gde_linux/CORE/HGLfile.c

#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);
}