set new value for data member

[tat]

Dear C++ experts,

I have a piece of code (see below).
Alignment object has a data member that is a vector of Sequence
objects.
Sequence object, in turn, has a data member that is a vector of Residue
objects.
Residue object has a data member called m_Number.
After initializing, I want to update data member (m_Number of Residue
object) via method setNumber(const string& number). This setNumber
method is supposed to change m_Number in the Residue object. However,
it does not (There is nothing on the third column of output). Changing
"string m_Number" to "mutable string m_Number" did not help.

Can someone explain me why?

Thanks,
tat

----------------------------------------------------------
#include<iostream>
#include<string>
#include<vector>
#include<fstream>

using namespace std;

class Residue {
public:
Residue(): m_Name(""), m_Number(""), m_Pos(0) {};
~Residue() {};

void initializeResidue(const char& name1, const int& align_pos) {
m_Name = name1;
m_Pos = align_pos;
}
void setName(const string& name)
{
m_Name = name;
}
string name() const
{
return m_Name;
}

void setNumber(const string& no)
{
m_Number = no;
}

string number() const {
return m_Number;
}

void setPos(const int& no)
{
m_Pos = no;
}

int pos() const {
return m_Pos;
}

private:
string m_Name;
string m_Number;
int m_Pos;
};

class Sequence {
string m_SeqName;
string m_Sequence;
vector<Residuem_Residues;
public:
Sequence(): m_SeqName(""), m_Sequence(""), m_Residues(0) {};
Sequence(const string& n, const string& s)
: m_SeqName(n), m_Sequence(s),m_Residues(0)
{
m_Residues.resize(m_Sequence.length());
for (int i = 0; i < int(m_Sequence.length()); i++) {
m_Residues.at(i).initializeResidue(m_Sequence.at(i ),i);
}
}

~Sequence() { m_Residues.clear();};

void setSequence(const string& seq) {
m_Sequence = seq;
m_Residues.resize(int(seq.length()));
for (int i = 0; i < int(seq.length()); i++) {
m_Residues.at(i).initializeResidue(seq.at(i),i);
}
}
string sequence() const {
return m_Sequence;
}
void setSeqName(const string& seq_name)
{
m_SeqName = seq_name;
}
string seqName() const {
return m_SeqName;
}

int length() const {
return m_Sequence.length();
}

Residue residue(const int& position) {
if (position >= m_Residues.size() || position < 0) {
cerr << "Index out of range\n";
exit(1);
}
else return m_Residues.at(position);
}
vector<Residueresidues() const {
return m_Residues;
}
void addResidue(Residue& res) {
m_Residues.push_back(res);
}
Sequence& operator=(const Sequence& xxx) {
if (this != &xxx) {
m_SeqName = xxx.seqName();
m_Sequence = xxx.sequence();
m_Residues = xxx.residues();
}
return *this;
}
};

typedef vector<SequenceVecS;

class Alignment {
Sequence m_RefSeq;
VecS m_ListOfSequences;
public:
Alignment(): m_ListOfSequences(0) {};
~Alignment() { m_ListOfSequences.clear(); };

Sequence refSeq() {
return m_RefSeq;
}
VecS listOfSeqs() const
{
return m_ListOfSequences;
}
void addSeq(Sequence& seq) {
m_ListOfSequences.push_back(seq);
}

void setRefSeq(const string& id) {
for (int i=0; i < int(m_ListOfSequences.size()); i++) {
if (m_ListOfSequences.at(i).seqName().find(id) != string::npos) {
m_RefSeq = m_ListOfSequences.at(i);
}
}
}

};

////////////////////////// MAIN ///////////////////////////////////

int main(int argc, char* argv[]) {
Alignment align;
Sequence seq1("1cje","KITVHFINRD");
Sequence seq2("Q5PPU4_XENLA","KLTVNFINRN");
Sequence seq3("Q9VZE1_DROME",".VNITFVRAN");
align.addSeq(seq1);align.addSeq(seq2);align.addSeq (seq3);
align.setRefSeq("1cje");
cout << align.refSeq().seqName() << "\t" << align.refSeq().sequence()
<< endl;

for (int i=0; i < align.refSeq().residues().size(); i++) {
cout << align.refSeq().residue(i).name() << "\t";
cout << align.refSeq().residue(i).pos() << "\t";
align.refSeq().residue(i).setNumber("pp");
cout << align.refSeq().residue(i).number() << "\n";
}
return 0;
}

[amirkam1]

hi tat,
The method

> Residue residue(const int& position);

is returning the "Residue" by val. So changes to object returned by
this method will not get reflected in the object stored in vector of
Sequence class.

regards,
amir
tat wrote:

Dear C++ experts,

I have a piece of code (see below).
Alignment object has a data member that is a vector of Sequence
objects.
Sequence object, in turn, has a data member that is a vector of Residue
objects.
Residue object has a data member called m_Number.
After initializing, I want to update data member (m_Number of Residue
object) via method setNumber(const string& number). This setNumber
method is supposed to change m_Number in the Residue object. However,
it does not (There is nothing on the third column of output). Changing
"string m_Number" to "mutable string m_Number" did not help.

