+++ /dev/null
-
-/* copyright (c) 1996, 1997, 1998, 1999 William R. Pearson and the
- U. of Virginia */
-
-/* $Name: fa_34_26_5 $ - $Id: mshowalign.c,v 1.43 2007/01/08 15:38:46 wrp Exp $ */
-
-/* mshowalign.c - show sequence alignments in pvcomplib */
-
-/*
- this is a merged version of showalign.c that works properly with
- both the comp_lib (serial, threaded) and PCOMPLIB parallel versions
- of the programs.
-
- In the serial and current threaded versions of the programs,
- showalign gets a list of high scoring sequences and must
- re_getlib() the sequence, do_walign(), and then calculate the
- alignment.
-
- In the PCOMPLIB parallel versions, the worker programs do the
- aligning, so showalign() must send them the appropriate messages to
- have the alignment done, and then collect the alignment results
-
-*/
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include "defs.h"
-#include "msg.h"
-#include "structs.h"
-#include "param.h"
-
-#ifdef PCOMPLIB
-#ifdef PVM_SRC
-#include "pvm3.h"
-extern int pinums[];
-#endif
-#ifdef MPI_SRC
-#include "mpi.h"
-#endif
-#include "p_mw.h"
-#else
-#include "mm_file.h"
-#include "mw.h"
-#endif
-
-#ifndef PCOMPLIB
-
-/* used to position the library sequence for re_getlib - also gets
- description */
-#define RANLIB (m_fptr->ranlib)
-
-extern struct lmf_str *
-re_openlib(struct lmf_str *, int outtty);
-
-int
-re_getlib(unsigned char *aa1, int maxn, int maxt,
- int loff, int cont, int term_code,
- long *loffset, long *l_off,
- struct lmf_str *m_fptr);
-
-#include "drop_func.h"
-
-#endif
-
-
-extern void cal_coord(int n0, int n1, long sq0off, long loffset,
- struct a_struct *aln);
-
-void initseq(char **, char **, char **, char **, int);
-void freeseq(char **, char **, char **, char **);
-
-void do_show(FILE *fp, int n0, int n1, int score,
- char *name0, char *name1, int nml,
- struct mngmsg m_msg, struct pstruct pst,
- char *seqc0, char *seqc0a, char *seqc1, char *seqca, int nc,
- float percent, float gpercent, int lc,
- struct a_struct *aln, long loffset);
-
-extern void discons(FILE *fd, struct mngmsg m_msg, struct pstruct pst,
- char *seqc0, char *seqc0a, char *seqc1, char *seqca,
- int nc,
- int n0, int n1, char *name0, char *name1, int nml,
- struct a_struct *aln,
- long loffset);
-
-extern void disgraph(FILE *fd, int n0, int n1,
- float percent, int score,
- int min0, int min1, int max0, int max1, long sq0off,
- char *name0, char *name1, int nml, int llen, int markx);
-
-extern double zs_to_bit(double, int, int);
-
-extern void
-do_url1(FILE *, struct mngmsg, struct pstruct, char *, int,
- struct a_struct , long);
-
-#ifndef A_MARK
-#define A_MARK ">>"
-#endif
-
-static char l_name[200]; /* link name */
-
-#ifdef PCOMPLIB
-#define BBP_INFO(info) bbp->desptr->info
-#else
-#define BBP_INFO(info) bbp->info
-#endif
-
-/* this version does not check for m_msg.e_cut because nshow/nbest has
