source: tags/arb-6.0/GDE/SUPPORT/Flatio.c

/* #include <malloc.h> */
#include <stdio.h>
#define TRUE 1
#define FALSE 0
#define MAX(a,b) ((a)>(b)?(a):(b))
#define MIN(a,b) ((a)<(b)?(a):(b))

struct data_format
{
        int length;
        char *nuc;
        int offset;
        char name[64];
        char type;
};


ErrorOut(code,string)
int code;
char *string;
{
        if (code == 0)
        {
                fprintf(stderr,"Error:%s\n",string);
                exit(1);
        }
        return 0;
}

char *Calloc2(count,size)
     int count,size;
{
        char *temp;

        temp = (char*)calloc(count,size);
        if(temp == NULL)
        {
                fprintf(stdout,"Error in Calloc\n");
                exit(-1);
        }
        else
                return(temp);
}

char *Realloc(block,size)
char *block;
int size;
{
    char *temp;
    temp =(char*)realloc(block,size);
    if(temp == NULL)
    {
                fprintf(stdout,"Error in Calloc\n");
                exit(-1);
    }
    else
        return(temp);
}



int ReadFlat(file,align,maxseqs)
FILE *file;
struct data_format align[];
int maxseqs;
{
        int j,len=0, count=-1,offset;
        unsigned maxlen = 1024;
        char Inline[1025];

        if(file == NULL)
            ErrorOut(0, "Cannot open data file");

        for(;fgets(Inline,1024,file) != NULL;)
        {
                Inline[strlen(Inline)-1] = '\0';
                switch(Inline[0])
                {
                        case '>':
                        case '#':
                        case '%':
                        case '"':
                        case '@':
                                offset = 0;
                                for(j=0;j<strlen(Inline);j++)
                                {
                                        if(Inline[j] == '(')
                                        {
                                                sscanf((char*)
                                                        (Inline+j+1),"%d",
                                                        &offset);
                                                Inline[j] = '\0';
                                        }
                                }

                                if(count != -1)
                                {
                                        align[count].length = len;
                                        align[count].nuc[len] = '\0';
                                        maxlen = len;
                                }

                                count++;
                                if(count > maxseqs)
                                    ErrorOut(0, "Sorry, alignment is too large");

                                align[count].nuc = Calloc2(maxlen,sizeof(char));
                                align[count].type = Inline[0];
                                align[count].offset = offset;
                                if( align[count].nuc == NULL)
                                    ErrorOut(0, "Calloc problem");

                                sscanf((char*)(Inline+1),"%s",
                                        align[count].name);
                                len = 0;
                                break;
                        default:
                                if(len+strlen(Inline) > maxlen)
                                {
                                        maxlen = (maxlen+strlen(Inline))*2;
                                        align[count].nuc =
                                        Realloc(align[count].nuc, maxlen);
                                }
                                for(j=0;j<strlen(Inline);j++)
                                        align[count].nuc[j+len] = Inline[j];
                                len += strlen(Inline);
                                break;
                }
        }
        if(count == -1) exit(1);

        align[count].length = len;
        align[count].nuc[len] = '\0';
        return(++count);
}


Errorout2(string)
char *string;
{
        fprintf(stderr,"%s\n",string);
        exit(1);
}

WriteData(file,data,count)
FILE *file;
struct data_format data[];
int count;
{
        int i,j;
        for(j = 0 ; j<count;j++)
        {
                if(data[j].offset)
                        fprintf(file,"\n%c%s(%d)",data[j].type,data[j].name,
                        data[j].offset);
                else
                        fprintf(file,"\n%c%s",data[j].type,data[j].name);

                for(i=0;i<data[j].length;i++)
                {
                        if(i%60 == 0)
                                fputc('\n',file);
                        fputc(data[j].nuc[i],file);
                }
        }
        return 0;
}