X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fastamap.cpp;h=bf55493faece21cbd6c0043ac89149826c83c166;hp=f5ac122112a633de7768b251568edda33623a81c;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=648ec37228eb16075ace911dd5a5773cdfe683da

diff --git a/fastamap.cpp b/fastamap.cpp
index f5ac122..bf55493 100644
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -15,12 +15,16 @@
 void FastaMap::readFastaFile(string inFileName) {
 	try {
 		ifstream in;
-		openInputFile(inFileName, in);
+		m->openInputFile(inFileName, in);
 		string name, sequence, line;
 		sequence = "";
 		string temp;
-
+		map<string, string>::iterator itName;
+		
+		
 		while(!in.eof()){
+			if (m->control_pressed) { break; }
+			
 			Sequence currSeq(in);
 			name = currSeq.getName();
 			
@@ -28,7 +32,10 @@ void FastaMap::readFastaFile(string inFileName) {
 				if(currSeq.getIsAligned())	{	sequence = currSeq.getAligned();	}
 				else						{	sequence = currSeq.getUnaligned();	}
 				
-				seqmap[name] = sequence;  
+				itName = seqmap.find(name);
+				if (itName == seqmap.end()) { seqmap[name] = sequence;  }
+				else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+				
 				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.
@@ -39,12 +46,12 @@ void FastaMap::readFastaFile(string inFileName) {
 					//				data[sequence].groupnumber++;
 				}	
 			}
-			gobble(in);
+			m->gobble(in);
 		}
 		in.close();		
 	}
 	catch(exception& e) {
-		errorOut(e, "FastaMap", "readFastaFile");
+		m->errorOut(e, "FastaMap", "readFastaFile");
 		exit(1);
 	}
 }
@@ -54,21 +61,27 @@ void FastaMap::readFastaFile(string inFileName) {
 void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prints data
 	
 	ifstream oldNameFile;
-	openInputFile(oldNameFileName, oldNameFile);
+	m->openInputFile(oldNameFileName, oldNameFile);
 	
 	map<string,string> oldNameMap;
+	map<string, string>::iterator itName;
 	string name, list;
 	while(!oldNameFile.eof()){
-		oldNameFile >> name >> list;
+		if (m->control_pressed) { break; }
+		
+		oldNameFile >> name; m->gobble(oldNameFile);
+		oldNameFile >> list;
 		oldNameMap[name] = list;
-		gobble(oldNameFile);
+		m->gobble(oldNameFile);
 	}
 	oldNameFile.close();
 	
 	ifstream inFASTA;
-	openInputFile(inFastaFile, inFASTA);
+	m->openInputFile(inFastaFile, inFASTA);
 	string sequence;
 	while(!inFASTA.eof()){
+		if (m->control_pressed) { break; }
+		
 		Sequence currSeq(inFASTA);
 		name = currSeq.getName();
 		
@@ -76,6 +89,10 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
 			if(currSeq.getIsAligned())	{	sequence = currSeq.getAligned();	}
 			else						{	sequence = currSeq.getUnaligned();	}
 			
+			itName = seqmap.find(name);
+			if (itName == seqmap.end()) { seqmap[name] = sequence;  }
+			else { m->mothurOut("You already have a sequence named " + name + ", sequence names must be unique, please correct."); m->mothurOutEndLine(); }
+			
 			seqmap[name] = sequence;  
 			map<string,group>::iterator it = data.find(sequence);
 			if (it == data.end()) { 	//it's unique.
@@ -87,7 +104,7 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
 				//			data[sequence].groupnumber++;
 			}	
 		}
-		gobble(inFASTA);
+		m->gobble(inFASTA);
 	}
 	
 	
@@ -141,16 +158,17 @@ int FastaMap::sizeUnique(){ //returns datas size which is the number of unique s
 void FastaMap::printNamesFile(string outFileName){ //prints data
 	try {
 		ofstream outFile;
-		openOutputFile(outFileName, outFile);
+		m->openOutputFile(outFileName, outFile);
 		
 		// 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);
 	}
 }
@@ -160,16 +178,17 @@ void FastaMap::printNamesFile(string outFileName){ //prints data
 void FastaMap::printCondensedFasta(string outFileName){ //prints data
 	try {
 		ofstream out;
-		openOutputFile(outFileName, out);
+		m->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);
 	}
 }