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gde_linux/CORE/HGLfile.c

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#include <sys/time.h>
#include <stdio.h>
#include <malloc.h>
#include <xview/xview.h>
#include <xview/panel.h>
#include "menudefs.h"
#include "defines.h"
/*
Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory.
All rights reserved.
*/
ReadGDE(filename,dataset,type)
char *filename;
NA_Alignment *dataset;
int type;
{
register int done = FALSE,len = 0, j=0;
int success,count,temp = 0;
char Inline[GBUFSIZ],c;
char *buffer,*line,*gencomments = NULL,fields[8][GBUFSIZ];
int buflen = GBUFSIZ,genclen = 0,curelem = 0,n = 0,flag = 0;
NA_Sequence *this_elem = NULL,temp_elem;
FILE *file;
extern int Default_DNA_Trans[], Default_RNA_Trans[];
extern int OVERWRITE,Default_NA_RTrans[], Default_PROColor_LKUP[];
ErrorOut("No such file",file = fopen(filename,"r"));
for(;fgets(Inline,GBUFSIZ,file) != 0;)
{
for(line = Inline;line[0]==' ' || line[0] == '\t';line++);
if(Find2(line,"{")==0)
{
this_elem = &temp_elem;
InitNASeq(this_elem,DNA);
this_elem->offset = -(dataset->rel_offset);
}
else if(Find2(line,"type")==0)
{
if(Find(line,"DNA"))
{
this_elem->elementtype = DNA;
this_elem->tmatrix = Default_DNA_Trans;
this_elem->rmatrix = Default_NA_RTrans;
}
else if(Find(line,"RNA"))
{
this_elem->elementtype = RNA;
this_elem->tmatrix = Default_RNA_Trans;
this_elem->rmatrix = Default_NA_RTrans;
}
else if(Find(line,"MASK"))
{
this_elem->elementtype = MASK;
this_elem->rmatrix = NULL;
this_elem->tmatrix = NULL;
this_elem->col_lut = NULL;
}
else if(Find(line,"TEXT"))
{
this_elem->elementtype = TEXT;
this_elem->rmatrix = NULL;
this_elem->tmatrix = NULL;
this_elem->col_lut = NULL;
}
else if(Find(line,"PROT"))
{
this_elem->elementtype = PROTEIN;
this_elem->rmatrix = NULL;
this_elem->tmatrix = NULL;
this_elem->col_lut = Default_PROColor_LKUP;
}
/*
this_elem->attr = DEFAULT_X_ATTR;
*/
}
else if(Find2(line,"circular")==0)
{
sscanf(line,"%*s %d",&temp);
if(temp == 1)
{
this_elem->attr |= IS_CIRCULAR;
}
else
{
this_elem->attr &= ~IS_CIRCULAR;
}
}
else if(Find2(line,"orig_direction")==0)
{
sscanf(line,"%*s %d",&temp);
if(temp == 1)
{
this_elem->attr |= IS_ORIG_5_TO_3;
this_elem->attr &= ~IS_ORIG_3_TO_5;
}
else
{
this_elem->attr |= IS_ORIG_3_TO_5;
this_elem->attr &= ~IS_ORIG_5_TO_3;
}
}
else if(Find2(line,"direction")==0)
{
sscanf(line,"%*s %d",&temp);
if(temp == 1)
{
this_elem->attr |= IS_5_TO_3;
this_elem->attr &= ~IS_3_TO_5;
}
else
{
this_elem->attr |= IS_3_TO_5;
this_elem->attr &= ~IS_5_TO_3;
}
}
else if(Find2(line,"orig_strand")==0)
{
sscanf(line,"%*s %d",&temp);
if(temp == 1)
{
this_elem->attr |= IS_ORIG_PRIMARY;
this_elem->attr &= ~IS_ORIG_SECONDARY;
}
else
{
this_elem->attr |= IS_ORIG_SECONDARY;
this_elem->attr &= ~IS_ORIG_PRIMARY;
}
}
else if(Find2(line,"strandedness")==0)
{
sscanf(line,"%*s %d",&temp);
if(temp == 1)
{
this_elem->attr |= IS_PRIMARY;
this_elem->attr &= ~IS_SECONDARY;
}
else
{
this_elem->attr |= IS_SECONDARY;
this_elem->attr &= ~IS_PRIMARY;
}
}
else if(Find2(line,"creator")==0)
{
sscanf(line,"%*s %[^\n]",this_elem->authority);
RemoveQuotes(this_elem->authority);
}
else if(Find2(line,"longname")==0)
{
sscanf(line,"%*s %[^\n]",this_elem->seq_name);
RemoveQuotes(this_elem->seq_name);
}
else if(Find2(line,"descrip")==0)