- already been set to limit on e_cut */
-
-void showalign (FILE *fp,
-#ifndef PCOMPLIB
- unsigned char **aa0, unsigned char *aa1, int maxn,
-#endif
- struct beststr **bptr, int nbest, int qlib,
- struct mngmsg m_msg, struct pstruct pst, char *gstring2
-#ifndef PCOMPLIB
- , void **f_str
-#endif
-)
-{
- char tmp_str[20];
- char info_str[200];
- char bline[2048], *bl_ptr, *bp, fmt[40];
- int tmp_len, l_llen;
- int t_have_ares;
- char name0[80], name0s[80], name1[200];
- int istart = 0, istop, i = 0, ib, nml;
- int n1tot;
- struct beststr *bbp;
- int nc, lc, maxc;
- float percent, gpercent;
- char *seqc0, *seqc0a, *seqc1, *seqca;
- long loffset, l_off;
-#ifdef PCOMPLIB
- struct stage2_str liblist;
- struct qmng_str qm_msg;
-#ifdef MPI_SRC
- int int_msg_b[10];
- MPI_Status mpi_status;
-#endif
-#else
- int n1;
- struct lmf_str *m_fptr;
- int ngap;
-#endif
-
-#ifdef PCOMPLIB
- /* this function has its own copy of qm_msg, so we must fill it
- appropriately */
- qm_msg.n0 = m_msg.n0;
- strncpy(qm_msg.libstr,m_msg.qtitle,sizeof(qm_msg.libstr));
-#endif
-
- /* set the name0,1 label length */
- if (m_msg.markx & MX_M10FORM) nml = 12;
- else nml = m_msg.nmlen;
-
- if (strlen(m_msg.qtitle) > 0) {
- if (m_msg.qtitle[0]=='>') strncpy(name0s,&m_msg.qtitle[1],sizeof(name0s));
- else strncpy(name0s,m_msg.qtitle,sizeof(name0s));
- }
- else {
- strncpy(name0s,m_msg.tname,sizeof(name0s));
- }
- name0s[sizeof(name0s)-1]='\0';
-
- if ((bp=strchr(name0s,' '))!=NULL) *bp='\0';
-
- if (m_msg.revcomp) name0[nml-1]='-';
-
- l_llen = m_msg.aln.llen;
- if ((m_msg.markx & MX_M9SUMM) && m_msg.show_code != SHOW_CODE_ID) {
- l_llen += 40;
- if (l_llen > 200) l_llen=200;
- }
-
- sprintf(fmt,"%s%%-%ds (%%d %s)\n",A_MARK,l_llen-5,m_msg.sqnam);
-
- if (!(m_msg.markx&MX_M10FORM)) fprintf(fp,"\n");
-
- if (m_msg.ashow < 0) m_msg.ashow = m_msg.nshow;
- istart = 0; istop = min(min(nbest,m_msg.ashow),m_msg.nshow);
-
- for (ib=istart; ib<istop; ib++) {
- bbp = bptr[ib];
-
-#ifdef SHOWUN
- if (BBP_INFO(nsfnum) > 0 && sfn_cmp(m_msg.qsfnum,BBP_INFO(sfnum))) {
- istop = min(istop+1,nbest);
- continue;
- }
-#endif
- if (bbp->score[0] <= 0) break;
-
- if (m_msg.quiet==1 && pst.zsflag>=0
- && bbp->escore < m_msg.e_low) continue;
-
-#ifndef PCOMPLIB
- /* get the alignment and score by re-aligning */
-
- if ((m_fptr=re_openlib(bbp->m_file_p,!m_msg.quiet))==NULL)
- exit(1);
-
- /* get the description - do not "edit" it yet */
-
- if (!(m_msg.markx & MX_M10FORM)){
- if (m_msg.long_info) {tmp_len = sizeof(bline)-1;}
- else {tmp_len = l_llen-5;}
- RANLIB(bline,tmp_len,bbp->lseek,bbp->libstr,bbp->m_file_p);
- bline[tmp_len]='\0';
- }
- else {
- RANLIB(bline,sizeof(bline),bbp->lseek,bbp->libstr,bbp->m_file_p);
- bline[sizeof(bline)-1]='\0';
- }
-
- n1 = re_getlib(aa1,maxn,m_msg.maxt3,m_msg.loff,bbp->cont,m_msg.term_code,
- &loffset,&l_off,bbp->m_file_p);
