source: tags/arb_5.3/ARB_GDE/GDE_HGLfile.cxx

#include <sys/time.h>
#include <stdio.h>
#include <stdlib.h>
// #include <malloc.h>
#include <string.h>
#include <time.h>

//#include <xview/xview.h>
//#include <xview/panel.h>

#include <arbdb.h>
#include <aw_root.hxx>
#include <aw_device.hxx>
#include <aw_window.hxx>
#include <awt.hxx>

#include "gde.hxx"
#include "GDE_menu.h"
#include "GDE_def.h"
#include "GDE_extglob.h"

/*
  Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory.
  All rights reserved.
*/

static void AdjustGroups(NA_Alignment *aln)
{
    size_t i;
    size_t j;
    int c,done=FALSE;

#ifdef HGL
    return;
#else
    for(c=0;c<200 && !done;c++)
    {
        for(j=1;j<=aln->numgroups;j++)
        {
            done = FALSE;
            for(i=0;i<aln->numelements;i++)
            {
                if(aln->element[i].groupid == j)
                {
                    if(aln->element[i].groupf!=NULL ||
                       aln->element[i].groupb!=NULL)
                        done = TRUE;
                    else
                        aln->element[i].groupid = 0;
                }
            }
            if(done == FALSE)
            {
                for(i=0;i<aln->numelements;i++)
                    if(aln->element[i].groupid == aln->numgroups)
                        aln->element[i].groupid = j;
                aln->numgroups--;
            }
        }
        if(aln->numgroups == 0)
            done = TRUE;
    }
    return;
#endif
}

static void StripSpecial(char *string)
{
    int i,j,len;
    i=0;

    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;
}


static void RemoveQuotes(char *string)
{
    int i, j, len;

    len = strlen(string);
    for(j=0;j<len;j++) {
        if(string[j] == '"') string[j] = ' ';
    }

    for(j=0;string[j]==' ' && j<(int)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;
}

/*
 *       OverWrite(), overwrite all non-default data from a sequence entry
 *       onto any entry with the same ID or short name.
 */
static int OverWrite(NA_Sequence *thiss,NA_Alignment *aln)
{
    size_t j;
    int indx = -1;
    NA_Sequence *that;
    for(j=0;j<aln->numelements;j++)
    {
        if(Find2(thiss->id,aln->element[j].id) != -1)
            if(Find2(aln->element[j].id,thiss->id) != -1)
                indx = j;
    }
    if(indx == -1)
        for(j=0;j<aln->numelements;j++)
        {
            if(Find2(thiss->short_name,aln->element[j].short_name)!= -1)
                if(Find2(aln->element[j].short_name,thiss->short_name)!= -1)
                    indx = j;
        }
    if(indx != -1)
    {
        that = &(aln->element[indx]);
        if(thiss->seq_name[0])
            strcpy(that->seq_name,thiss->seq_name);
        if(thiss->barcode[0])
            strcpy(that->barcode,thiss->barcode);
        if(thiss->contig[0])
            strcpy(that->contig,thiss->contig);
        if(thiss->membrane[0])
            strcpy(that->membrane,thiss->membrane);
        if(thiss->authority[0])
            strcpy(that->authority,thiss->authority);
        if(thiss->short_name[0])
            strcpy(that->short_name,thiss->short_name);
        if(thiss->description[0])
            strcpy(that->description,thiss->description);
        if(thiss->sequence)
        {
            free((char*)that->sequence);
            that->sequence = thiss->sequence;
            that->seqlen = thiss->seqlen;
            that->seqmaxlen = thiss->seqmaxlen;
        }
        if(thiss->baggage)
        {
            that->baggage_len += thiss->baggage_len;
            that->baggage_maxlen += thiss->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,thiss->baggage,that->baggage_maxlen);
        }
        if(thiss->comments)
        {
            that->comments_len += thiss->comments_len;
            that->comments_maxlen += thiss->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,thiss->comments,that->comments_maxlen);
        }
        if(thiss->cmask)
        {
            free((char*)that->cmask);
            that->cmask = thiss->cmask;
        }
        if(thiss->offset != that->offset)
            that->offset = thiss->offset;
        if(thiss->attr != 0)
            that->attr = thiss->attr;
        if(thiss->groupid != 0)
        {
            that->groupid = thiss->groupid;
        }
        that->groupb = NULL;
        that->groupf = NULL;
    }

    return(indx);
}

void ReadGDE(char *filename,NA_Alignment *dataset,int type)
{
    int          done               = FALSE;
    size_t       len                = 0, j=0;
    int          success,count,temp = 0;
    char         in_line[GBUFSIZ],c;
    char        *buffer,*line;
    size_t       buflen             = GBUFSIZ;
    int          genclen            = 0,curelem = 0;
    NA_Sequence *this_elem          = NULL,temp_elem;
    FILE        *file;

    type=0;count=0;c=0;

    ErrorOut5(0!=(file = fopen(filename,"r")),"No such file");

    for(;fgets(in_line,GBUFSIZ,file) != 0;)
    {
        for(line = in_line;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 %zu",&(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')
                    ErrorOut5(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(in_line,GBUFSIZ,file) == 0)
                        done = TRUE;
                    line = in_line;
                }
            }
            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')
                    ErrorOut5(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(in_line,GBUFSIZ,file) == 0)
                        done = TRUE;
                    line = in_line;
                }
            }
            if(this_elem->rmatrix) {
                for(j=0;j<len;j++) {
                    buffer[j]=this_elem->rmatrix[(unsigned char)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((char*)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 = strdup(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;
}


int WriteGDE(NA_Alignment *aln,char *filename,int method,int maskable)
{
    int i;
    size_t j;
    int k,mask = -1;
    FILE *file;
    NA_Sequence *this_elem;
    //extern char month[12][6];

    if(aln == NULL)
        return(1);
    //ARB
    //if(aln->na_ddata == NULL)
    //      return(1);
    //ARB END
    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 && (int)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          %zu\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(0);
}



/*
 *       Normalize seq (remove leading indels in the sequence;
 */
void SeqNorm(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 *uniqueID()
{
    static char vname[32];
    time_t *tp;
    static int cnt = 0;

    tp = (time_t *)Calloc(1, sizeof(time_t));

    time(tp);
    sprintf(vname, "host:%d:%ld", cnt, *tp);
    cnt++;
    Cfree((char*)tp);
    return(vname);
}