Can someone explain me why?

Thanks,
tat

----------------------------------------------------------
#include<iostream>
#include<string>
#include<vector>
#include<fstream>

using namespace std;

class Residue {
public:
Residue(): m_Name(""), m_Number(""), m_Pos(0) {};
~Residue() {};

void initializeResidue(const char& name1, const int& align_pos) {
m_Name = name1;
m_Pos = align_pos;
}
void setName(const string& name)
{
m_Name = name;
}
string name() const
{
return m_Name;
}

void setNumber(const string& no)
{
m_Number = no;
}

string number() const {
return m_Number;
}

void setPos(const int& no)
{
m_Pos = no;
}

int pos() const {
return m_Pos;
}

private:
string m_Name;
string m_Number;
int m_Pos;
};

class Sequence {
string m_SeqName;
string m_Sequence;
vector<Residuem_Residues;
public:
Sequence(): m_SeqName(""), m_Sequence(""), m_Residues(0) {};
Sequence(const string& n, const string& s)
: m_SeqName(n), m_Sequence(s),m_Residues(0)
{
m_Residues.resize(m_Sequence.length());
for (int i = 0; i < int(m_Sequence.length()); i++) {
m_Residues.at(i).initializeResidue(m_Sequence.at(i ),i);
}
}

~Sequence() { m_Residues.clear();};

void setSequence(const string& seq) {
m_Sequence = seq;
m_Residues.resize(int(seq.length()));
for (int i = 0; i < int(seq.length()); i++) {
m_Residues.at(i).initializeResidue(seq.at(i),i);
}
}
string sequence() const {
return m_Sequence;
}
void setSeqName(const string& seq_name)
{
m_SeqName = seq_name;
}
string seqName() const {
return m_SeqName;
}

int length() const {
return m_Sequence.length();
}

Residue residue(const int& position) {
if (position >= m_Residues.size() || position < 0) {
cerr << "Index out of range\n";
exit(1);
}
else return m_Residues.at(position);
}
vector<Residueresidues() const {
return m_Residues;
}
void addResidue(Residue& res) {
m_Residues.push_back(res);
}
Sequence& operator=(const Sequence& xxx) {
if (this != &xxx) {
m_SeqName = xxx.seqName();
m_Sequence = xxx.sequence();
m_Residues = xxx.residues();
}
return *this;
}
};

typedef vector<SequenceVecS;

class Alignment {
Sequence m_RefSeq;
VecS m_ListOfSequences;
public:
Alignment(): m_ListOfSequences(0) {};
~Alignment() { m_ListOfSequences.clear(); };

Sequence refSeq() {
return m_RefSeq;
}
VecS listOfSeqs() const
{
return m_ListOfSequences;
}
void addSeq(Sequence& seq) {
m_ListOfSequences.push_back(seq);
}

void setRefSeq(const string& id) {
for (int i=0; i < int(m_ListOfSequences.size()); i++) {
if (m_ListOfSequences.at(i).seqName().find(id) != string::npos) {
m_RefSeq = m_ListOfSequences.at(i);
}
}
}

};

////////////////////////// MAIN ///////////////////////////////////

int main(int argc, char* argv[]) {
Alignment align;
Sequence seq1("1cje","KITVHFINRD");
Sequence seq2("Q5PPU4_XENLA","KLTVNFINRN");
Sequence seq3("Q9VZE1_DROME",".VNITFVRAN");
align.addSeq(seq1);align.addSeq(seq2);align.addSeq (seq3);
align.setRefSeq("1cje");
cout << align.refSeq().seqName() << "\t" << align.refSeq().sequence()
<< endl;

for (int i=0; i < align.refSeq().residues().size(); i++) {
cout << align.refSeq().residue(i).name() << "\t";
cout << align.refSeq().residue(i).pos() << "\t";
align.refSeq().residue(i).setNumber("pp");
cout << align.refSeq().residue(i).number() << "\n";
}
return 0;
}

[tat]

Hi Amir,

Thanks very much. I missed that. I actually make two mistakes. One is
what you pointed out. The other is the same kind of mistake but in the
Alignment class (Sequence refSeq()).
Now, it worked.