{
sscanf(line,"%*s %[^\n]",this_elem->description);
RemoveQuotes(this_elem->description);
}
else if(Find2(line,"name")==0)
{
sscanf(line,"%*s %[^\n]",this_elem->short_name);
RemoveQuotes(this_elem->short_name);
}
else if(Find2(line,"group-ID")==0)
{
sscanf(line,"%*s %d",&(this_elem->groupid));
dataset->numgroups =
MAX(this_elem->groupid, dataset->numgroups);
}
else if(Find2(line,"sequence-ID")==0)
{
sscanf(line,"%*s %[^\n]",this_elem->id);
RemoveQuotes(this_elem->id);
}
else if(Find2(line,"barcode")==0)
{
sscanf(line,"%*s %[^\n]",this_elem->barcode);
RemoveQuotes(this_elem->barcode);
}
else if(Find2(line,"membrane")==0)
{
sscanf(line,"%*s %[^\n]",this_elem->membrane);
RemoveQuotes(this_elem->membrane);
}
else if(Find2(line,"contig")==0)
{
sscanf(line,"%*s %[^\n]",this_elem->contig);
RemoveQuotes(this_elem->contig);
}
else if(Find2(line,"creation-date")==0)
{
sscanf(line,"%*s %2d%*c%2d%*c%2d%*c%2d%*c%2d%*c%2d\n",
&(this_elem->t_stamp.origin.mm),
&(this_elem->t_stamp.origin.dd),
&(this_elem->t_stamp.origin.yy),
&(this_elem->t_stamp.origin.hr),
&(this_elem->t_stamp.origin.mn),
&(this_elem->t_stamp.origin.sc));
}
else if(Find2(line,"offset")==0)
{
sscanf(line,"%*s %d",&(this_elem->offset));
this_elem->offset -= dataset->rel_offset;
}
else if(Find2(line,"comments")==0)
{
if(this_elem->comments_maxlen ==0)
buflen = 2048;
else
buflen = this_elem->comments_maxlen;
done = FALSE;
len = this_elem->comments_len;
for(;line[0] != '"';line++)
if(line[0] == '\0')
ErrorOut(0,"Error in input file");
line++;
buffer = Calloc(buflen,sizeof(char));
for(;!done;)
{
for(j=0;j<strlen(line);j++)
{
if(len+strlen(line) >= buflen)
{
buflen *=2;
buffer = Realloc(buffer,
buflen*sizeof(char));
}
if(line[j] == '"') done = TRUE;
else
buffer[len++] = line[j];
}
/*
* Check pad with null
*/
buffer[len] = '\0';
if(!done)
{
if(fgets(Inline,GBUFSIZ,file) == 0)
done = TRUE;
line = Inline;
}
}
this_elem->comments = buffer;
this_elem->comments_len = strlen(buffer);
this_elem->comments_maxlen = buflen;
RemoveQuotes(this_elem->comments);
}
else if(Find2(line,"sequence")==0)
{
buflen = GBUFSIZ;
done = FALSE;
len = 0;
buffer = Calloc(buflen,sizeof(char));
for(;line[0] != '"';line++)
if(line[0] == '\0')
ErrorOut(0,"Error in input file");
line++;
for(;!done;)
{
for(j=0;j<strlen(line);j++)
{
if(len+strlen(line) >= buflen)
{
buflen *=2;
buffer = Realloc(buffer,
buflen*sizeof(char));
}
if(line[j] == '"') done = TRUE;
else
{
/*
* If not text, ignore spaces...
*/
if(this_elem->elementtype !=TEXT)
{
if(line[j]!=' ' && line[j] !=
'\t' && line[j] != '\n')
buffer[len++] = line[j];
}
else
if(line[j] != '\t' && line[j] != '\n')
buffer[len++] = line[j];
}
}
if(!done)
{
if(fgets(Inline,GBUFSIZ,file) == 0)
done = TRUE;
line = Inline;
}
}
if(this_elem->rmatrix)
for(j=0;j<len;j++)
buffer[j]=this_elem->rmatrix[buffer[j]];
this_elem->sequence =(NA_Base*)buffer;
this_elem->seqlen = len;
this_elem->seqmaxlen = buflen;
}
else if (Find2(line,"}")==0)
{
if(this_elem->id[0] == '\0')
strncpy(this_elem->id,uniqueID(),79);
if(this_elem->short_name[0] == '\0')
strncpy(this_elem->short_name,this_elem->id,79);
if(this_elem->seqlen == 0)
this_elem->protect=
PROT_BASE_CHANGES+
PROT_GREY_SPACE+
PROT_WHITE_SPACE+
PROT_TRANSLATION;
genclen = 0;
/*
* Make a new sequence entry...
