Help me to find out what is wrong with this code

[vermarajeev]

Hello everybody,
This is my second query in this post. Firstly thankx to Banfa, for helping me solve my first query.

Here is the code which I have written.

#include<iostream>
#include<fstream>
using namespace std;
 
class myClass
{
public:
    myClass(){}
    friend std::istream& operator>>(std::istream& i, myClass& ct);
    std::istream& extractor(std::istream& i);
};
 
std::istream& myClass::extractor(std::istream& i)
{
    char line[256];
    char keyword[64];
    char origKeyword[64];
    int  p;
    char cp;
    bool finished = false;
    bool endct = false;    
 
    while( i && !finished )
        {
            if( (p = i.peek()) == ';' || p == '#' )
            {
            // read the comment line and discard it
            i.getline( line, 255 );
            continue;
            }        
            // check for eof or error
            if( !i )
                continue;
            while( i && isspace( p = i.peek() ) )
            {
            i.get(cp);
            }
            // check for error or eof
            if( !i )
                continue;
 
            if( !endct )
            {
            // check for a digit, and if we don't get one it means we
            // are done with tablecounting
                if( ( p = i.peek() ) != EOF && isdigit( p ) )
                {
                    i.getline(line, sizeof(line));    
                    continue;
                }
                else
                {
                // this is the end of the connection table proper
                endct = true;
                }
            }
 
            if( ( p = i.peek() ) != EOF && isalpha( p ) )
            {
            // read the keyword, and deal with the input
            i >> origKeyword;
            // make a copy of the keyword, in case we need to put it back in the stream
            strcpy( keyword, origKeyword );
            // change to lower case
            for( char *lp = keyword; *lp; ++lp )
            {
            *lp = tolower( *lp );
            }
            if( i )
                {
                    if( !strncmp( keyword, "cis", 3 ) )
                    {
                        i.getline(line, sizeof(line));
                    }
                    else if( !strncmp( keyword, "trans", 5 ) )
                    {
                        i.getline(line, sizeof(line));
                    }
                    else if( !strncmp( keyword, "entgegen", 8 ) )
                    {
                        i.getline(line, sizeof(line));
                    }
                    else if( !strncmp( keyword, "zusammen", 8 ) )
                    {
                        i.getline(line, sizeof(line));
                    }
                    else if( !strncmp( keyword, "chiral", 6 ) )
                    {
                        i.getline(line, sizeof(line));
                    }
                    else if( !strncmp( keyword, "donttouch", 9 ) )
                    {
                        i.getline(line, sizeof(line));
                    }
                    else if( !strncmp( keyword, "startwith", 9 ) )
                    {
                        i.getline(line, sizeof(line));
                    }
                    else if( !strncmp( keyword, "keybond", 7 ) )
                    {
                        i.getline(line, sizeof(line));
                    }
                    else if( !strncmp( keyword, "planetrans", 10 ) )
                    {
                        i.getline(line, sizeof(line));
                    }
                    else if( !strncmp( keyword, "planecis", 8 ) )
                    {
                        i.getline(line, sizeof(line));
                    }
                    else if( !strncmp( keyword, "available", 9 ) )
                    {
                        i.getline(line, sizeof(line));
                    }
                    else
                    {
                        int len = strlen( origKeyword );
                        for(char c = origKeyword[len-1]; len>0; --len)
                        {
                            c = origKeyword[len - 1];                            
                            i.putback(c);
                        }
                        finished = true;
                    }
                }//if i
                continue;
            }
 
        if( EOF == i.peek() )
            break;
        }//while
        return i;
}
 
std::istream& operator>>(std::istream& i, myClass& ct)
{
    return ct.extractor( i );
}
 
bool loadFile( std::istream &i )
{
    if(i)
    {
        int ii = 1;
        char line[256];
        int  p;
        char cp;        
        bool finished = false;
        int  routesw = 2;        // routesw == 2 means the beginning of the file
 
        int  ctsw = 0;
        int  infosw = 0;        
        myClass* ct = NULL;
 
        while( i && !finished )
            {
                if( (p = i.peek()) == ';' || p == '#' )
                {
                // read the comment line and discard it
                i.getline( line, sizeof() );
                continue;
                }
 
