X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequencedb.cpp;h=9ddb40f44a7e9ded9ba12a625e647c5abd3bed43;hb=6e81846c8e5b2614f6b06643a9f558fb0e6669fa;hp=e0bd10033459896f10c2d42fb9b3b4f6921add7f;hpb=faf4e99552d6fb4595ff348b1f909ddc74536da2;p=mothur.git

diff --git a/sequencedb.cpp b/sequencedb.cpp
index e0bd100..9ddb40f 100644
--- a/sequencedb.cpp
+++ b/sequencedb.cpp
@@ -15,7 +15,7 @@
 
 /***********************************************************************/
 
-SequenceDB::SequenceDB() {}
+SequenceDB::SequenceDB() {  m = MothurOut::getInstance();  }
 /***********************************************************************/
 //the clear function free's the memory
 SequenceDB::~SequenceDB() { clear(); }
@@ -23,31 +23,20 @@ SequenceDB::~SequenceDB() { clear(); }
 /***********************************************************************/
 
 SequenceDB::SequenceDB(int newSize) {
-	data.resize(newSize, NULL);
+	data.resize(newSize, Sequence());
 }
 
 /***********************************************************************/
 
 SequenceDB::SequenceDB(ifstream& filehandle) {
 	try{
-		string name, sequence, line;
-		sequence = "";
-		int c;
-		string temp;
-		
-		
+				
 		//read through file
-		while ((c = filehandle.get()) != EOF) {
-			name = ""; sequence = ""; 
-			//is this a name
-			if (c == '>') { 
-				name = readName(filehandle); 
-				sequence = readSequence(filehandle); 
-			}else {  cout << "Error fasta in your file. Please correct." << endl; }
-
+		while (!filehandle.eof()) {
 			//input sequence info into sequencedb
-			Sequence* newSequence = new Sequence(name, sequence);
-			data.push_back(newSequence);
+			Sequence newSequence(filehandle);
+			
+			if (newSequence.getName() != "") {   data.push_back(newSequence);  }
 			
 			//takes care of white space
 			gobble(filehandle);
@@ -57,11 +46,7 @@ SequenceDB::SequenceDB(ifstream& filehandle) {
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function SequenceDB. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SequenceDB class function SequenceDB. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SequenceDB", "SequenceDB");
 		exit(1);
 	}
 }
@@ -82,11 +67,7 @@ string SequenceDB::readName(ifstream& in) {
 		return name;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SequenceDB class function readName. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SequenceDB", "readName");
 		exit(1);
 	}
 }
@@ -115,11 +96,7 @@ string SequenceDB::readSequence(ifstream& in) {
 		return sequence;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SequenceDB class function readSequence. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SequenceDB", "readSequence");
 		exit(1);
 	}
 }
@@ -134,41 +111,29 @@ int SequenceDB::getNumSeqs() {
 
 void SequenceDB::set(int index, string newUnaligned) {
 	try {
-		if (data[index] != NULL) {  delete data[index];  } //free memory
-	
-		Sequence* newSeq = new Sequence(data[index]->getName(), newUnaligned);
-		data[index] = newSeq;
+		data[index] = Sequence(data[index].getName(), newUnaligned);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SequenceDB class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SequenceDB", "set");
 		exit(1);
 	}
 }
 
 /***********************************************************************/
 
-void SequenceDB::set(int index, Sequence* newSeq) {
+void SequenceDB::set(int index, Sequence newSeq) {
 	try {
-		if (data[index] != NULL) {  delete data[index];  } //free memory
 		data[index] = newSeq;
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SequenceDB class function set. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SequenceDB", "set");
 		exit(1);
 	}
 }
 
 /***********************************************************************/
 
-Sequence* SequenceDB::get(int index) {
+Sequence SequenceDB::get(int index) {
 	return data[index];
 }
 
@@ -176,17 +141,10 @@ Sequence* SequenceDB::get(int index) {
 
 void SequenceDB::resize(int newSize) {
 	try {
-		int size = data.size();
-	
-		for (int i = size; i > newSize; i--) {	delete data[i];	}
 		data.resize(newSize);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function resize. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SequenceDB class function resize. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SequenceDB", "resize");
 		exit(1);
 	}
 }
@@ -195,15 +153,10 @@ void SequenceDB::resize(int newSize) {
 
 void SequenceDB::clear() {
 	try {
-		for (int i = 0; i < data.size(); i++) { delete data[i];  }
 		data.clear();
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SequenceDB class function clear. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SequenceDB", "clear");
 		exit(1);
 	}
 }
@@ -219,31 +172,23 @@ int SequenceDB::size() {
 void SequenceDB::print(ostream& out) {
 	try {
 		for(int i = 0; i < data.size(); i++) {
-			data[i]->printSequence(out);
+			data[i].printSequence(out);
 		}
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SequenceDB class function print. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SequenceDB", "print");
 		exit(1);
 	}
 }
 	
 /***********************************************************************/
 
-void SequenceDB::push_back(Sequence* newSequence) {
+void SequenceDB::push_back(Sequence newSequence) {
 	try {
 		data.push_back(newSequence);
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the SequenceDB class Function add. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}
-	catch(...) {
-		cout << "An unknown error has occurred in the SequenceDB class function add. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "SequenceDB", "push_back");
 		exit(1);
 	}
 }