*/
success = -1;
if(OVERWRITE)
success = OverWrite(this_elem,dataset);
if(success == -1)
{
curelem = dataset->numelements++;
if(curelem == 0)
{
dataset->element=(NA_Sequence*)
Calloc(5,sizeof(NA_Sequence));
dataset->maxnumelements = 5;
}
else if (curelem==dataset->maxnumelements)
{
(dataset->maxnumelements) *= 2;
dataset->element =(NA_Sequence*)
Realloc(dataset->element,
dataset->maxnumelements * sizeof(NA_Sequence));
}
dataset->element[curelem] = *this_elem;
}
}
else if(this_elem != NULL)
{
if (this_elem->baggage == NULL)
{
this_elem->baggage = String(line);
this_elem->baggage_maxlen =
this_elem->baggage_len =
strlen(this_elem->baggage)+1;
}
else
{
this_elem->baggage_len += strlen(line)+1;
this_elem->baggage = Realloc(
this_elem->baggage,this_elem->baggage_len *
sizeof(char));
this_elem->baggage_maxlen =
this_elem->baggage_len;
strncat(this_elem->baggage,line,GBUFSIZ);
}
}
}
fclose(file);
NormalizeOffset(dataset);
Regroup(dataset);
AdjustGroups(dataset);
return;
}
WriteGDE(aln,filename,method,maskable)
NA_Alignment *aln;
char *filename;
int method,maskable;
{
int i,j,k,mask = -1;
FILE *file;
NA_Sequence *this_elem;
extern char month[12][6];
if(aln == NULL)
return;
if(aln->na_ddata == NULL)
return;
file = fopen(filename,"w");
if(file == NULL)
{
Warning("Cannot open file for output");
return(1);
}
if(maskable && method != SELECT_REGION)
for(j=0;j<aln->numelements;j++)
if(aln->element[j].elementtype == MASK &&
aln->element[j].selected)
mask = j;
for(j=0;j<aln->numelements;j++)
{
if((aln->element[j].selected && j!=mask && method!=SELECT_REGION)
|| (method == ALL)
|| (aln->element[j].subselected && method == SELECT_REGION))
{
this_elem = &(aln->element[j]);
SeqNorm(this_elem);
fprintf(file,"{\n");
if(this_elem->short_name[0])
fprintf(file,"name \"%s\"\n",this_elem->short_name);
switch(this_elem->elementtype)
{
case DNA:
fprintf(file,"type \"DNA\"\n");
break;
case RNA:
fprintf(file,"type \"RNA\"\n");
break;
case PROTEIN:
fprintf(file,"type \"PROTEIN\"\n");
break;
case MASK:
fprintf(file,"type \"MASK\"\n");
break;
case TEXT:
fprintf(file,"type \"TEXT\"\n");
break;
}
if(this_elem->seq_name[0])
fprintf(file,"longname %s\n",this_elem->seq_name);
if(this_elem->id[0])
fprintf(file,"sequence-ID \"%s\"\n",this_elem->id);
RemoveQuotes(this_elem->barcode);
RemoveQuotes(this_elem->contig);
if(this_elem->barcode[0])
fprintf(file,"barcode \"%s\"\n",this_elem->barcode);
if(this_elem->membrane[0])
fprintf(file,"membrane \"%s\"\n",this_elem->membrane);
if(this_elem->contig[0])
fprintf(file,"contig \"%s\"\n",this_elem->contig);
if(this_elem->description[0])
fprintf(file,"descrip \"%s\"\n",this_elem->description);
if(this_elem->authority[0])
fprintf(file,"creator \"%s\"\n",this_elem->authority);
if(this_elem->groupid)
fprintf(file,"group-ID %d\n",
this_elem->groupid);
if(this_elem->offset+aln->rel_offset && method!=SELECT_REGION)
fprintf(file,"offset %d\n",this_elem->offset+aln->rel_offset);
if(method == SELECT_REGION)
{
/*
* If selecting a region, the offset should be moved to the first
* non-'0' space in the mask.
*/
for(k=this_elem->offset;k<aln->selection_mask_len &&
aln->selection_mask[k] == '0';k++);
fprintf(file,"offset %d\n", aln->rel_offset+k);
}
if(this_elem->t_stamp.origin.mm != 0)
fprintf(file,
"creation-date %2d/%2d/%2d %2d:%2d:%2d\n",
this_elem->t_stamp.origin.mm,
this_elem->t_stamp.origin.dd,
(this_elem->t_stamp.origin.yy)>1900?