                // check for eof or error
                if( !i )
                    continue;
 
                // If we haven't reached EOF, read the line, and parse.
                // Otherwise break the loop and finish.
                // The getline() function reads to the '\n' (or sizeof(line) - 1),
                // discards it, and appends a '\0' to the line.
                if( ( p = i.peek() ) != EOF )
                {
                    i.getline( line, sizeof(line) );
                    cout<<line<<endl;    
                    if(ii == 4017)
                    {
                        cout<<ii<<endl;
                    }
                    ii++;
                }
                else
                    break;
                if(i)
                {
                    if( strstr(line,"CONNECTION TABLE") )
                    {
                        // The connection table starts on the next line,
                        // and so we read it here. 
                        // skip blank space at the beginning of the line
                        while( i && isspace( p = i.peek() ) )
                        {
                            i.get(cp);
                        }
 
                        // check for error or eof
                        if( !i )
                            continue;
 
                        // Check for a digit, meaning we are about to read a 
                        // ConnectionTable.  Only allocate a new ct if we
                        // are not at EOF and the next line begins with a digit.
                        if( ( p = i.peek() ) != EOF && isdigit( p ) )
                        {
                            // Allocate a new connection table
                            ct = new myClass;                                        
                             i >> *ct;                                        
                        }
                        i.clear();
                        // if we are at EOF then break
                        if( EOF == i.peek() )
                        {
                            finished = true;
                            break;
                        }
                    }                    
                } //if(i)
                // check whether we are at the end of the file
            if( EOF == i.peek() )
                break;
            }//while
    return true;
    }//if(i)
    return false;
}
 
int main(int argc, char* argv[])
{
    ifstream t("eugene.ct.syn", std::ios::in );
    if(t)
    {
        t.seekg( 0, std::ios::beg );
        if(loadFile( t ))
        {
            cout<<"File loaded completely"<<endl;
        }
        else
            cout<<"File failed to load"<<endl;
    }
    t.close();
 
    return 0;
}

Please dont get scared with the size of the code. I'm trying to read a file called "eugene.ct.syn" (given below as attached file). Now I want to read the entire file from starting till end. When I run this code on Visual C++ Editor, the program doesnt read the entire file, but I get the message "File loaded completely" written in main. Finally the program throws an exception at the end. I want to read the entire file. If you open the file with Microsoft word you can see some text contents in it. My target is to read the file till "THE PROGRAM HAS NOW FINISHED THE PROBLEM." (which you can see in the file(eugene.ct. syn) given below as attchment after you open it). I'm attaching the program too for you easiness.
Also I'm not able to guess why this program throws an exception.

Thankx in advance,
Rajeev

[vermarajeev]

Hey sorry, there is some syntax error in that program.

bool loadFile( std::istream &i )
{
    if(i)
    {
        int ii = 1;
        char line[256];
        int  p;
        char cp;        
        bool finished = false;
        int  routesw = 2;        // routesw == 2 means the beginning of the file
 
        int  ctsw = 0;
        int  infosw = 0;        
        myClass* ct = NULL;
 
        while( i && !finished )
            {
                if( (p = i.peek()) == ';' || p == '#' )
                {
                // read the comment line and discard it
                i.getline( line, sizeof(line) );
                continue;
                }

There should be "sizeof(line) instead of sizeof()", Please correct that and run the program.

[vermarajeev]

Hi guys,
Aah! I think I have confused you guys. Or is that the code seems confusing.

Never mind. Let me clear. This is a simple program to read a text file. Firstly in main I call a method called "loadFile" which takes a stream as an argument.

int main(int argc, char* argv[])
{
    ifstream t("eugene.ct.syn", std::ios::in );
    if(t)
    {
      t.seekg( 0, std::ios::beg );
     if(loadFile( t ))
      {
          cout<<"File loaded completely"<<endl;
      }
     else
         cout<<"File failed to load"<<endl;
    }
    t.close();
    return 0;
}

Then in method loadFile( t ), I just start reading the file till end. During this process, I check whether if I have read any "CONNECTION TABLE" which contains only digits in the file and if yes, then I create an object of myClass and allocate space for that, then I use overloaded operator ">>" defined in myClass to read that table(containin g digits). This operation is performed by the following code.

