merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / sequencedb.cpp

diff --git a/sequencedb.cpp b/sequencedb.cpp
index e0bd10033459896f10c2d42fb9b3b4f6921add7f..bc8523aa78b5d217fd5cfd12c8bade6bbb630721 100644 (file)
--- a/sequencedb.cpp
+++ b/sequencedb.cpp
@@ -23,7 +23,7 @@ SequenceDB::~SequenceDB() { clear(); }
 /***********************************************************************/
 
 SequenceDB::SequenceDB(int newSize) {
-       data.resize(newSize, NULL);
+       data.resize(newSize, Sequence());
 }
 
 /***********************************************************************/
@@ -46,7 +46,7 @@ SequenceDB::SequenceDB(ifstream& filehandle) {
                        }else {  cout << "Error fasta in your file. Please correct." << endl; }
 
                        //input sequence info into sequencedb
-                       Sequence* newSequence = new Sequence(name, sequence);
+                       Sequence newSequence(name, sequence);
                        data.push_back(newSequence);
                        
                        //takes care of white space
@@ -134,10 +134,7 @@ 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";
@@ -151,9 +148,8 @@ void SequenceDB::set(int index, string newUnaligned) {
 
 /***********************************************************************/
 
-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) {
@@ -168,7 +164,7 @@ void SequenceDB::set(int index, Sequence* newSeq) {
 
 /***********************************************************************/
 
-Sequence* SequenceDB::get(int index) {
+Sequence SequenceDB::get(int index) {
        return data[index];
 }
 
@@ -176,9 +172,6 @@ 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) {
@@ -195,7 +188,6 @@ 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) {
@@ -219,7 +211,7 @@ 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) {
@@ -234,7 +226,7 @@ void SequenceDB::print(ostream& out) {
        
 /***********************************************************************/
 
-void SequenceDB::push_back(Sequence* newSequence) {
+void SequenceDB::push_back(Sequence newSequence) {
        try {
                data.push_back(newSequence);
        }