466 lines
10 KiB
C
466 lines
10 KiB
C
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#include <sys/time.h>
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#include <stdio.h>
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#include <malloc.h>
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#include <xview/xview.h>
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#include <xview/panel.h>
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#include "menudefs.h"
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#include "defines.h"
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/*
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Copyright (c) 1989-1990, University of Illinois board of trustees. All
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rights reserved. Written by Steven Smith at the Center for Prokaryote Genome
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Analysis. Design and implementation guidance by Dr. Gary Olsen and Dr.
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Carl Woese.
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Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory.
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all rights reserved.
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Copyright (c) 1993, Steven Smith, all rights reserved.
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*/
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ReadGen(filename,dataset,type)
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char *filename;
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NA_Alignment *dataset;
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int type;
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{
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register int done = FALSE,len = 0, j=0;
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int count,IS_REALLY_AA = FALSE;
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char Inline[GBUFSIZ],c;
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char *buffer,*gencomments = NULL,fields[8][GBUFSIZ];
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int buflen = 0,genclen = 0,curelem = 0,n = 0,flag = 0;
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int start_col = -1;
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NA_Sequence *this_elem;
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FILE *file;
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extern int Default_DNA_Trans[], Default_RNA_Trans[];
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extern int Default_NA_RTrans[];
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extern int Default_PROColor_LKUP[],Default_NAColor_LKUP[];
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ErrorOut("No such file",file = fopen(filename,"r"));
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for(;fgets(Inline,GBUFSIZ,file) != 0;)
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{
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if(Inline[strlen(Inline)-1] == '\n')
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Inline[strlen(Inline)-1] = '\0';
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if(Find(Inline,"LOCUS"))
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{
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curelem = dataset->numelements++;
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if(curelem == 0)
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{
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dataset->element=(NA_Sequence*)
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Calloc(5,sizeof(NA_Sequence));
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dataset->maxnumelements = 5;
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}
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else if (curelem==dataset->maxnumelements)
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{
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(dataset->maxnumelements) *= 2;
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dataset->element =(NA_Sequence*)
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Realloc(dataset->element,
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dataset->maxnumelements * sizeof(NA_Sequence));
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}
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this_elem = &(dataset->element[curelem]);
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n = sscanf(Inline,"%s %s %s %s %s %s %s %s",
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fields[0],fields[1],fields[2],fields[3],fields[4],
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fields[5],fields[6],fields[7]);
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if(IS_REALLY_AA)
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{
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InitNASeq(this_elem,PROTEIN);
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}
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else if(Find(Inline,"DNA"))
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{
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InitNASeq(this_elem,DNA);
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}
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else if(Find(Inline,"RNA"))
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{
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InitNASeq(this_elem,RNA);
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}
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else if(Find(Inline,"MASK"))
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{
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InitNASeq(this_elem,MASK);
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}
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else if(Find(Inline,"TEXT"))
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{
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InitNASeq(this_elem,TEXT);
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}
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else if(Find(Inline,"PROT"))
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{
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InitNASeq(this_elem,PROTEIN);
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}
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else
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InitNASeq(this_elem,DNA);
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strncpy(this_elem->short_name,fields[1],31);
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AsciiTime(&(this_elem->t_stamp.origin),fields[n-1]);
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this_elem->attr = DEFAULT_X_ATTR;
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if( Find(Inline, "Circular") )
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this_elem->attr |= IS_CIRCULAR;
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gencomments = NULL;
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genclen = 0;
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}
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else if(Find(Inline,"DEFINITION"))
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strncpy(this_elem->description,&(Inline[12]),79);
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else if(Find(Inline,"AUTHOR"))
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strncpy(this_elem->authority,&(Inline[12]),79);
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else if(Find(Inline," ORGANISM"))
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strncpy(this_elem->seq_name,&(Inline[12]),79);
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else if(Find(Inline,"ACCESSION"))
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strncpy(this_elem->id,&(Inline[12]),79);
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else if(Find(Inline,"ORIGIN"))
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{
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done = FALSE;
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len = 0;
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for(;done == FALSE && fgets(Inline,GBUFSIZ,file) != 0;)
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{
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if(Inline[0] != '/')
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{
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if(buflen == 0)
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{
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buflen = GBUFSIZ;
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buffer = Calloc(sizeof(char) ,
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buflen);
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}
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else if (len+strlen(Inline) >= buflen)
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{
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buflen += GBUFSIZ;
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buffer = Realloc(buffer,
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sizeof(char)*buflen);
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for(j=buflen-GBUFSIZ
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;j<buflen;j++)
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buffer[j] = '\0';
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}
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/*
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* Search for the fist column of data (whitespace-number-whitespace)data
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*/
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if(start_col == -1)
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{
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for(start_col=0; Inline[start_col] == ' ' ||
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Inline[start_col] == '\t';start_col++);
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for(start_col++;strchr("1234567890",
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Inline[start_col]) != NULL;start_col++);
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for(start_col++; Inline[start_col] == ' ' ||
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Inline[start_col] == '\t';start_col++);
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}
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for(j=start_col;(c = Inline[j]) != '\0';j++)
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{
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if((c != '\n') &&
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((j-start_col + 1) % 11 !=0))
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buffer[len++] = c;
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}
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}
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else
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{
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AppendNA(buffer,len,&(dataset->
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element[curelem]));
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for(j=0;j<len;j++)
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buffer[j] = '\0';
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len = 0;
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done = TRUE;
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dataset->element[curelem].comments
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= gencomments;
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dataset->element[curelem].comments_len=
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genclen - 1;
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dataset->element[curelem].