-#ifdef DEBUG
- if (n1 != bbp->n1) {
- fprintf(stderr," library sequence: %s lengths differ: %d != %d\n",
- bline,bbp->n1, n1);
- fprintf(stderr, "offset is: %lld\n",bbp->lseek);
- }
-#endif
-
- if (!bbp->have_ares) {
- bbp->sw_score =
- do_walign(aa0[bbp->frame],m_msg.n0, aa1, n1, bbp->frame, &pst,
- f_str[bbp->frame], &bbp->a_res, &t_have_ares);
- }
- else {
- pre_cons(aa1,n1,bbp->frame,f_str[bbp->frame]);
- }
-
- aln_func_vals(bbp->frame, &m_msg.aln);
-
-#else /* PCOMPLIB - get the alignment information from a worker */
-
- /* we have a sequence that we need an alignment for -
- send a message to the appropriate worker to produce an alignment
- qm_msg.slist == 1 -> one alignment
- qm_msg.s_func == DO_ALIGN_FLG -> use the alignment function
- send mngmsg (MSEQTYPE)
- then send number of sequence to be aligned
- */
-
- qm_msg.slist = 1;
- qm_msg.s_func = DO_ALIGN_FLG;
-
- liblist.seqnm = bbp->seqnm;
- liblist.frame = bbp->frame;
-#ifdef PVM_SRC
- pvm_initsend(PvmDataRaw);
- pvm_pkbyte((char *)&qm_msg,sizeof(struct qmng_str),1);
- pvm_send(pinums[bbp->wrkr],MSEQTYPE);
-
- pvm_initsend(PvmDataRaw);
- pvm_pkbyte((char *)&liblist,sizeof(struct stage2_str),1);
- pvm_send(pinums[bbp->wrkr],LISTTYPE);
-#endif
-#ifdef MPI_SRC
- MPI_Send(&qm_msg,sizeof(struct qmng_str),MPI_BYTE,bbp->wrkr,
- MSEQTYPE,MPI_COMM_WORLD);
- MPI_Send(&liblist,sizeof(struct stage2_str),MPI_BYTE,bbp->wrkr,
- LISTTYPE,MPI_COMM_WORLD);
-#endif
- /* information should be sent */
- /* pick up description */
- strncpy(bline,bbp->desptr->bline,l_llen-5);
- bline[l_llen-5]='\0';
-#endif /* PCOMPLIB */
-
- if (strlen(bline)==0) {
- bline[0]='>';
- strncpy(&bline[1],m_msg.lname,l_llen-5);
- bline[l_llen-5]='\0';
- }
- /* re-format bline */
- while ((bp=strchr(bline,'\n'))!=NULL) *bp=' ';
- if (m_msg.long_info) {
- tmp_len = strlen(bline);
- bl_ptr = bline;
- if (!(m_msg.markx & MX_M10FORM)) while (tmp_len > l_llen) {
- for (i=l_llen; i>10; i--)
- if (bl_ptr[i]==' ') {
- bl_ptr[i]='\n';
- break;
- }
- if (i <= 10) break;
- tmp_len -= i;
- bl_ptr += i;
- }
- bline[sizeof(bline)-1]='\0';
- }
-
- n1tot = (BBP_INFO(n1tot_p)) ? *BBP_INFO(n1tot_p) : bbp->n1;
-
- strncpy(name1,bline,sizeof(name1));
-
- if ((!m_msg.markx & MX_M10FORM)) name1[nml]='\0';
- if ((bp = strchr(name1,' '))!=NULL) *bp = '\0';
-
- /* l_name is used to build an HTML link from the bestscore line to
- the alignment. It can also be used to discriminate multiple hits
- from the same long sequence. Text must match that in showbest.c */
-
- strncpy(name1,bline,sizeof(name1));
- name1[sizeof(name1)-1]='\0';
- if ((bp = strchr(name1,' '))!=NULL) *bp = '\0';
- strncpy(l_name,name1,sizeof(l_name));
- l_name[sizeof(l_name)-1]='\0';
- if ((bp=strchr(&l_name[3],'|'))!=NULL) *bp='\0';
- if (m_msg.nframe > 2) sprintf(&l_name[strlen(l_name)],"_%d",bbp->frame+1);
- else if (m_msg.qframe >= 0 && bbp->frame == 1)
