Merge two strings by overlapped region

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# 15  
Old 04-02-2014
When I saw your answers, I did not know what I should reply, but my feeling is a mixture of embarrassment (so little I know about C), disappointment (buggy code), discourage (so much to learn) and maybe, hopelessness (not working code). I am so far away from catching the spirits of C language as compared with your catch!
From your code I need go back the bitwise and other stuffs, not my string merge anymore. I wish I could have any comments with my code corrected side by side, so I know the correct way in that situation.
Thank you very much for your time and effort, Corona688!
# 16  
Old 04-02-2014
Originally Posted by yifangt
From your code I need go back the bitwise and other stuffs
Don't worry, you can ignore everything but main() in my code like I said. They're not relevant to your problem -- they're for debugging, they print memory, I whipped them up to make those charts.

If you can start using 'char * const', that would really help I think. The compiler would catch that mistake -- just wouldn't let you do it. (Which is mostly what const is for, FYI -- a label to inform the programmer what they can and cannot do to a variable.)
I wish I could have any comments with my code corrected side by side, so I know the correct way in that situation.
You post such large programs that fixing them pretty much means rewriting them. I can update the first two lines, sure -- but if all the lines after it are written on false assumptions, that's not much help.

It'd help us if you showed your entire program again when you made changes.

Last edited by Corona688; 04-02-2014 at 07:21 PM..
This User Gave Thanks to Corona688 For This Post:
# 17  
Old 04-02-2014
I wonder if learning assembly language would help. The way pointers work is mostly because of how the CPU works. Seeing that can be revealing.
# 18  
Old 04-02-2014
What I wanted is to concatenate two strings by joining the overlapping suffix of string1 and prefix of string2. The overlapping region is merged. Here is the entire program.
#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#define MAXLEN 4096                            //Line 5, at this moment no string longer than 4096 is allowed.

//strmerg was from:
char *strmerg(char *dst, char *src)                    //Line 8
    size_t dstLen = strlen(dst);
    size_t srcLen = strlen(src);

    char *p = dst + dstLen + srcLen;            /* Line 13, Pointer to the end of the concatenated string */
    char *q = src + srcLen - 1;                    /* Line 14, Pointer to the last character of the src */
    char *r = dst + dstLen - 1;                    /* Line 15, Temp Pointer to the last character of the dst */
    char *end = r;                                /* Line 16, Permanent Pointer to the last character of the dst */
    *p = '\0';                                    /*terminating the concatened string with NULL character */

    while (q >= src) 
{                                                /*Copy src in reverse */
    if (*r == *q) {                                /*Till it matches with the src, decrement r */
    } else {
        r = end;
        if (*r == *q) {

    *p-- = *q--;

    while (r >= dst)                            /*Copy dst, ending with r */
    *p-- = *r--;

    return p + 1;                                //pointer of string, i.e. the start of string

int main(int argc, char **argv)                    //Line 39
    const char *str1 = argv[1];                 //Line 41, Original two strings
    const char *str2 = argv[2];                    //Line 42, Original two strings
    char *str3;                                    //Line 43, resulting string

    str1 = malloc(sizeof(char) * MAXLEN);        //Line 45, allocate memory
    str2 = malloc(sizeof(char) * MAXLEN);        //Line 46, allocate memory

    if (argc != 3) {
    printf("Error! \nUsage: ./arg[0]=program argv[1]=string1 argv[2]=string2\n");

    strcpy(str1, argv[1]);                        //Line 53, 
    strcpy(str2, argv[2]);                        //Line 54, 

    str3=strmerg(str1, str2);                    //Line 56,
    printf("Input strings are: \nSeq1=%s\nSeq2=%s\n", str1, str2);
    printf("\nConcatenated string is: Seq_merged=%s\n", str3);
    printf("\nConcatenated string is: Seq_merged=%s\n", strmerg(str1, str2));
    return 0;

Two questions:
1a) Syntax related: accroding to the replies, what are the right way for Lines 8, 41, 42, & 43 (and probably within the strmerg() function, Lines 13, 14, 15 may need change too)?
./prog ACGTGatatat  atatGTGTGTGT  
Input strings are: 

Concatenated string is: Seq_merged=ACGTGatatatGTGTGTGT
Concatenated string is: Seq_merged=ACGTGACGTGatatatGTGTGTGT           //Extra ACGTG

1b)Similar to 1a) Syntax related: Lines 53, 54, & 56 that should be changed coordingly, especially Line 56;
2) Algorithm related: If the repetitive overlapping region in src is longer than those in dest, merged string is NOT correct!
./prog ACGTGatat   atatatGTGTGTGT  
Input strings are: 

Concatenated string is: Seq_merged=ACGTGatatatatGTGTGTGT
Concatenated string is: Seq_merged=ACGTGACGTGatatatatGTGTGTGT           //Extra ACGTG

This is a bug with the strmerg() function.
The extra ACGTG part in seq1 seems related to the const char * str1 delcaration, but I am not sure.

Thank you again!
# 19  
Old 04-03-2014
I repeat: You've written your program around assumptions which don't hold water -- like the very idea of "str3" being a separate entity from "str1" and "str2" just because you threw pointers to the same memory into a different function. You're still modifying the memory pointed to by str1 whenever you do that!

Also, you are calling strmerge twice before you print its output -- considering str1 gets modified each time, I'm not surprised its output is doubly strange.

I suggest rewriting it from scratch with this new knowledge in mind, using that pointer suggestion I told you about so you're forced to break these habits.

Last edited by Corona688; 04-03-2014 at 01:40 AM..
# 20  
Old 04-03-2014
Since all you need to reconstruct the last try is the length of str1 you used, it is easy to reconstruct the winner even though you need to go too far to find the limit. You might even use bisection to find the right number! If str1 has 6 bytes, try 3, then 1 or 5, then 0, 2, 4, 6 to find the highest substring that works. Use the shorter length of str1 and str2, as the max overlap is that length and the min is always 0.

I helps in C to know what is going on, at least in a sensible model. Imagine a char* in a 32 bit system is a 4 byte unsigned integer offset from the bottom of memory. Values in the environment are in the heap below free memory. The heap grows up like stalagmites. Subroutine arguments and auto variables are on the stack at the top of memory growing down like stalactites. When you call, automatics may have whatever old ram content in them, so write before you read. When you exit a subroutine, the stack pointer rises above the automatics and passed variables, and the space is reused/overwritten on the next call. When you create a static or global variable, the compiler/linker allocates it on the heap. When you malloc, that is on the heap, too. Since you can free, someone has to keep track of the holes and try to reuse them. Fancy items like structs and such may be allocated on a mod 4 or 8 address, for speed. Some CPUs need aligned variables -- 4 byte integers have to have mod-4 addresses. So, space can be wasted when little and big items are mixed. If you mmap() a file region, address space is allocated, but rather than setting it up to swap to swap space, it is tied to the file. Some people do not like calling everything at the bottom 'the heap'. Dynamically linked code is mmap'd into several places. Itmight have initialized variables and constants with it, which are put in different areas, sometimes because code is on executable pages but data may be not executable, even not writable. If you run a command under truss, tusc or strace, you can see all this going on -- very educational.
This User Gave Thanks to DGPickett For This Post:
# 21  
Old 04-03-2014
Thanks DGPickett!
That's too comprehensive to integrate your idea into my code. What I lack is the practice, and I was wondering if anyone can correct my code. I like to learn by example, and not sure I should take some theory courses, if that would help.
For sure I have not yet caught the whole picture of "stack" and "heap" in theory, blank with them when handle situations in real C code.
Thank you again.
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