bool loadFile( std::istream &i )
{
    if(i)
    {
      char line[256];
      int  p;
      char cp;        
      bool finished = false;    
      int  ctsw = 0;
      int  infosw = 0;        
      myClass* ct = NULL;
 
      while( i && !finished )
      {
         if( (p = i.peek()) == ';' || p == '#' )
         {
            // read the comment line and discard it
             i.getline( line, sizeof(line) );
            continue;
         }
         // check for eof or error
         if( !i )
             continue;
          // If we haven't reached EOF, read the line, and parse.
          // Otherwise break the loop and finish.
          // The getline() function reads to the '\n' (or sizeof(line) - 1),
          // discards it, and appends a '\0' to the line.
           if( ( p = i.peek() ) != EOF )
            {
               i.getline( line, sizeof(line) );
               cout<<line<<endl;                    
            }
           else
               break;
            if(i)
             {
                 if( strstr(line,"CONNECTION TABLE") )
                  {
                    // The connection table starts on the next line,
                    // and so we read it here. 
                    // skip blank space at the beginning of the line
                    while( i && isspace( p = i.peek() ) )
                     {
             i.get(cp);
                     }    
                     // check for error or eof
                     if( !i )
                       continue;
                     // Check for a digit, meaning we are about to read a 
                     // ConnectionTable.  Only allocate a new ct if we
                     // are not at EOF and the next line begins with a digit.
                     if( ( p = i.peek() ) != EOF && isdigit( p ) )
                     {
            // Allocate a new connection table
           ct = new myClass;
           i >> *ct;                
                     }
                     i.clear();
                     // if we are at EOF then break
          if( EOF == i.peek() )
         {
                   finished = true;
                       break;
         }
                  }                
             } //if(i)
       // check whether we are at the end of the file
       if( EOF == i.peek() )
          break;
      }//while
    return true;
   }//if(i)
   return false;
}

After this because of operator overloading "<<", this part of code is called

std::istream& operator>>(std::istream& i, myClass& ct)
{
    return ct.extractor( i );
}

Finally in ct.extractor(i) , Firstly I'm reading all the connection table(all digits),
shown in this part of code defined in extractor(i)

if( !endct )
{
    // check for a digit, and if we don't get one it means we
    // are done with tablecounting
    if( ( p = i.peek() ) != EOF && isdigit( p ) )
    {
       i.getline(line, sizeof(line));    
       continue;
    }
    else
    {
        // this is the end of the connection table proper
       endct = true;
    }
}

Then, I check for various conditions, If I find the particular keyword I process that otherwise I put the keyword back to stream and return that stream. As in this part of code

if( ( p = i.peek() ) != EOF && isalpha( p ) )
{
   // read the keyword, and deal with the input
   i>> origKeyword;
   // make a copy of the keyword, in case we need to put it back in the stream
   strcpy( keyword, origKeyword );
   // change to lower case
   for( char *lp = keyword; *lp; ++lp )
   {
      *lp = tolower( *lp );
   }
   if( i )
   {
   if( !strncmp( keyword, "cis", 3 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "trans", 5 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "entgegen", 8 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "zusammen", 8 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "chiral", 6 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "donttouch", 9 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "startwith", 9 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "keybond", 7 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "planetrans", 10 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "planecis", 8 ) )
   {
      i.getline(line, sizeof(line));
   } 
   else if( !strncmp( keyword, "available", 9 ) )
   {
      i.getline(line, sizeof(line));
   }
   else
   {
      int len = strlen( origKeyword );
      for(char c = origKeyword[len-1]; len>0; --len)
      {
         c = origKeyword[len - 1];                
         i.putback(c);
      }
        finished = true;
   }
   }//if i
   continue;
}

Now the problem is since the file is too large, the program reads the contents of the file(eugene.ct. syn) but not completely. Finally the program throws an exception. I'm using Visual C++ 2003 to run this program. My target is to read complete file without any runtime error.

Please help me. I'm seeking your help at the earliest.

