source: src/helpers.hpp@ 02da9e

/** \file helpers.hpp
 *
 * Declaration of some auxiliary functions for memory dis-/allocation and so on
 */

#ifndef HELPERS_HPP_
#define HELPERS_HPP_

using namespace std;

#include <iostream>
#include <iomanip>
#include <fstream>
#include <sstream>
#include <math.h>
#include <string>
#include <string.h>
#include <stdio.h>
#include <stdlib.h>
#include <time.h>

#include "defs.hpp"

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

/********************************************** helpful functions *********************************/

// taken out of TREMOLO
/*@-namechecks@*/
#ifndef __GNUC__
# undef __attribute__
# define __attribute__(x)
#endif
/*@=namechecks@*/

/* Behandelt aufgetretene Fehler. error ist der Fehlertyp(enum Errors)
         void *SpecialData ist ein untypisierter Zeiger auf Spezielle Daten zur Fehlerbehandlung.
         Man koennte auch noch einen Zeiger auf eine Funktion uebergeben */
extern void /*@exits@*/ debug(const char *output);
        //__attribute__ ((__return__));
#define debug(data) debug_in((data), __FILE__, __LINE__)

extern void /*@exits@*/ debug_in(const char *output,
                const char *file, const int line);
        //__attribute__ ((__return__));

double ask_value(const char *text);
bool check_bounds(double *x, double *cell_size);
void bound(double *b, double lower_bound, double upper_bound);
void flip(double *x, double *y);
int pot(int base, int n);
void * Malloc(size_t size, const char* output);
void * Calloc(size_t size, const char* output);
void * ReAlloc(void * OldPointer, size_t size, const char* output);
char* MallocString(size_t size, const char* output);
void Free(void ** buffer, const char* output);
char *FixedDigitNumber(const int FragmentNumber, const int digits);
bool IsValidNumber( const char *string);

/********************************************** helpful template functions *********************************/

/** Creates a lookup table for true father's Atom::Nr -> atom ptr.
 * \param *out output stream for debugging
 * \param *start begin of chain list
 * \paran *end end of chain list
 * \param **Lookuptable pointer to return allocated lookup table (should be NULL on start)
 * \param count optional predetermined count for table (otherwise we set the count to highest true father id)
 * \return true - success, false - failure
 */
template <typename T> bool CreateFatherLookupTable(ofstream *out, T *start, T *end, T **&LookupTable, int count = 0)
{
        bool status = true;
        T *Walker = NULL;
        int AtomNo;

        if (LookupTable != NULL) {
                *out << "Pointer for Lookup table is not NULL! Aborting ..." <<endl;
                return false;
        }

        // count them
        if (count == 0) {
                Walker = start;
                while (Walker->next != end) { // create a lookup table (Atom::nr -> atom) used as a marker table lateron
                        Walker = Walker->next;
                        count = (count < Walker->GetTrueFather()->nr) ? Walker->GetTrueFather()->nr : count;
                }
        }
        if (count <= 0) {
                *out << "Count of lookup list is 0 or less." << endl;
                return false;
        }

        // allocat and fill
        LookupTable = (T **) Malloc(sizeof(T *)*count, "CreateFatherLookupTable - **LookupTable");
        if (LookupTable == NULL) {
                cerr << "LookupTable memory allocation failed!" << endl;
                status = false;
        } else {
                for (int i=0;i<count;i++)
                        LookupTable[i] = NULL;
                Walker = start;
                while (Walker->next != end) { // create a lookup table (Atom::nr -> atom) used as a marker table lateron
                        Walker = Walker->next;
                        AtomNo = Walker->GetTrueFather()->nr;
                        if ((AtomNo >= 0) && (AtomNo < count)) {
                                //*out << "Setting LookupTable[" << AtomNo << "] to " << *Walker << endl;
                                LookupTable[AtomNo] = Walker;
                        } else {
                                *out << "Walker " << *Walker << " exceeded range of nuclear ids [0, " << count << ")." << endl;
                                status = false;
                                break;
                        }
                }
        }

        return status;
};

/******************************** Some templates for list management ***********************************/

/** Adds linking of an item to a list.
 * \param *walker
 * \return true - adding succeeded, false - error in list
 */
template <typename X> void link(X *walker, X *end)
{
        X *vorher = end->previous;
        if (vorher != NULL)
                vorher->next = walker;
        end->previous = walker;
        walker->previous = vorher;
        walker->next = end;
};