- strncat(l_name,"_r",sizeof(l_name));
- if (bbp->cont-1 > 0) {
- sprintf(tmp_str,":%d",bbp->cont-1);
- strncat(l_name,tmp_str,sizeof(l_name)-strlen(l_name));
- }
-
- if (!(m_msg.markx & MX_M10FORM)) name1[nml]='\0';
-
- /* print out score information; */
-
- if (m_msg.markx & MX_HTML ) {
- fprintf (fp,"<A name=%s>\n<tt><pre>\n",l_name);
- }
- strncpy(name0,name0s,nml);
- name0[nml]='\0';
-
- if (pst.zsflag%10 == 6) {
- sprintf(info_str," comp: %.5f H: %.5f",bbp->comp,bbp->H);
- }
- else info_str[0]='\0';
-
- if ((m_msg.markx & MX_ATYPE)!=7 && !(m_msg.markx & MX_M10FORM)) {
- fprintf (fp, fmt,bp=bline,n1tot);
- if (m_msg.nframe > 2)
- fprintf (fp, "Frame: %d",bbp->frame+1);
- else if (m_msg.nframe > 1)
- fprintf (fp, "Frame: %c",(bbp->frame? 'r': 'f'));
- else if (m_msg.qframe >= 0 && bbp->frame > 0 ) {
- fputs("rev-comp",fp);
- name0[nml-1]='\0';
- strcat(name0,"-");
- }
-
- if (m_msg.arelv > 0)
- fprintf (fp, " %s: %3d", m_msg.alab[0],bbp->score[0]);
- if (m_msg.arelv > 1)
- fprintf (fp, " %s: %3d", m_msg.alab[1],bbp->score[1]);
- if (m_msg.arelv > 2)
- fprintf (fp, " %s: %3d", m_msg.alab[2],bbp->score[2]);
- fprintf(fp,"%s",info_str);
- if (pst.zsflag>=0)
- fprintf (fp, " Z-score: %4.1f bits: %3.1f E(): %4.2g",
- bbp->zscore,zs_to_bit(bbp->zscore,m_msg.n0,bbp->n1),bbp->escore);
- fprintf (fp, "\n");
- }
- else if (m_msg.markx & MX_M10FORM) {
- fprintf(fp,">>%s\n",bline);
- if (m_msg.qframe > -1) {
- if (m_msg.nframe > 2) {
- fprintf(fp,"; %s_frame: %d\n",m_msg.f_id0,bbp->frame+1);
- }
- else {
- fprintf(fp,"; %s_frame: %c\n",m_msg.f_id0,(bbp->frame > 0? 'r':'f'));
- }
- }
- fprintf (fp, "; %s_%s: %3d\n", m_msg.f_id0,m_msg.alab[0],bbp->score[0]);
- if (m_msg.arelv > 1)
- fprintf (fp,"; %s_%s: %3d\n", m_msg.f_id0,m_msg.alab[1],bbp->score[1]);
- if (m_msg.arelv > 2)
- fprintf (fp,"; %s_%s: %3d\n", m_msg.f_id0,m_msg.alab[2],bbp->score[2]);
- if (info_str[0]) fprintf(fp,"; %s_info: %s\n",m_msg.f_id0,info_str);
- if (pst.zsflag>=0)
- fprintf (fp,"; %s_z-score: %4.1f\n; %s_bits: %3.1f\n; %s_expect: %6.2g\n",
- m_msg.f_id0,bbp->zscore,
- m_msg.f_id0,zs_to_bit(bbp->zscore,m_msg.n0,bbp->n1),
- m_msg.f_id0,bbp->escore);
- }
-
-
-#ifdef PCOMPLIB
- /* get the sw_score, alignment information, get seqc0, seqc1 */
-
-#ifdef PVM_SRC
- /* get alignment lengths, percents */
- pvm_recv(pinums[bbp->wrkr],ALN1TYPE);
- pvm_upkint(&nc,1,1);
- pvm_upkint(&lc,1,1);
- pvm_upkint(&maxc,1,1);
-
- pvm_upkfloat(&percent,1,1);
- pvm_upkfloat(&gpercent,1,1);
-
- pvm_upkint(&bbp->sw_score,1,1);
- pvm_upkbyte((char *)&m_msg.aln,sizeof(struct a_struct),1);
-
- initseq(&seqc0, &seqc0a, &seqc1, &seqca, maxc);
-
- pvm_recv(pinums[bbp->wrkr],ALN2TYPE);
- pvm_upkbyte(seqc0,maxc,1);
- if (m_msg.ann_flg) pvm_upkbyte(seqc0a,maxc,1);
- pvm_upkbyte(seqc1,maxc,1);
- pvm_upkbyte(seqca,maxc,1);
-#endif
-#ifdef MPI_SRC
- MPI_Recv(int_msg_b,4,MPI_INT,bbp->wrkr,ALN1TYPE,MPI_COMM_WORLD,