Thanks,
Rajeev

[Ashaman0]

Nothing obviously wrong has popped out at me yet, ill try downloading your attachments to look at your code a little closer.

What is the exception you are getting thou? And have you tried using a debuging utility to try and find out where the exception is being thrown and to see exactly what your code is actually doing?

[Ashaman0]

hmm. I just compiled and ran your code on linux. Seems to work fine, no exceptions, and i think it ran all the way through.


heres the end of the output. Is that right?

LIST OF EQUIVALENT ATOMS
TOP[11] IS 11
TOP[12] IS 11
THERE IS ONE CHIRAL ATOM IN THE MOLECULE
complexity = 9
sumofcomplexity = 19
 
END OF DUMP OF m[2].
}
CT OF REACTANT
THIS IS THE CONNECTION TABLE OF m[3].
THE PRODUCT IS 2
THE COREACTANT IS 0
firstreactant 4
PRODUCTATOMS 2 1 3 4 6 7 5 8 9 10 11 12
FUNGP 4: 132 7: 115
 
REACTANTS WERE GENERATED 8293 TIMES
5793 DUPLICATE MOLECULES WERE ELIMINATED.
21 ROUTES WERE PROPOSED.
THE PROGRAM HAS NOW FINISHED THE PROBLEM.
 
Fri Sep 26 15:45:30 EDT 2003
File loaded completely

The only problem i had, was you were missing a variable on line 160.
it was
i.getline( line, sizeof( ) );
needed to be
i.getline( line, sizeof(line) );
that should have not compiled thou, not thrown an exception. Maybe a typo?

[vermarajeev]

Hi,
Thanx for your reply

That is what is more interesting about this code. Currently I'm using Microsoft Visual Studio .NET 2003 to run this program. When I run the same program on linux or Visual C++ Express Edition, it works fine.

Yeah, there was a syntax error which I have already mentioned in my previous post.
Try running the code on Microsoft Visual Studio .NET 2003 you will get an exception as "Run Time exception".

Can you suggest me why is this unusual scenario occuring?????

Thankx

[Banfa]

Microsoft aren't any good at writing software :p

Try running lint/splint over your code. If any bits are particularly complex (multiple levels of pointers to structures to pointers etc) then try re-writing them using additional local variables to simplify the code.

Use the symbolic debugger to locate the exact error and line it is occuring on. It may give you a clue.

[vermarajeev]

Hi Banfa,
I was desperately waiting for your reply. Thanks for replying my post.

Could you please tell me what is lint/splint???, I have absolutely no idea about that.
Please explain me how I can correct that error.

Thanks

[Banfa]

lint/splint/pclint are all versions (splint being free) of a utility that you can run on C/C++ code. This untility checks the code and reports Errors and Warnings much as a compiler would, however the errors and warnings it produces are normally much more detailed than most compilers and also contain information about errors that could occur at run time.

It is a useful to to ensure the rigerousness and robustness of your code.

If your code is working with 1 version of VC++ and not another version then one of the following errors has occured

1. You have used an extension that is only available in one of the versions (unlikely since it also works in Linux).

2. You have constructued the code in a way that causes a compiler bug to become apparent in the non-working version.

3. You have an error in the code that is not effecting the versions the code works on but is effecting the version that the code does not work on.

(sp)lint may help locate the problem if it is in category 3.

Using the symbolic debugger may help identify the location of the troublesome code, then visual examination may help fix the problem if it is in category 3 or if it is in category 2 then it may highlight a partiularly complex code syntax that could be simplified.

Good Luck, this is often a really hard type of bug to fix :-)

[vermarajeev]

Hi,
Glad to receive your reply :)

I just debuged the program and got to know that the stream which I'm using in my code, fails. As you can see the contents of the file "eugene", there are several strings like "Chiral", "available" , "CONNECTION TABLE" etc. As seen here for example

THIS IS STEP NUMBER 1
CONNECTION TABLE
35  0  0    6  0  0  0  0  0            0            0  0  1
17  0  0    6  0  0  0  0  0            0            0  0  1
8   4  0    5  5  0  0  0  0            0            0  0  1
8   0  1    5  0  0  0  0  0            0            0  0  0
6   4  0    3  3  4  6  0  0        1.037       0.6625  0  1
6   0  1    1  2  5  0  0  0        1.381         0.85  1  1
CHIRAL 6 C
available Name:        BROMOCHLOROACETIC ACID
available Supplier:        ALDRICH
available Price:        61.95USD/5g 97%
 