/** Removes linking of an item in a list.
 * \param *walker
 * \return true - removing succeeded, false - given item not found in list
 */
template <typename X> void unlink(X *walker)
{
        if (walker->next != NULL)
                walker->next->previous = walker->previous;
        if (walker->previous != NULL)
                walker->previous->next = walker->next;
};

/** Adds new item before an item \a *end in a list.
 * \param *pointer       item to be added
 * \param *end  end of list
 * \return true - addition succeeded, false - unable to add item to list
 */
template <typename X>   bool add(X *pointer, X *end)
{
        if (end != NULL) {
                link(pointer, end);
        } else {
                pointer->previous = NULL;
                pointer->next = NULL;
        }
        return true;
};

/** Finds item in list
 * \param *suche        search criteria
 * \param *start        begin of list
 * \param *end  end of list
 * \return X - if found, NULL - if not found
 */
template <typename X, typename Y> X * find(Y *suche, X *start, X *end)
{
        X *walker = start;
        while (walker->next != end) { // go through list
                walker = walker->next; // step onward beforehand
                if (*walker->sort == *suche) return (walker);
        }
        return NULL;
};

/** Removes an item from the list without check.
 * \param *walker item to be removed
 * \return true - removing succeeded, false - given item not found in list
 */
template <typename X> void removewithoutcheck(X *walker)
{
        if (walker != NULL) {
                unlink(walker);
                delete(walker);
                walker = NULL;
        }
};

/** Removes an item from the list, checks if exists.
 * Checks beforehand if atom is really within molecule list.
 * \param *pointer       item to be removed
 * \param *start        begin of list
 * \param *end  end of list
 * \return true - removing succeeded, false - given item not found in list
 */
template <typename X> bool remove(X *pointer, X *start, X *end)
{
        X *walker = find (pointer->sort, start, end);
/*      while (walker->next != pointer) { // search through list
                walker = walker->next;
                if (walker == end) return false;        // item not found in list
        }*/
        // atom found, now unlink
        if (walker != NULL)
                removewithoutcheck(walker);
        else
                return false;
        return true;
};

/** Cleans the whole list.
 * \param *start begin of list
 * \param *end end of list
 * \return true - list was cleaned successfully, false - error in list structure
 */
template <typename X> bool cleanup(X *start, X *end)
{
        X *pointer = start->next;
        X *walker;
        while (pointer != end) { // go through list
                walker = pointer; // mark current
                pointer = pointer->next; // step onward beforehand
                // remove walker
                unlink(walker);
                delete(walker);
                walker = NULL;
        }
        return true;
};

/** Returns the first marker in a chain list.
 * \param *me one arbitrary item in chain list
 * \return poiner to first marker
 */
template <typename X> X *GetFirst(X *me)
{
        X *Binder = me;
        while(Binder->previous != NULL)
                Binder = Binder->previous;
        return Binder;
};

/** Returns the last marker in a chain list.
 * \param *me one arbitrary item in chain list
 * \return poiner to last marker
 */
template <typename X> X *GetLast(X *me)
{
        X *Binder = me;
        while(Binder->next != NULL)
                Binder = Binder->next;
        return Binder;
};

/** Frees a two-dimensional array.
 * \param *ptr pointer to array
 * \param dim first dim of array
 */
template <typename X> void Free2DArray(X **ptr, int dim)
{
        int i;
        if (ptr != NULL) {
                for(i=dim;i--;)
                        if (ptr[i] != NULL)
                                free(ptr[i]);
                free(ptr);
        }
};

/************************************* Class Verbose & Binary *******************************/

/** Verbose is an IO manipulator, that writes tabs according to \a Verbosity level.
 */
class Verbose
{
        public:
                Verbose(int value) : Verbosity(value) { }

                ostream& print (ostream &ost) const;
        private:
                int Verbosity;
};

ostream& operator<<(ostream& ost,const Verbose& m);

/** Binary is an IO manipulator, that writes 0 and 1 according to number \a Binary.
 */
class Binary
{
        public:
                Binary(int value) : BinaryNumber(value) { }

                ostream& print (ostream &ost) const;
        private:
                int BinaryNumber;
};

ostream& operator<<(ostream& ost,const Binary& m);



#endif /*HELPERS_HPP_*/