X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequencedb.cpp;h=e0bd10033459896f10c2d42fb9b3b4f6921add7f;hb=faf4e99552d6fb4595ff348b1f909ddc74536da2;hp=f948bf355c84f18f7e67573ab77952d0f1e0cbf3;hpb=d5d2761f88b41f1006d0b700e0ab51e2ce48b875;p=mothur.git

diff --git a/sequencedb.cpp b/sequencedb.cpp
index f948bf3..e0bd100 100644
--- a/sequencedb.cpp
+++ b/sequencedb.cpp
@@ -16,16 +16,113 @@
 /***********************************************************************/
 
 SequenceDB::SequenceDB() {}
+/***********************************************************************/
+//the clear function free's the memory
+SequenceDB::~SequenceDB() { clear(); }
 
 /***********************************************************************/
 
 SequenceDB::SequenceDB(int newSize) {
-	data.resize(newSize);
+	data.resize(newSize, NULL);
 }
 
 /***********************************************************************/
 
-SequenceDB::SequenceDB(ifstream&) {}
+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; }
+
+			//input sequence info into sequencedb
+			Sequence* newSequence = new Sequence(name, sequence);
+			data.push_back(newSequence);
+			
+			//takes care of white space
+			gobble(filehandle);
+		}
+
+		filehandle.close();
+		
+	}
+	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";
+		exit(1);
+	}
+}
+/*******************************************************************************/
+string SequenceDB::readName(ifstream& in) {
+	try{
+		string name = "";
+		int c;
+		string temp;
+		
+		while ((c = in.get()) != EOF) {
+			//if c is not a line return
+			if (c != 10) {
+				name += c;
+			}else { break;  }
+		}
+			
+		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";
+		exit(1);
+	}
+}
+
+/*******************************************************************************/
+string SequenceDB::readSequence(ifstream& in) {
+	try{
+		string sequence = "";
+		string line;
+		int pos, c;
+		
+		while (!in.eof()) {
+			//save position in file in case next line is a new name.
+			pos = in.tellg();
+			line = "";
+			in >> line;			
+			//if you are at a new name
+			if (line[0] == '>') {
+				//put file pointer back since you are now at a new name
+				in.seekg(pos, ios::beg);
+				c = in.get();  //because you put it back to a newline char
+				break;
+			}else {  sequence += line;	}
+		}
+			
+		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";
+		exit(1);
+	}
+}
 	
 /***********************************************************************/
 
@@ -36,32 +133,79 @@ int SequenceDB::getNumSeqs() {
 /***********************************************************************/
 
 void SequenceDB::set(int index, string newUnaligned) {
-	Sequence newSeq(data[index].getName(), newUnaligned);
-	data[index] = newSeq;
+	try {
+		if (data[index] != NULL) {  delete data[index];  } //free memory
+	
+		Sequence* newSeq = new Sequence(data[index]->getName(), newUnaligned);
+		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";
+		exit(1);
+	}
 }
 
 /***********************************************************************/
 
-void SequenceDB::set(int index, Sequence newSeq) {
-	data[index] = 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";
+		exit(1);
+	}
 }
 
 /***********************************************************************/
 
-Sequence SequenceDB::get(int index) {
+Sequence* SequenceDB::get(int index) {
 	return data[index];
 }
 
 /***********************************************************************/
 
-void SequenceDB::changeSize(int newSize) {
-	data.resize(newSize);
+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";
+		exit(1);
+	}
 }
 
 /***********************************************************************/
 
 void SequenceDB::clear() {
-	data.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";
+		exit(1);
+	}
 }
 
 /***********************************************************************/
@@ -73,22 +217,36 @@ int SequenceDB::size() {
 /***********************************************************************/
 
 void SequenceDB::print(ostream& out) {
-	for(int i = 0; i < data.size(); i++)
-		data[i].printSequence(out);
+	try {
+		for(int i = 0; i < data.size(); i++) {
+			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";
+		exit(1);
+	}
 }
 	
 /***********************************************************************/
 
-void SequenceDB::add(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 RAbundVector class Function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		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 RAbundVector class function push_back. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		cout << "An unknown error has occurred in the SequenceDB class function add. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 		exit(1);
 	}
-}
\ No newline at end of file
+}
+
+/***********************************************************************/
+