X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=sequencedb.cpp;h=e798ee14ac70837e795a7be3191a14f68788c234;hp=e8aade76284c73749af5799233a1ded3ef90f0a1;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b

diff --git a/sequencedb.cpp b/sequencedb.cpp
index e8aade7..e798ee1 100644
--- a/sequencedb.cpp
+++ b/sequencedb.cpp
@@ -3,7 +3,7 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 4/13/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
@@ -15,17 +15,100 @@
 
 /***********************************************************************/
 
-SequenceDB::SequenceDB() {}
+SequenceDB::SequenceDB() {  m = MothurOut::getInstance();  length = 0; samelength = true; }
+/***********************************************************************/
+//the clear function free's the memory
+SequenceDB::~SequenceDB() { clear(); }
 
 /***********************************************************************/
 
 SequenceDB::SequenceDB(int newSize) {
-	data.resize(newSize);
+	data.resize(newSize, Sequence());
+	length = 0; samelength = true;
 }
 
 /***********************************************************************/
 
-SequenceDB::SequenceDB(ifstream&) {}
+SequenceDB::SequenceDB(ifstream& filehandle) {
+	try{
+		length = 0; samelength = true;
+				
+		//read through file
+		while (!filehandle.eof()) {
+			//input sequence info into sequencedb
+			Sequence newSequence(filehandle);
+			
+			if (newSequence.getName() != "") {   
+				if (length == 0) { length = newSequence.getAligned().length(); }
+				if (length != newSequence.getAligned().length()) { samelength = false; }
+				data.push_back(newSequence);  
+			}
+			
+			//takes care of white space
+			m->gobble(filehandle);
+		}
+
+		filehandle.close();
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SequenceDB", "SequenceDB");
+		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) {
+		m->errorOut(e, "SequenceDB", "readName");
+		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;	}
+		}
+		
+		if (length == 0) { length = sequence.length(); }
+		if (length != sequence.length()) { samelength = false; }
+		
+		return sequence;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SequenceDB", "readSequence");
+		exit(1);
+	}
+}
 	
 /***********************************************************************/
 
@@ -36,14 +119,31 @@ int SequenceDB::getNumSeqs() {
 /***********************************************************************/
 
 void SequenceDB::set(int index, string newUnaligned) {
-	Sequence newSeq(data[index].getName(), newUnaligned);
-	data[index] = newSeq;
+	try {
+		if (length == 0) { length = newUnaligned.length(); }
+		if (length != newUnaligned.length()) { samelength = false; }
+		
+		data[index] = Sequence(data[index].getName(), newUnaligned);
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SequenceDB", "set");
+		exit(1);
+	}
 }
 
 /***********************************************************************/
 
 void SequenceDB::set(int index, Sequence newSeq) {
-	data[index] = newSeq;
+	try {
+		if (length == 0) { length = newSeq.getAligned().length(); }
+		if (length != newSeq.getAligned().length()) { samelength = false; }
+
+		data[index] = newSeq;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SequenceDB", "set");
+		exit(1);
+	}
 }
 
 /***********************************************************************/
@@ -54,14 +154,26 @@ Sequence SequenceDB::get(int index) {
 
 /***********************************************************************/
 
-void SequenceDB::changeSize(int newSize) {
-	data.resize(newSize);
+void SequenceDB::resize(int newSize) {
+	try {
+		data.resize(newSize);
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SequenceDB", "resize");
+		exit(1);
+	}
 }
 
 /***********************************************************************/
 
 void SequenceDB::clear() {
-	data.clear();
+	try {
+		data.clear();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SequenceDB", "clear");
+		exit(1);
+	}
 }
 
 /***********************************************************************/
@@ -73,22 +185,31 @@ 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) {
+		m->errorOut(e, "SequenceDB", "print");
+		exit(1);
+	}
 }
 	
 /***********************************************************************/
 
-void SequenceDB::add(Sequence newSequence) {
+void SequenceDB::push_back(Sequence newSequence) {
 	try {
+		if (length == 0) { length = newSequence.getAligned().length(); }
+		if (length != newSequence.getAligned().length()) { samelength = false; }
+
 		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";
+		m->errorOut(e, "SequenceDB", "push_back");
 		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";
-		exit(1);
-	}
-}
\ No newline at end of file
+}
+
+/***********************************************************************/
+