196 lines
3.8 KiB
C
Executable File
196 lines
3.8 KiB
C
Executable File
#include "global_defs.h"
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main(ac,av)
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int ac;
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char **av;
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{
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Sequence *data;
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int i,j,k,numseqs=0,maxlen = 0,minlen=999999999;
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int lines_printed, Success, maxsize, ss;
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int width,scale = 0;
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int len[1000];
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FILE *infile;
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char a,b, style[32];
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int WIDTH;
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if(ac == 1)
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{
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fprintf(stderr,"Usage:%s\n", av[0]);
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fprintf(stderr, " -in alignment_file [-width max_line_width (50)]\n");
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fprintf(stderr, " [-scale scale (1)] [-style comp|poster (comp)]\n");
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exit(0);
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}
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for(i = 1; i < ac; i+=2)
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{
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if(av[i][0] != '-')
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{
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fprintf(stderr, "\nInvalid flag %s.\n", av[i]);
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fprintf(stderr, "Type %s for usage.\n\n", av[0]);
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exit(1);
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}
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if(i+1 == ac)
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{
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fprintf(stderr, "\nMissing value for flag %s.\n\n", av[i]);
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exit(1);
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}
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}
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i = 1;
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scale = 1;
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WIDTH = 50;
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infile = NULL;
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strcpy(style, "comp");
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while(i < ac)
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{
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if(strcmp(av[i], "-in") == 0)
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{
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if((infile = fopen(av[++i],"r")) == NULL)
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{
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fprintf(stderr,"Cannot open %s\n",av[i]);
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exit(1);
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}
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}
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else if(strcmp(av[i], "-scale") == 0)
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{
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sscanf(av[++i],"%d",&scale);
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if(scale == 0)
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scale = 1;
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}
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else if(strcmp(av[i], "-width") == 0)
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{
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sscanf(av[++i], "%d", &WIDTH);
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}
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else if(strcmp(av[i], "-style") == 0)
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{
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strcpy(style, av[++i]);
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}
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else
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{
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fprintf(stderr, "\nUnknow flag %s\n\n", av[i]);
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exit(1);
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}
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i++;
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}
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if(infile == NULL)
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{
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fprintf(stderr, "\nWhat do you want to print.%c\n\n", 7);
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exit(1);
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}
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/*
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* Read in alignment...
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*/
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maxsize = 64;
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data = (Sequence *)Calloc(maxsize, sizeof(Sequence));
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for(numseqs = 0;Success != -1;numseqs++)
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{
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Success = ReadRecord(infile,&(data[numseqs]));
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if(numseqs == maxsize-1)
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{
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maxsize *= 2;
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data = (Sequence*)Realloc(data,
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maxsize*sizeof(Sequence));
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}
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for(j=0; j<data[numseqs].seqlen; j++)
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{
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if(data[numseqs].c_elem[j] == 'u')
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data[numseqs].c_elem[j] = 't';
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}
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}
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if(Success == FALSE)
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ErrorOut(0,"Problem reading sequences");
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numseqs --;
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/*
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* Done. Alignment is now in data[].
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*/
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fclose(infile);
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if(numseqs == 0) exit(1);
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width = WIDTH*scale;
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for(k=0;k<numseqs;k++)
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{
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if(data[k].seqlen > 0 || strcmp(style, "poster") == 0)
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{
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minlen = MIN(minlen,data[k].offset);
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maxlen = MAX(maxlen,data[k].seqlen+data[k].offset);
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}
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}
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for(j=minlen;j<maxlen;j+=width)
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{
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lines_printed = FALSE;
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for (i=0;i<numseqs;i++)
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{
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data[i].name[19] = '\0';
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if(strcmp(style, "comp") == 0 &&
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(data[i].offset > j+width ||
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data[i].offset+data[i].seqlen<j));
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else
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{
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lines_printed = TRUE;
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printf("\n%20s%5d ", data[i].name,
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indx(j,&(data[i])));
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for(k=j;k<j+width;k+=scale)
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{
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if((k<data[i].seqlen+data[i].offset)
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&& (k>=data[i].offset))
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if(scale == 1)
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putchar(data[i].c_elem[k-data[i].offset]);
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else
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putchar('-');
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else putchar(' ');
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}
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}
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}
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if(lines_printed)
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{
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printf("\n ");
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ss = j+1;
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while(ss < MIN(j+WIDTH*scale, maxlen+1))
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{
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printf("|---------");
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ss += 10*scale;
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}
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printf("\n ");
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ss = j+1;
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while(ss < MIN(j+WIDTH*scale, maxlen+1))
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{
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printf("%-10d",ss);
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ss += 10*scale;
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}
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printf("\n");
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}
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if(strcmp(style, "poster") == 0)
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printf("\f");
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}
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putchar('\n');
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exit(0);
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}
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int indx(pos,seq)
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int pos;
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Sequence *seq;
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{
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int j,count=0;
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if(pos < seq->offset)
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return (0);
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if(pos>seq->offset+seq->seqlen)
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pos = seq->offset+seq->seqlen;
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pos -= seq->offset;
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for(j=0;j<pos;j++)
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if(seq->c_elem[j] != '-')
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if(seq->c_elem[j] != '~')
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count++;
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return (count);
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}
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