- &mpi_status);
- nc = int_msg_b[0];
- lc = int_msg_b[1];
- maxc = int_msg_b[2];
- bbp->sw_score = int_msg_b[3];
- MPI_Recv(&percent,1,MPI_FLOAT,bbp->wrkr,ALN2TYPE,MPI_COMM_WORLD,
- &mpi_status);
- MPI_Recv(&gpercent,1,MPI_FLOAT,bbp->wrkr,ALN2TYPE,MPI_COMM_WORLD,
- &mpi_status);
- MPI_Recv(&m_msg.aln,sizeof(struct a_struct),MPI_BYTE,
- bbp->wrkr,ALN3TYPE,MPI_COMM_WORLD,&mpi_status);
-
- initseq(&seqc0, &seqc0a, &seqc1, &seqca, maxc);
- MPI_Recv(seqc0,maxc,MPI_BYTE,bbp->wrkr,ALN2TYPE,MPI_COMM_WORLD,&mpi_status);
- if (m_msg.ann_flg)
- MPI_Recv(seqc0a,maxc,MPI_BYTE,bbp->wrkr,ALN2TYPE,MPI_COMM_WORLD,&mpi_status);
- MPI_Recv(seqc1,maxc,MPI_BYTE,bbp->wrkr,ALN3TYPE,MPI_COMM_WORLD,&mpi_status);
- MPI_Recv(seqca,maxc,MPI_BYTE,bbp->wrkr,ALN3TYPE,MPI_COMM_WORLD,&mpi_status);
-#endif
-
- /* l_off is the coordinate of the first residue */
- l_off = 1;
- /* loffset is the offset of the aa1 in the full sequence */
- loffset = bbp->desptr->loffset-l_off;
-
-#else /* not PCOMPLIB */
-
- /* estimate space for alignment consensus */
- if (m_msg.aln.showall==1) {
- maxc = bbp->a_res.nres + max(bbp->a_res.min0,bbp->a_res.min1)+
- max((m_msg.n0-bbp->a_res.max0),(n1-bbp->a_res.max1))+4;
- }
- else {
- maxc = bbp->a_res.nres + 4*m_msg.aln.llen+4;
- }
-
- /* get space to put the sequence alignment consensus */
- initseq(&seqc0, &seqc0a, &seqc1, &seqca, maxc);
-
- /* build consensus from res, nres (done by workers if PCOMPLIB) */
- if (!m_msg.ann_flg) {
- nc=calcons(aa0[bbp->frame],m_msg.n0,aa1,n1,
- &lc,&m_msg.aln, bbp->a_res, pst, seqc0, seqc1, seqca,
- f_str[bbp->frame]);
- memset(seqc0a,' ',nc);
- seqc0a[nc]='\0';
- }
- else {
- nc=calcons_a(aa0[bbp->frame],m_msg.aa0a,m_msg.n0,aa1,n1,
- &lc,&m_msg.aln,bbp->a_res,pst, seqc0, seqc0a,
- seqc1, seqca, m_msg.ann_arr,f_str[bbp->frame]);
- }
-
- /* PCOMPLIB workers return percent, gpercent, so calculate it here */
- if (lc > 0) percent = (100.0*(float)m_msg.aln.nident)/(float)lc;
- else percent = -1.00;
- ngap = m_msg.aln.ngap_q + m_msg.aln.ngap_l;
-#ifndef SHOWSIM
- if (lc-ngap> 0) gpercent =(100.0*(float)m_msg.aln.nident)/(float)(lc-ngap);
-#else
- if (lc > 0) gpercent =(100.0*(float)m_msg.aln.nsim)/(float)lc;
-#endif
- else gpercent = -1.00;
-#endif
-
- if (max(strlen(seqc0),strlen(seqc1)) > nc) {
- fprintf(stderr," mshowalign: nc/maxc: %d/%d seqc0/1: %u/%u\n",
- nc,maxc,strlen(seqc0),strlen(seqc1));
- }
-
- /* here PCOMPLIB/comp_lib logic is the same */
-
-#ifdef DEBUG
- if (bbp->sw_score < bbp->score[pst.score_ix]) {
- fprintf(stderr," *** warning - SW score=%d < opt score=%d ***\n",
- bbp->sw_score, bbp->score[pst.score_ix]);
- }
-#endif
-
- cal_coord(m_msg.n0,bbp->n1,m_msg.sq0off,loffset+l_off-1,&m_msg.aln);
-
-#ifndef PCOMPLIB
- if (bbp->a_res.nres > 0)
-#endif
- do_show(fp, m_msg.n0, bbp->n1, bbp->sw_score, name0, name1, nml,
- m_msg, pst, seqc0, seqc0a, seqc1, seqca,