Regards,
tat

am******@yahoo.com wrote:

hi tat,
The method

Residue residue(const int& position);

is returning the "Residue" by val. So changes to object returned by
this method will not get reflected in the object stored in vector of
Sequence class.

regards,
amir
tat wrote:

Dear C++ experts,

I have a piece of code (see below).
Alignment object has a data member that is a vector of Sequence
objects.
Sequence object, in turn, has a data member that is a vector of Residue
objects.
Residue object has a data member called m_Number.
After initializing, I want to update data member (m_Number of Residue
object) via method setNumber(const string& number). This setNumber
method is supposed to change m_Number in the Residue object. However,
it does not (There is nothing on the third column of output). Changing
"string m_Number" to "mutable string m_Number" did not help.

Can someone explain me why?

Thanks,
tat

----------------------------------------------------------
#include<iostream>
#include<string>
#include<vector>
#include<fstream>

using namespace std;

class Residue {
public:
Residue(): m_Name(""), m_Number(""), m_Pos(0) {};
~Residue() {};

void initializeResidue(const char& name1, const int& align_pos) {
m_Name = name1;
m_Pos = align_pos;
}
void setName(const string& name)
{
m_Name = name;
}
string name() const
{
return m_Name;
}

void setNumber(const string& no)
{
m_Number = no;
}

string number() const {
return m_Number;
}

void setPos(const int& no)
{
m_Pos = no;
}

int pos() const {
return m_Pos;
}

private:
string m_Name;
string m_Number;
int m_Pos;
};

class Sequence {
string m_SeqName;
string m_Sequence;
vector<Residuem_Residues;
public:
Sequence(): m_SeqName(""), m_Sequence(""), m_Residues(0) {};
Sequence(const string& n, const string& s)
: m_SeqName(n), m_Sequence(s),m_Residues(0)
{
m_Residues.resize(m_Sequence.length());
for (int i = 0; i < int(m_Sequence.length()); i++) {
m_Residues.at(i).initializeResidue(m_Sequence.at(i ),i);
}
}

~Sequence() { m_Residues.clear();};

void setSequence(const string& seq) {
m_Sequence = seq;
m_Residues.resize(int(seq.length()));
for (int i = 0; i < int(seq.length()); i++) {
m_Residues.at(i).initializeResidue(seq.at(i),i);
}
}
string sequence() const {
return m_Sequence;
}
void setSeqName(const string& seq_name)
{
m_SeqName = seq_name;
}
string seqName() const {
return m_SeqName;
}

int length() const {
return m_Sequence.length();
}

Residue residue(const int& position) {
if (position >= m_Residues.size() || position < 0) {
cerr << "Index out of range\n";
exit(1);
}
else return m_Residues.at(position);
}
vector<Residueresidues() const {
return m_Residues;
}
void addResidue(Residue& res) {
m_Residues.push_back(res);
}
Sequence& operator=(const Sequence& xxx) {
if (this != &xxx) {
m_SeqName = xxx.seqName();
m_Sequence = xxx.sequence();
m_Residues = xxx.residues();
}
return *this;
}
};

typedef vector<SequenceVecS;

class Alignment {
Sequence m_RefSeq;
VecS m_ListOfSequences;
public:
Alignment(): m_ListOfSequences(0) {};
~Alignment() { m_ListOfSequences.clear(); };

Sequence refSeq() {
return m_RefSeq;
}
VecS listOfSeqs() const
{
return m_ListOfSequences;
}
void addSeq(Sequence& seq) {
m_ListOfSequences.push_back(seq);
}

void setRefSeq(const string& id) {
for (int i=0; i < int(m_ListOfSequences.size()); i++) {
if (m_ListOfSequences.at(i).seqName().find(id) != string::npos) {
m_RefSeq = m_ListOfSequences.at(i);
}
}
}

};

////////////////////////// MAIN ///////////////////////////////////

int main(int argc, char* argv[]) {
Alignment align;
Sequence seq1("1cje","KITVHFINRD");
Sequence seq2("Q5PPU4_XENLA","KLTVNFINRN");
Sequence seq3("Q9VZE1_DROME",".VNITFVRAN");
align.addSeq(seq1);align.addSeq(seq2);align.addSeq (seq3);
align.setRefSeq("1cje");
cout << align.refSeq().seqName() << "\t" << align.refSeq().sequence()
<< endl;

for (int i=0; i < align.refSeq().residues().size(); i++) {
cout << align.refSeq().residue(i).name() << "\t";
cout << align.refSeq().residue(i).pos() << "\t";
align.refSeq().residue(i).setNumber("pp");
cout << align.refSeq().residue(i).number() << "\n";
}
return 0;
}