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Top Forums Programming C++ getline, parse and take first tokens by condition Post 302917837 by Corona688 on Thursday 18th of September 2014 06:44:13 PM
Old 09-18-2014
Quote:
Originally Posted by yifangt
For this practice, I am struggling to catch the flow of the
Code:
 sPtr = strtok(NULL, " ")

strtok() is pretty simple once you know what it does, which is why it's so fast.
Quote:
The part I am still not sure is:
1) In the line with ">", the first field is stored as one string, except the '>' char which is a separator for each record (like RS in awk).
Which line of what now?

Quote:
2) All the rest of the field next to the ">" line are concatenated to have a single string. It is easy for printing, but to track them in memory with
Code:
 sPtr = strtok(NULL, " ")

I am not sure at all.
Code:
FastaSeq[entryID] += sPtr;   // assign more token to sequence

For example, the entry:
Code:
>seq01 some description protein 
AGCTAC GTACAT C
AGTCGTGT GAT 
CGAGC GGG

Only seq01 is picked up for key on the first line, the other part are discarded; from the second row of the entry all is concatenated: AGCTACGTACATCAGTCGTGTGATCGAGCGGG for value of the map (if I insist map be used!)
strtok() discards the spaces replacing them with NULL terminators. Instead of printing a space, the string ends early. This even lets it break it into a bunch of separate mini-strings without copying it anywhere or using any more memory.

Let me illustrate it. What does this code print?

Code:
char str[]="abc def ghi jkl";

str[3]='\0';
cout << str << endl;

str[7]='\0';
cout << str+4 << endl;

str[11]='\0';
cout << str+8 << endl;

This is all strtok does, change your spaces into NULs and tell you where it started.

Quote:
I seem to understand the syntax, as I can print out the individual field parsed, but do not know how to combine certain fields together if needed.
There's much less technically wrong with your programs now, most of your problems are innocent mistakes. But an innocent mistake with a pointer makes your program explode without even telling you where or why.

This leaves you trying to fix your program by wild guessing, which is incredibly frustrating. Let me help you out.

Code:
#include <stdio.h>
#include <string.h>
#include <assert.h>

int main() {
         char str[]="abc def ghi";
         char *ptr=strtok(str, " ");

        // printf would crash if we fed it NULL.
        // so we tell assert, "we are assuming ptr != NULL"
        // and if your assumption is incorrect, it dies.
        assert(ptr != NULL);
        printf("%s\n", ptr);

        ptr=strtok(NULL, " ");
        assert(ptr != NULL);
        printf("%s\n", ptr);

        ptr=strtok(NULL, " ");
        assert(ptr != NULL);
        printf("%s\n", ptr);

        ptr=strtok(NULL, " ");
        assert(ptr != NULL);
        printf("%s\n", ptr);

        ptr=strtok(NULL, " ");
        assert(ptr != NULL);
        printf("%s\n", ptr);
}

Code:
$ gcc myassert.c
$ ./a.out
abc
def
ghi
a.out: assert.c:24: main: Assertion `ptr != ((void *)0)' failed.
Aborted

$

You can consider an assert to be a "controlled crash". This should take a lot of the mystery out of your programs because, unlike a segfault, it tells you exactly where and why it broke down. You can dump them wherever you want without changing your program logic.

Quote:
Maybe I should not say I understand the syntax.

How the pointer/reference is manipulated behind is the bottleneck for me to catch the whole point. Can you elaborate that? Thanks!
It might surprise you just how short a function strtok() is. Here's a simplified one for clarity:

Code:
#include <stdio.h>

char *last; /* Store the last value my_strtok used */

/**
 * A simplified strtok that only uses one char as a token.
 * The real strtok takes a string, and stops at ANY char in it.
 *
 * 'first' points to the first character in the string.
 * If we give it NULL, it assumes 'last'.
 *
 * It points to wherever it left off in the global variable 'last'.
 */
char *my_tok(char *first, char c)
{
        int pos=0;

        /* If given a string, start over here */
        if(first != NULL)       last=first;

        first=last;     /* Pick up wherever we left off */

        /* Our very first char is NULL?  Give up. */
        if(first[0] == '\0') return(NULL);

        /* Increment 'pos' until we find c or NULL */
        while(first[pos] && (first[pos] != c)) pos++;

        /**
         * If we found a separator, replace it with a NULL terminator
         * The string beginning in 'first' will now stop early, here.
         *
         * A 'while' loop is used to catch several in a row.
         */
        while(first[pos]==c)
        {
                first[pos]='\0';
                pos++;
        }

        // Remember exactly where we left off.
        last += pos;

        // Return a pointer to where we started.
        return(first);
}

int main(void) {
        char buf[128]="abcd  efgh  jklm  nop";
        char *tok=my_tok(buf, ' ');

        while(tok != NULL)
        {
                fprintf(stderr, "tok=%s\n", tok);
                tok=my_tok(NULL, ' ');
        }
}

Code:
$ gcc mystr.c
$ ./a.out

tok=abcd
tok=efgh
tok=jklm
tok=nop

$


Last edited by Corona688; 09-18-2014 at 07:52 PM..
This User Gave Thanks to Corona688 For This Post:
 

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