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comments_maxlen = genclen;
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gencomments = NULL;
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genclen = 0;
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}
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}
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/*
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* Test if sequence should be converted by the translation table
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* If it looks like a protein...
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*/
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if(dataset->element[curelem].rmatrix &&
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IS_REALLY_AA == FALSE)
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{
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IS_REALLY_AA = CheckType(dataset->element[curelem].
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sequence,dataset->element[curelem].seqlen);
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if(IS_REALLY_AA == FALSE)
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Ascii2NA(dataset->element[curelem].sequence,
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dataset->element[curelem].seqlen,
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dataset->element[curelem].rmatrix);
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else
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/*
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* Force the sequence to be AA
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*/
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{
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dataset->element[curelem].elementtype = PROTEIN;
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dataset->element[curelem].rmatrix = NULL;
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dataset->element[curelem].tmatrix = NULL;
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dataset->element[curelem].col_lut =
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Default_PROColor_LKUP;
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}
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}
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}
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else if (Find(Inline,"ZZZZZ"))
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{
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Cfree(gencomments);
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genclen = 0;
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}
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else
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{
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if (gencomments == NULL)
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{
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gencomments = String(Inline);
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genclen = strlen(gencomments)+1;
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}
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else
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{
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genclen += strlen(Inline)+1;
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gencomments = Realloc(gencomments,genclen *
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sizeof(char));
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strncat(gencomments,Inline,GBUFSIZ);
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strncat(gencomments,"\n",GBUFSIZ);
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}
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}
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}
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Cfree(buffer);
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fclose(file);
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for(j=0;j<dataset->numelements;j++)
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dataset->maxlen = MAX(dataset->maxlen,
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dataset->element[j].seqlen+dataset->element[j].offset);
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return;
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}
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typedef struct mya {
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int yy;
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int mm;
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int dd;
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int hr;
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int mn;
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int sc;
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} sA;
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AsciiTime(sA *a,char *asciitime)
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{
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int j;
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char temp[GBUFSIZ];
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extern char month[12][6];
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a->dd = 0;
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a->yy = 0;
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a->mm = 0;
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sscanf(asciitime,"%d%5c%d",&(a->dd),temp,&(a->yy));
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temp[5] = '\0';
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for(j=0;j<12;j++)
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if(strcmp(temp,month[j]) == 0)
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a->mm = j+1;
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if(a->dd <0 || a->dd > 31 || a->yy < 0 || a->mm > 11)
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SetTime(a);
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return;
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}
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WriteGen(aln,filename,method,maskable)
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NA_Alignment *aln;
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char *filename;
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int method,maskable;
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{
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int i,j,k,mask = -1;
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FILE *file;
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NA_Sequence *this_elem;
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extern char month[12][6];
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char c;
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if(aln == NULL)
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return;
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if(aln->na_ddata == NULL)
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return;
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file = fopen(filename,"w");
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if(file == NULL)
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{
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Warning("Cannot open file for output");
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return(1);
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}
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if(maskable && method != SELECT_REGION)
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for(j=0;j<aln->numelements;j++)
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if(aln->element[j].elementtype == MASK &&
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aln->element[j].selected)
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mask = j;
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for(j=0;j<aln->numelements;j++)
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{
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if((aln->element[j].selected && j!=mask && method != SELECT_REGION)