CONNECTION TABLE
8   0  0    2  3  0  0  0  0            0            0  0  1
7   0  1    1  4  0  0  0  0            0            0  0  1
6   0  3    1  0  0  0  0  0            0            0  0  1
6   0  3    2  0  0  0  0  0            0            0  0  1
available Name:        N,O-DIMETHYLHYDROXYLAMINE HYDROCHLORIDE
available Supplier:        ALDRICH
available Price:        173.70USD/100g 98%

Now suppose I'm at below shown position in the file

CHIRAL 6 C
available Name:        BROMOCHLOROACETIC ACID
available Supplier:        ALDRICH
available Price:        61.95USD/5g 97%

So when I'm at this part of the program(as shown below)

if( ( p = i.peek() ) != EOF && isalpha( p ) )
{
   // read the keyword, and deal with the input
   i>> origKeyword;
   // make a copy of the keyword, in case we need to put it back in the stream
   strcpy( keyword, origKeyword );
   // change to lower case
   for( char *lp = keyword; *lp; ++lp )
   {
      *lp = tolower( *lp );
   }
   if( i )
   {
   if( !strncmp( keyword, "cis", 3 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "trans", 5 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "entgegen", 8 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "zusammen", 8 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "chiral", 6 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "donttouch", 9 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "startwith", 9 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "keybond", 7 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "planetrans", 10 ) )
   {
      i.getline(line, sizeof(line));
   }
   else if( !strncmp( keyword, "planecis", 8 ) )
   {
      i.getline(line, sizeof(line));
   } 
   else if( !strncmp( keyword, "available", 9 ) )
   {
      i.getline(line, sizeof(line));
   }
   else
   {
      int len = strlen( origKeyword );
      for(char c = origKeyword[len-1]; len>0; --len)
      {
         c = origKeyword[len - 1];                
         i.putback(c);
      }
        finished = true;
   }
   }//if i
   continue;
}

Here in the code above the origKeyword is "CHIRAL" which I convert to lowercase and check the various conditions which satisfies this condition

else if( !strncmp( keyword, "chiral", 6 ) )
   {
      i.getline(line, sizeof(line));
   }

Then the next three line after "CHIRAL" in the file is "available" which too satisfies this part of code

else if( !strncmp( keyword, "available", 9 ) )
   {
      i.getline(line, sizeof(line));
   }

Finally when I read the next string which is "CONNECTION TABLE", else part in my code is called which is

 else
   {
      int len = strlen( origKeyword );
      for(char c = origKeyword[len-1]; len>0; --len)
      {
         c = origKeyword[len - 1];                
         i.putback(c);
      }
        finished = true;
   }

here my len is 10, so char c = 'N' , hence 'N' is pushed back to stream. The stream now contains N ...(some data in the buffer).
Next c = 'O' is pushed stream contains ON...(some data in the buffer).
Next c = 'I' is pushed stream contains ION...(some data in the buffer).
Next c = 'T' is pushed stream contains TION...(some data in the buffer).
Next c = 'C' is pushed stream contains CTION...(some data in the buffer).
Next c = 'E' is pushed stream contains ECTION...(some data in the buffer).
Next c = 'N' is pushed stream contains NECTION...(some data in the buffer).

Now peroblem starts here,
When the next c = 'N' is pushed into the stream, stream still contains "NECTION...(som e data in the buffer)" instread of "NNECTION...(so me data in the buffer)". From here onwards if whatever is pushed onto the stream "i", It shows me "NECTION...(som e data in the buffer)". But the original sequence which I want is

"NNECTION...(some data in the buffer)"
"ONNECTION...(some data in the buffer)"
"CONNECTION...(some data in the buffer)"

Because the stream is not able to push back the character after N, it fails and throws exception.
Now, what can I do to solve this problem????. I just tried using

i.seekg(ios::cur, -len)

but this too fails, as the stream fails to return the correct position.
Please help me.