Comperssion/Encoding

Dear People,

I have been struggling with the following problem for about a week allready, which spans several C and Java programs (i believe the problem is in the final C program however) which i will try to distill in readable segments below.

1. The true first input is a file containg a varying number of lines, where each line contains 2 floats seperated by a space.

2. The first program compresses and encodes this file using the following code:

Code:

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  /* mz values */
  error=compress2(comp_buffer, &comp_length,(const Bytef*)data.mz ,(uLongf)length,Z_DEFAULT_COMPRESSION); /* compression */
  if (error != Z_OK) {fprintf(stderr,"zlib error..exiting"); exit(EXIT_FAILURE);}
  printf("Computational (m/z) length is %i\n",(int)comp_length); /* Length needed for uncompress later */
  mz_binary=g_base64_encode (comp_buffer,comp_length); /* encoding */
  mz_length=strlen(mz_binary);
  printf("mz: %s\n",mz_binary);
  printf("mz encoded length: %d\n",mz_length);

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3. This data is entered in a DB and a subsequent Java program retrieves specific data yielding a file that has a XML-like formatting with <something>value</something>. Important aspect here is that the length of the computational_buffer is printed in the XML-like file like

Code:

---

<decoded mz length>value</decoded mz length>

---

.

4. The C program i am struggling with attempts to restore the original data and so far i have come up with the following code (yielding a segmentation fault):

Code:

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sscanf(spectral_buffer,"<decoded mz length>%i</decoded length>\n",&(glycan+teller)->decoded_mz_length);
        if (p_str=(char*)strstr(spectral_buffer,"<m/z>")) {
            p_begin=p_str+5;
            p_end=(char*)strstr(spectral_buffer,"</m/z>");
            length=p_end-p_begin;
            ((glycan+teller)->mz)=(char*)malloc(sizeof(char)*MAX_SIZE1);
            gchar *decoded_result;                                              /* pointer to memory for result in decoding */
            decoded_result=(char*)malloc(sizeof(char)*MAX_SIZE1);              /* allocating memory to the result 'block' */
            gsize decoded_mz_length;                                            /* variable for result length in decoding */
            strncpy(((glycan+teller)->mz),p_begin,length);
            *((glycan+teller)->mz+length)='\0';
            decoded_result = g_base64_decode((glycan+teller)->mz, &decoded_mz_length);  /* decoding */
            printf("length of decoded mz string is %i\n",decoded_mz_length);
            guchar *uncompressed_result;                                        /* pointer to memory for result of uncompress */
            uncompressed_result=(char*)malloc(sizeof(char)*MAX_SIZE1);          /* allocating memory to the result 'block' */
            uncompress(uncompressed_result,((glycan+teller)->decoded_mz_length),decoded_result,decoded_mz_length); /* MAGIC */
            printf("decoded & uncompressed string is %s\n",uncompressed_result);
        }

---

The header for this program is:

Code:

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#ifndef SPECTRAL_MATCHER
#define SPECTRAL_MATCHER
#define MAX_SIZE1 5120
#define MAX_SIZE2 512
char spectral_buffer[MAX_SIZE1];
/* structure to store spectral data GOES into header file */
typedef struct {
    float prec;
    int decoded_mz_length;
    int decoded_int_length;
    char* desc;
    char* mz;
    char* intensity;
} glycopeptide;
#endif

---

Could anyone point me to where i am going wrong? I think that i am giving the correct length of the uncompressed/decoded string to uncompress (printed the value in the first C program) but somehow, something goes wrong :(

Any help would be greatly appreciated.

Kind Regards,
Bas Jansen
(C-Newbie)

Forgot to add tags, can someone still do that for clarity?

If you're getting a segmentation fault, then the first thing I would suggest is to compile in debug mode and run it in the debugger. That will help pinpoint the problem for you.

If you're programming in C, the casts of the return value of malloc are unnecessary and should not be in the code.

Quote:

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The C program i am struggling with attempts to restore the original data and so far i have come up with the following code (yielding a segmentation fault):

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Did you run this code through your debugger? The debugger should be able to tell you the line number where the fault was detected, and you should be able to look at the variables to see what looks out of whack.

Jim

I use the command line gcc, it does give 2 warnings that i am not explicitly casting a variable but beyond that nothing. I will google a bit to see how debugging mode works for gcc.

@rags: I didn't know that, i'll try it ;)

You will use gdb as your debugger, and compile with -ggdb3 to compile with gcc in debug mode.

That shaves a few minutes off the googling heh

I will try this straight away once i managed to get everything set (environment wise) on my netbook (as i allready left the office for today).

You 're not checking the return value from scanf. If you do, I suspect it will return 0 since your XML end tag is incorrect.

Meh, that was a copy/paste fault on my part, i would fix it in the original post if i could o.O

Meh yourself. Rather odd copy/paste error.

I found the problem when i re-examined ramp.c. I wasn't rebuilding the structure during decoding which meant that the uncompress would never make sense to begin with. Now.. time to fix them memory leaks :P