- nc, percent, gpercent, lc, &m_msg.aln,
- loffset+l_off-1);
-
- if (m_msg.markx & MX_HTML) fprintf(fp,"</pre></tt>\n<hr>\n");
- fflush(fp);
-
- freeseq(&seqc0,&seqc0a,&seqc1, &seqca);
- }
- if (fp!=stdout) fprintf(fp,"\n");
-}
-
-void do_show(FILE *fp, int n0,int n1, int score,
- char *name0, char *name1, int nml,
- struct mngmsg m_msg, struct pstruct pst,
- char *seqc0, char *seqc0a, char *seqc1, char *seqca, int nc,
- float percent, float gpercent, int lc,
- struct a_struct *aln, long loffset)
-{
- int tmp;
-
- if (m_msg.markx & MX_AMAP && (m_msg.markx & MX_ATYPE)==7)
- disgraph(fp, n0, n1, percent, score,
- aln->amin0, aln->amin1, aln->amax0, aln->amax1, m_msg.sq0off,
- name0, name1, nml, aln->llen, m_msg.markx);
- else if (m_msg.markx & MX_M10FORM) {
- if (pst.sw_flag && m_msg.arelv>0)
- fprintf(fp,"; %s_score: %d\n",m_msg.f_id1,score);
- fprintf(fp,"; %s_ident: %5.3f\n",m_msg.f_id1,percent/100.0);
-#ifndef SHOWSIM
- fprintf(fp,"; %s_gident: %5.3f\n",m_msg.f_id1,gpercent/100.0);
-#else
- fprintf(fp,"; %s_sim: %5.3f\n",m_msg.f_id1,gpercent/100.0);
-#endif
-
- fprintf(fp,"; %s_overlap: %d\n",m_msg.f_id1,lc);
- discons(fp, m_msg, pst, seqc0, seqc0a, seqc1, seqca, nc,
- n0, n1, name0, name1, nml, aln, loffset);
- }
- else {
- if (pst.sw_flag) fprintf(fp,"Smith-Waterman score: %d; ",score);
- else fprintf(fp,"banded Smith-Waterman score: %d; ",score);
-#ifndef SHOWSIM
- fprintf(fp," %6.3f%% identity (%6.3f%% ungapped) in %d %s overlap (%ld-%ld:%ld-%ld)\n",
- percent,gpercent,lc,m_msg.sqnam,aln->d_start0,aln->d_stop0,
- aln->d_start1,aln->d_stop1);
-#else
- fprintf(fp," %6.3f%% identity (%6.3f%% similar) in %d %s overlap (%ld-%ld:%ld-%ld)\n",
- percent,gpercent,lc,m_msg.sqnam,aln->d_start0,aln->d_stop0,
- aln->d_start1,aln->d_stop1);
-#endif
-
- if (m_msg.markx & MX_HTML) {
- do_url1(fp, m_msg, pst, l_name,n1,*aln,loffset);
- }
-
- if (m_msg.markx & MX_AMAP && (m_msg.markx & MX_ATYPE)!=7) {
- fputc('\n',fp);
- tmp = n0;
-
- if (m_msg.qdnaseq == SEQT_DNA && m_msg.ldnaseq== SEQT_PROT)
- tmp /= 3;
-
- disgraph(fp, tmp, n1, percent, score,
- aln->amin0, aln->amin1,
- aln->amax0, aln->amax1,
- m_msg.sq0off,
- name0, name1, nml, aln->llen,m_msg.markx);
- }
-
- discons(fp, m_msg, pst, seqc0, seqc0a, seqc1, seqca, nc,
- n0, n1, name0, name1, nml, aln, loffset);
-
- fputc('\n',fp);
-
- }
-}
-
-
-#ifndef MPI_SRC
-void /* initialize consensus arrays */
-initseq(char **seqc0, char **seqc0a, char **seqc1, char **seqca, int seqsiz)
-{
- *seqc0=(char *)calloc((size_t)seqsiz*4,sizeof(char));
- if (*seqc0==NULL)
- {fprintf(stderr,"cannot allocate consensus arrays %d\n",seqsiz);
- exit(1);}
- *seqc0a=*seqc0 + seqsiz;
- *seqc1=*seqc0a + seqsiz;
- *seqca=*seqc1 + seqsiz;
-}
-
-void freeseq(char **seqc0, char **seqc0a, char **seqc1, char **seqca)
-{
- free(*seqc0);
-}
-#endif
git://source.jalview.org / jabaws.git / blobdiff