(this_elem->t_stamp.origin.yy-1900):
(this_elem->t_stamp.origin.yy),
this_elem->t_stamp.origin.hr,
this_elem->t_stamp.origin.mn,
this_elem->t_stamp.origin.sc);
if((this_elem->attr & IS_ORIG_5_TO_3) &&
((this_elem->attr & IS_ORIG_3_TO_5) == 0))
fprintf(file,"orig_direction 1\n");
if((this_elem->attr & IS_CIRCULAR) )
fprintf(file,"circular 1\n");
if((this_elem->attr & IS_5_TO_3) &&
((this_elem->attr & IS_3_TO_5) == 0))
fprintf(file,"direction 1\n");
if((this_elem->attr & IS_ORIG_3_TO_5) &&
((this_elem->attr & IS_ORIG_5_TO_3) == 0))
fprintf(file,"orig_direction -1\n");
if((this_elem->attr & IS_3_TO_5) &&
((this_elem->attr & IS_5_TO_3) == 0))
fprintf(file,"direction -1\n");
if((this_elem->attr & IS_ORIG_PRIMARY) &&
((this_elem->attr & IS_ORIG_SECONDARY) == 0))
fprintf(file,"orig_strand 1\n");
if((this_elem->attr & IS_PRIMARY) &&
((this_elem->attr & IS_SECONDARY) == 0))
fprintf(file,"strandedness 1\n");
if(((this_elem->attr & IS_ORIG_PRIMARY) == 0) &&
(this_elem->attr & IS_ORIG_SECONDARY))
fprintf(file,"orig_strand 2\n");
if(((this_elem->attr & IS_PRIMARY) == 0) &&
(this_elem->attr & IS_SECONDARY))
fprintf(file,"strandedness 2\n");
if(this_elem->comments != NULL)
{
StripSpecial(this_elem->comments);
fprintf(file,"comments \"%s\"\n",this_elem->comments);
}
if(this_elem->baggage != NULL)
{
if(this_elem->
baggage[strlen(this_elem->baggage)-1] == '\n')
fprintf(file,"%s",this_elem->baggage);
else
fprintf(file,"%s\n",this_elem->baggage);
}
fprintf(file,"sequence \"");
if(this_elem->tmatrix)
{
if(mask == -1)
{
for(k=this_elem->offset;k<this_elem->seqlen+this_elem->offset;k++)
{
if(k%60 == 0)
putc('\n',file);
if(method == SELECT_REGION)
{
if(aln->selection_mask[k] == '1')
putc(this_elem->tmatrix[getelem(this_elem,k)],
file);
}
else
putc(this_elem->tmatrix[getelem(this_elem,k)],
file);
}
}
else
{
for(i=0,k=this_elem->offset;k<this_elem->seqlen+this_elem->offset;k++)
if(aln->element[mask].seqlen+this_elem->offset>k)
if((char)getelem(&(aln->element[mask]),k) != '0'
&& ((char)getelem(&(aln->element[mask]),k) != '-'))
{
if(i%60 == 0)
putc('\n',file);
putc(this_elem->tmatrix[getelem(this_elem,k)],
file);
i++;
}
}
fprintf(file,"\"\n");
}
else
{
if(mask == -1)
{
for(k=this_elem->offset;k<this_elem->seqlen+this_elem->offset;k++)
{
if(k%60 == 0)
putc('\n',file);
if(method == SELECT_REGION)
{
if(aln->selection_mask[k] == '1')
putc(getelem(this_elem,k),file);
}
else
putc(getelem(this_elem,k),file);
}
}
else
{
for(i=0,k=this_elem->offset;k<this_elem->seqlen+this_elem->offset;k++)
if(((aln->element[mask].seqlen)+(aln->element[mask].
