X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=fastamap.cpp;h=bf55493faece21cbd6c0043ac89149826c83c166;hp=9b2438f4e18986f7fc362c71f77c3e71caa448a3;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=163b300cfd7d4ca4e70c454be20f07b1d8346650

diff --git a/fastamap.cpp b/fastamap.cpp
index 9b2438f..bf55493 100644
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -15,39 +15,43 @@
 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();
 			
-			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);
+			if (name != "") {
+				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(); }
+				
+				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++;
+				}	
+			}
+			m->gobble(in);
 		}
 		in.close();		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the FastaMap class function readFastaFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "FastaMap", "readFastaFile");
 		exit(1);
 	}
 }
@@ -57,39 +61,50 @@ 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();
 		
-		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);
+		if (name != "") {
+			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.
+				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++;
+			}	
+		}
+		m->gobble(inFASTA);
 	}
 	
 	
@@ -143,20 +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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the FastaMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "FastaMap", "printNamesFile");
 		exit(1);
 	}
 }
@@ -166,20 +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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the FastaMap class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the FastaMap class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "FastaMap", "printCondensedFasta");
 		exit(1);
 	}
 }