X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fastamap.cpp;h=36b072121b044490332a8926f0f3f287bf816fab;hb=44b464979e91c2a1f144ac45ca12c14fcf6579f0;hp=57754667da593265618aa0d9e5c046e18b2b7203;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/fastamap.cpp b/fastamap.cpp
index 5775466..36b0721 100644
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -21,29 +21,32 @@ void FastaMap::readFastaFile(string inFileName) {
 		string temp;
 
 		while(!in.eof()){
+			if (m->control_pressed) { break; }
+			
 			Sequence currSeq(in);
 			name = currSeq.getName();
 			
-			if(currSeq.getIsAligned())	{	sequence = currSeq.getAligned();	}
-			else						{	sequence = currSeq.getUnaligned();	}
-			
-			seqmap[name] = sequence;  
-			map<string,group>::iterator it = data.find(sequence);
-			if (it == data.end()) { 	//it's unique.
-				data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
-//				data[sequence].groupnumber = 1;
-				data[sequence].names = name;
-			}else { // its a duplicate.
-				data[sequence].names += "," + name;
-//				data[sequence].groupnumber++;
-			}	
-			
+			if (name != "") {
+				if(currSeq.getIsAligned())	{	sequence = currSeq.getAligned();	}
+				else						{	sequence = currSeq.getUnaligned();	}
+				
+				seqmap[name] = sequence;  
+				map<string,group>::iterator it = data.find(sequence);
+				if (it == data.end()) { 	//it's unique.
+					data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
+					//				data[sequence].groupnumber = 1;
+					data[sequence].names = name;
+				}else { // its a duplicate.
+					data[sequence].names += "," + name;
+					//				data[sequence].groupnumber++;
+				}	
+			}
 			gobble(in);
 		}
 		in.close();		
 	}
 	catch(exception& e) {
-		errorOut(e, "FastaMap", "readFastaFile");
+		m->errorOut(e, "FastaMap", "readFastaFile");
 		exit(1);
 	}
 }
@@ -58,6 +61,8 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
 	map<string,string> oldNameMap;
 	string name, list;
 	while(!oldNameFile.eof()){
+		if (m->control_pressed) { break; }
+		
 		oldNameFile >> name >> list;
 		oldNameMap[name] = list;
 		gobble(oldNameFile);
@@ -68,23 +73,26 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
 	openInputFile(inFastaFile, inFASTA);
 	string sequence;
 	while(!inFASTA.eof()){
+		if (m->control_pressed) { break; }
+		
 		Sequence currSeq(inFASTA);
 		name = currSeq.getName();
 		
-		if(currSeq.getIsAligned())	{	sequence = currSeq.getAligned();	}
-		else						{	sequence = currSeq.getUnaligned();	}
-		
-		seqmap[name] = sequence;  
-		map<string,group>::iterator it = data.find(sequence);
-		if (it == data.end()) { 	//it's unique.
-			data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
-//			data[sequence].groupnumber = 1;
-			data[sequence].names = oldNameMap[name];
-		}else { // its a duplicate.
-			data[sequence].names += "," + oldNameMap[name];
-//			data[sequence].groupnumber++;
-		}	
-		
+		if (name != "") {
+			if(currSeq.getIsAligned())	{	sequence = currSeq.getAligned();	}
+			else						{	sequence = currSeq.getUnaligned();	}
+			
+			seqmap[name] = sequence;  
+			map<string,group>::iterator it = data.find(sequence);
+			if (it == data.end()) { 	//it's unique.
+				data[sequence].groupname = name;  //group name will be the name of the first duplicate sequence found.
+				//			data[sequence].groupnumber = 1;
+				data[sequence].names = oldNameMap[name];
+			}else { // its a duplicate.
+				data[sequence].names += "," + oldNameMap[name];
+				//			data[sequence].groupnumber++;
+			}	
+		}
 		gobble(inFASTA);
 	}
 	
@@ -143,12 +151,13 @@ void FastaMap::printNamesFile(string outFileName){ //prints data
 		
 		// two column file created with groupname and them list of identical sequence names
 		for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+			if (m->control_pressed) { break; }
 			outFile << it->second.groupname << '\t' << it->second.names << endl;
 		}
 		outFile.close();
 	}
 	catch(exception& e) {
-		errorOut(e, "FastaMap", "printNamesFile");
+		m->errorOut(e, "FastaMap", "printNamesFile");
 		exit(1);
 	}
 }
@@ -161,13 +170,14 @@ void FastaMap::printCondensedFasta(string outFileName){ //prints data
 		openOutputFile(outFileName, out);
 		//creates a fasta file
 		for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+			if (m->control_pressed) { break; }
 			out << ">" << it->second.groupname << endl;
 			out << it->first << endl;
 		}
 		out.close();
 	}
 	catch(exception& e) {
-		errorOut(e, "FastaMap", "printCondensedFasta");
+		m->errorOut(e, "FastaMap", "printCondensedFasta");
 		exit(1);
 	}
 }