X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alignmentdb.cpp;h=51fb17517f3598fa975c5349fcf9fe4af1dbec90;hb=aba5f8811829037b0a3004ef33f0ad4ed5e5fcf8;hp=52eedf80cbdc0991249d9eb6deca30e006d665a8;hpb=c82900be3ceed3d9bc491bdc98b1819ef85c1af7;p=mothur.git

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index 52eedf8..51fb175 100644
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -16,17 +16,20 @@
 /**************************************************************************************************/
 AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch){		//	This assumes that the template database is in fasta format, may 
 	try {											//	need to alter this in the future?
+		m = MothurOut::getInstance();
 		longest = 0;
-		
+
 		ifstream fastaFile;
 		openInputFile(fastaFileName, fastaFile);
 		
-		mothurOutEndLine();
-		mothurOut("Reading in the " + fastaFileName + " template sequences...\t");	cout.flush();
+		m->mothurOutEndLine();
+		m->mothurOut("Reading in the " + fastaFileName + " template sequences...\t");	cout.flush();
 		
 		while (!fastaFile.eof()) {
 			Sequence temp(fastaFile);  gobble(fastaFile);
 			
+			if (m->control_pressed) {  templateSequences.clear(); break;  }
+			
 			if (temp.getName() != "") {
 				templateSequences.push_back(temp);
 				//save longest base
@@ -39,8 +42,8 @@ AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, floa
 		fastaFile.close();
 		//all of this is elsewhere already!
 		
-		mothurOut("DONE.");
-		mothurOutEndLine();	cout.flush();
+		m->mothurOut("DONE.");
+		m->mothurOutEndLine();	cout.flush();
 		
 		//in case you delete the seqs and then ask for them
 		emptySequence = Sequence();
@@ -61,28 +64,29 @@ AlignmentDB::AlignmentDB(string fastaFileName, string method, int kmerSize, floa
 		else if(method == "suffix")		{	search = new SuffixDB(numSeqs);								}
 		else if(method == "blast")		{	search = new BlastDB(gapOpen, gapExtend, match, misMatch);	}
 		else {
-			mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
-			mothurOutEndLine();
+			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);
 		}
 		
-		if (needToGenerate) {
-		
-			//add sequences to search 
-			for (int i = 0; i < templateSequences.size(); i++) {
-				search->addSequence(templateSequences[i]);
+		if (!(m->control_pressed)) {
+			if (needToGenerate) {
+				//add sequences to search 
+				for (int i = 0; i < templateSequences.size(); i++) {
+					search->addSequence(templateSequences[i]);
+				}
+				search->generateDB();
+				
+			}else if ((method == "kmer") && (!needToGenerate)) {
+				ifstream kmerFileTest(kmerDBName.c_str());
+				search->readKmerDB(kmerFileTest);	
 			}
-			search->generateDB();
 			
-		}else if ((method == "kmer") && (!needToGenerate)) {
-			ifstream kmerFileTest(kmerDBName.c_str());
-			search->readKmerDB(kmerFileTest);	
+			search->setNumSeqs(numSeqs);
 		}
-		
-		search->setNumSeqs(numSeqs);
 	}
 	catch(exception& e) {
-		errorOut(e, "AlignmentDB", "AlignmentDB");
+		m->errorOut(e, "AlignmentDB", "AlignmentDB");
 		exit(1);
 	}
 }
@@ -99,7 +103,7 @@ Sequence AlignmentDB::findClosestSequence(Sequence* seq) {
 		
 	}
 	catch(exception& e) {
-		errorOut(e, "AlignmentDB", "findClosestSequence");
+		m->errorOut(e, "AlignmentDB", "findClosestSequence");
 		exit(1);
 	}
 }