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||(aln->element[j].subselected && method == SELECT_REGION)
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|| (method == ALL))
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{
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this_elem = &(aln->element[j]);
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fprintf(file,
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"LOCUS %10s%8d bp %4s %10s %2d%5s%4d\n",
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this_elem->short_name,this_elem->seqlen+this_elem->offset,
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(this_elem->elementtype == DNA) ? "DNA":
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(this_elem->elementtype ==RNA)?"RNA":
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(this_elem->elementtype == MASK)?"MASK":
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(this_elem->elementtype == PROTEIN)?"PROT":"TEXT",
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this_elem->attr & IS_CIRCULAR?"Circular":"",
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this_elem->t_stamp.origin.dd,
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month[this_elem->t_stamp.origin.mm-1],
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this_elem->t_stamp.origin.yy>1900?this_elem->t_stamp.origin.yy:
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this_elem->t_stamp.origin.yy+1900);
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if(this_elem->description[0])
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fprintf(file,"DEFINITION %s\n",this_elem->description);
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if(this_elem->seq_name[0])
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fprintf(file," ORGANISM %s\n",this_elem->seq_name);
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if(this_elem->id[0])
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fprintf(file," ACCESSION %s\n",this_elem->id);
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if(this_elem->authority[0])
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fprintf(file," AUTHORS %s\n",this_elem->authority);
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if(this_elem->comments)
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fprintf(file,"%s\n",this_elem->comments);
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fprintf(file,"ORIGIN");
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if(this_elem->tmatrix)
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{
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if(mask == -1)
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{
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for(i=0,k=0;k<this_elem->seqlen+this_elem->offset;k++)
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{
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if(method == SELECT_REGION)
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{
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if(aln->selection_mask[k] == '1')
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{
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if(i%60 == 0)
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fprintf(file,"\n%9d",i+1);
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if(i%10 == 0)
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fprintf(file," ");
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fprintf(file,"%c",this_elem->tmatrix
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[getelem(this_elem,k)]);
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i++;
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}
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}
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else
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{
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if(i%60 == 0)
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fprintf(file,"\n%9d",i+1);
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if(i%10 == 0)
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fprintf(file," ");
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fprintf(file,"%c",this_elem->tmatrix
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[getelem(this_elem,k)]);
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i++;
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}
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}
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}
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else
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{
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for(k=0;k<this_elem->seqlen+this_elem->offset;k++)
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{
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c =(char)getelem(&(aln->element[mask]),k);
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if(c != '0' && c!= '-')
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{
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if(k%60 == 0)
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fprintf(file,"\n%9d",k+1);
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if(k%10 == 0)
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fprintf(file," ");
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fprintf(file,"%c",this_elem->tmatrix
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[getelem(this_elem,k)]);
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}
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}
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}
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}
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else
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{
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if(mask == -1)
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{
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for(i=0,k=0;k<this_elem->seqlen+this_elem->offset;k++)
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{
|
||
|
|
if(method == SELECT_REGION)
|
||
|
|
{
|
||
|
|
if(aln->selection_mask[k] == '1')
|
||
|
|
{
|
||
|
|
if(i%60 == 0)
|
||
|
|
fprintf(file,"\n%9d",i+1);
|
||
|
|
if(i%10 == 0)
|
||
|
|
fprintf(file," ");
|
||
|
|
fprintf(file,"%c", getelem(this_elem,k));
|
||
|
|
i++;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
else
|
||
|
|
{
|
||
|
|
if(i%60 == 0)
|
||
|
|
fprintf(file,"\n%9d",i+1);
|
||
|
|
if(i%10 == 0)
|
||
|
|
fprintf(file," ");
|
||
|
|
fprintf(file,"%c",getelem(this_elem,k));
|
||
|
|
i++;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
else
|
||
|
|
{
|
||
|
|
for(k=0;k<this_elem->seqlen+this_elem->offset;k++)
|
||
|
|
{
|
||
|
|
c =(char)getelem(&(aln->element[mask]),k);
|
||
|
|
if(c != '0' && c!= '-')
|
||
|
|
{
|
||
|
|
if(k%60 == 0)
|
||
|
|
fprintf(file,"\n%9d",k+1);
|
||
|
|
if(k%10 == 0)
|
||
|
|
fprintf(file," ");
|
||
|
|
fprintf(file,"%c",getelem(this_elem,k));
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
fprintf(file,"\n//\n");
|
||
|
|
}
|
||
|
|
}
|
||
|
|
fclose(file);
|
||
|
|
return;
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
SetTime(sA *a)
|
||
|
|
{
|
||
|
|
struct tm *tim,*localtime();
|
||
|
|
long clock;
|
||
|
|
|
||
|
|
clock = time(0);
|
||
|
|
tim = localtime(&clock);
|
||
|
|
|
||
|
|
a->yy = tim->tm_year;
|
||
|
|
a->mm = tim->tm_mon+1;
|
||
|
|
a->dd = tim->tm_mday;
|
||
|
|
a->hr = tim->tm_hour;
|
||
|
|
a->mn = tim->tm_min;
|
||
|
|
a->sc = tim->tm_sec;
|
||
|
|
return;
|
||
|
|
}
|
||
|
|
|
||
|
|
/*
|
||
|
|
* CheckType: Check base composition to see if the sequence
|
||
|
|
* appears to be an amino acid sequence. If it is, pass back
|
||
|
|
* TRUE, else FALSE.
|
||
|
|
*/
|
||
|
|
CheckType(seq,len)
|
||
|
|
char *seq;
|
||
|
|
int len;
|
||
|
|
{
|
||
|
|
|
||
|
|
int j,count1 = 0,count2 = 0;
|
||
|
|
|
||
|
|
for(j=0;j<len;j++)
|
||
|
|
if(((seq[j]|32) < 'z') && ((seq[j]|32) > 'a'))
|
||
|
|
{
|
||
|
|
count1++;
|
||
|
|
if(index("ACGTUNacgtun",seq[j]) == NULL)
|
||
|
|
count2++;
|
||
|
|
}
|
||
|
|
|
||
|
|
return( (count2 > count1/4)?TRUE:FALSE);
|
||
|
|
}
|