offset)) > k)
if((char)getelem(&(aln->element[mask]),k) == '1')
{
if(i%60 == 0)
putc('\n',file);
putc(getelem(this_elem,k),file);
i++;
}
}
fprintf(file,"\"\n");
}
fprintf(file,"}\n");
}
}
fclose(file);
return;
}
StripSpecial(string)
char *string;
{
register int i,j,len;
len = strlen(string);
for(j=0;j<len;j++)
{
if(string[j] == '"')
string[j] = '`';
else if(string[j] == '{')
string[j] = '(';
else if(string[j] == '}')
string[j] = ')';
}
return;
}
RemoveQuotes(string)
char *string;
{
register int i,j,len;
len = strlen(string);
for(j=0;j<len;j++)
if(string[j] == '"')
string[j] = ' ';
for(j=0;string[j]==' ' && j<strlen(string);j++);
len = strlen(string);
for(i=0;i<len - j;i++)
string[i] = string[i+j];
for(j=strlen(string)-1;j>=0 && (string[j]=='\n'||string[j]==' '); j--)
string[j] = '\0';
return;
}
/*
* Normalize seq (remove leading indels in the sequence;
*/
void SeqNorm(seq)
NA_Sequence *seq;
{
int len,j,shift_width,trailer;
char *sequence;
len = seq->seqlen;
sequence =(char*)seq->sequence;
if(len == 0) return;
if(seq->tmatrix)
for(shift_width=0; (shift_width<len) &&
((sequence[shift_width]&15) == '\0'); shift_width++);
else
for(shift_width=0; (shift_width<len) &&
(sequence[shift_width] == '-'); shift_width++);
for(j=0;j<len-shift_width;j++)
sequence[j] = sequence[j+shift_width];
seq->seqlen -= shift_width;
seq->offset += shift_width;
for(trailer=seq->seqlen-1;(sequence[trailer] =='-' ||
sequence[trailer] == '\0') && trailer>=0;
trailer--)
sequence[trailer] = '\0';
seq->seqlen = trailer+1;
return;
}
/* ALWAYS COPY the result from uniqueID() to a char[32],
* (strlen(hostname)+1+10). Memory is lost when the function
* is finished.
*/
char vname[32];
char *uniqueID()
{
char hname[32]; /* ,vname[32]; rtm 18.III.98 */
int hnamelen = 32;
time_t *tp;
static cnt = 0;
tp = (time_t *)Calloc(1, sizeof(time_t));
if(gethostname(hname, 10) == -1)
{
fprintf(stderr, "UniqueID(): Failed to get host name.\n");
exit(1);
}
time(tp);
sprintf(vname, "%s:%d:%ld", hname, cnt, *tp);
cnt++;
Cfree(tp);
return(vname);
}
/*
* OverWrite(), overwrite all non-default data from a sequence entry
* onto any entry with the same ID or short name.
*/
OverWrite(this,aln)
NA_Sequence *this;
NA_Alignment *aln;
{
int j,indx = -1;
NA_Sequence *that;
for(j=0;j<aln->numelements;j++)
{
if(Find2(this->id,aln->element[j].id) != -1)
if(Find2(aln->element[j].id,this->id) != -1)
indx = j;
}
if(indx == -1)
for(j=0;j<aln->numelements;j++)
{
if(Find2(this->short_name,aln->element[j].short_name)!= -1)
if(Find2(aln->element[j].short_name,this->short_name)!= -1)
indx = j;
}
if(indx != -1)
{
that = &(aln->element[indx]);
if(this->seq_name[0])
strcpy(that->seq_name,this->seq_name);
if(this->barcode[0])
strcpy(that->barcode,this->barcode);
if(this->contig[0])
strcpy(that->contig,this->contig);
if(this->membrane[0])
strcpy(that->membrane,this->membrane);
if(this->authority[0])
strcpy(that->authority,this->authority);
if(this->short_name[0])
strcpy(that->short_name,this->short_name);
if(this->description[0])
strcpy(that->description,this->description);
if(this->sequence)
{
cfree(that->sequence);
that->sequence = this->sequence;
that->seqlen = this->seqlen;
that->seqmaxlen = this->seqmaxlen;
}
if(this->baggage)
{
that->baggage_len += this->baggage_len;
that->baggage_maxlen += this->baggage_maxlen;
if(that->baggage)
that->baggage =
Realloc(that->baggage,that->baggage_maxlen*sizeof(char));
else
that->baggage = Calloc(that->baggage_maxlen,sizeof(char));
strncat(that->baggage,this->baggage,that->baggage_maxlen);
}
if(this->comments)
{
that->comments_len += this->comments_len;
that->comments_maxlen += this->comments_maxlen;
if(that->comments)
that->comments =
Realloc(that->comments,that->comments_maxlen*sizeof(char));
else
that->comments = Calloc(that->comments_maxlen,sizeof(char));
strncat(that->comments,this->comments,that->comments_maxlen);
}
if(this->cmask)
{
cfree(that->cmask);
that->cmask = this->cmask;
}
if(this->offset != that->offset)
that->offset = this->offset;
if(this->attr != 0)
that->attr = this->attr;
if(this->groupid != 0)
{
that->groupid = this->groupid;
}
that->groupb = NULL;
that->groupf = NULL;
}
/*
NormalizeOffset(aln);
Regroup(aln);
AdjustGroups(aln);
*/
return(indx);
}
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