}
+		else if(method == "blast")		{	search = new BlastDB(fastaFileName.substr(0,fastaFileName.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch, "", threadID);	}
 		else {
+			method = "kmer";
 			m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
 			m->mothurOutEndLine();
 			search = new KmerDB(fastaFileName, 8);
@@ -198,7 +214,7 @@ AlignmentDB::AlignmentDB(string s){
 		method = s;
 		
 		if(method == "suffix")		{	search = new SuffixDB();	}
-		else if(method == "blast")	{	search = new BlastDB("");		}
+		else if(method == "blast")	{	search = new BlastDB("", 0);		}
 		else						{	search = new KmerDB();		}