+++ /dev/null
-/* dispn.c associated subroutines for matching sequences */
-
-/* $Name: fa_34_26_5 $ - $Id: c_dispn.c,v 1.21 2005/10/25 20:22:52 wrp Exp $ */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <ctype.h>
-
-#include "defs.h"
-#include "structs.h"
-#include "param.h"
-
-#define XTERNAL
-
-#define YES 1
-#define NO 0
-
-#define MAXOUT 201
-
-/* the seqca[] array has the following codes:
- 0 - no alignment symbol
- 1 - align; pam < 0
- 2 - align; pam == 0
- 3 - align; pam > 0
- 4 - align; ident
- 5 - align; del
-
- the map_sym arrays determine the value to be displayed with each
- type of aligned residue
-*/
-
-static char *map_sym_0 =" ..: ";
-static char *map_sym_1 =" Xxx ";
-static char *map_sym_2 =" . ";
-#ifdef M10_CONS_L
-static char *map_sym_10=" mzp=-";
-#else
-static char *map_sym_10=" ..:-";
-#endif
-
-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)
-{
- char line[3][MAXOUT], cline[2][MAXOUT+10], *clinep[2];
- int il, i, lend, loff, id;
- int del0, del1, ic, ll0, ll1, ll01, cl0, cl1, rl0, rl1;
- int ic_save;
- char *map_sym_p;
- int l_llen;
- int ioff0, ioff00, ioff1, ioff10;
- long qqoff, lloff, qoffset;
- int llsgn, llfact, qlsgn, qlfact, qfx0, qfxn, lfx0, lfxn;
- int have_res;
- char *name01, *sq;
- char blank[MAX_UID], afmt[32];
-
- memset(blank,' ',sizeof(blank)-1);
- blank[sizeof(blank)-1]='\0';
-
- if (nml > 6) {
- blank[nml-6]='\0';
- sprintf(afmt,"%%-%ds %%s\n",nml);
- }
- else {
- blank[0]='\0';
- strncpy(afmt,"%-6s %s\n",sizeof(afmt));
- }
- if (pst.ext_sq_set) sq = pst.sqx; else sq = pst.sq;
-
- clinep[0]=cline[0]+1;
- clinep[1]=cline[1]+1;
-
- if (aln->qlfact == 0) {qlfact = 1;}
- else qlfact = aln->qlfact;
- if (aln->qlrev == 1) {
- qoffset = n0;
- qlsgn = -1;
- qfx0 = 0;
- qfxn = 1;
- }
- else {
- qoffset = 0;
- qlsgn = 1;
- qfx0 = 1;
- qfxn = 0;
- }
-
- if (aln->llfact == 0) {llfact = 1;}
- else llfact = aln->llfact;
-
- if (aln->llrev == 1) {
- loffset += n1;
- llsgn = -1;
- lfx0 = 0;
- lfxn = 1;
- }
- else {
- llsgn = 1;
- lfx0 = 1;
- lfxn = 0;
- }
-
- l_llen = aln->llen;
- if ((m_msg.markx & MX_M9SUMM) && m_msg.show_code != 1) { l_llen += 40; }
-
- if ((m_msg.markx & MX_ATYPE)==2) name01=name1;
- else name01 = "\0";
-
- ioff0=aln->smin0;
- ioff00 = ioff0;
- ioff1=aln->smin1;
- ioff10 = ioff1;
-
- if (m_msg.markx& MX_AMAP && (m_msg.markx & MX_ATYPE)==7) return;
-
- /* set *map_sym_p to correct match symbol */
- if ((m_msg.markx&MX_ATYPE)==1) {map_sym_p = map_sym_1;}
- else if ((m_msg.markx&MX_ATYPE)==2) {map_sym_p = map_sym_2;}
- else if (m_msg.markx&MX_M10FORM) {map_sym_p = map_sym_10;}
- else {map_sym_p = map_sym_0;}
-
- if (m_msg.markx & MX_ASEP) {
- fprintf(fd,">%s ..\n",name0);
- for (i=0; i<nc && seqc0[i]; i++) {
- /* if (seqc0[i]=='-') fputc('.',fd); else */
- fputc(seqc0[i],fd);
- if (i%50 == 49) fputc('\n',fd);
- }
- if ((i-1)%50 != 49) fputc('\n',fd);
- fprintf(fd,">%s ..\n",name1);
- for (i=0; i<nc && seqc1[i]; i++) {
- /* if (seqc1[i]=='-') fputc('.',fd); else */
- fputc(seqc1[i],fd);
- if (i%50 == 49) fputc('\n',fd);
- }
- if ((i-1)%50 != 49) fputc('\n',fd);
- return;
- }
-
- if (m_msg.markx & MX_M10FORM) {
- fprintf(fd,">%s ..\n",name0);
- fprintf(fd,"; sq_len: %d\n",n0);
- fprintf(fd,"; sq_offset: %ld\n",m_msg.sq0off);
- fprintf(fd,"; sq_type: %c\n",m_msg.sqtype[0]);
- fprintf(fd,"; al_start: %ld\n",aln->d_start0);
- fprintf(fd,"; al_stop: %ld\n",aln->d_stop0);
- fprintf(fd,"; al_display_start: %ld\n",
- qoffset+qlsgn*ioff0*aln->llmult+qfx0);
-
- have_res = 0;
- for (i=0; i<nc && seqc0[i]; i++) {
- if (!have_res && seqc0[i]==' ') fputc('-',fd);
- else if (seqc0[i]==' ') break;
- else {
- have_res = 1;
- fputc(seqc0[i],fd);
- }
- if (i%50 == 49) fputc('\n',fd);
- }
- if ((i-1)%50!=49 || seqc0[i-1]==' ') fputc('\n',fd);
- fprintf(fd,">%s ..\n",name1);
- fprintf(fd,"; sq_len: %d\n",n1);
- fprintf(fd,"; sq_type: %c\n",m_msg.sqtype[0]);
- fprintf(fd,"; al_start: %ld\n",aln->d_start1);
- fprintf(fd,"; al_stop: %ld\n",aln->d_stop1);
- fprintf(fd,"; al_display_start: %ld\n",loffset+llsgn*ioff1+lfx0);
-
- have_res = 0;
- for (i=0; i<nc && seqc1[i]; i++) {
- if (!have_res && seqc1[i]==' ') fputc('-',fd);
- else if (seqc1[i]==' ') break;
- else {
- have_res = 1;
- fputc(seqc1[i],fd);
- }
- if (i%50 == 49) fputc('\n',fd);
- }
- if ((i-1)%50!=49 || seqc1[i-1]==' ') fputc('\n',fd);
-#ifdef M10_CONS
- fprintf(fd,"; al_cons:\n");
- for (i=0,del0=0,id=ioff0; id-del0<aln->amax0 && i < nc; i++,id++) {
- if (seqc0[i] == '\0' || seqc1[i] == '\0') break;
- if (seqc0[i]=='-' || seqc0[i]==' ' || seqc0[i]=='\\') del0++;
- else if (seqc0[i]=='/') del0++;
- if (id-del0<aln->amin0) fputc(' ',fd);
- else if (seqc0[i]=='-'||seqc1[i]=='-') fputc('-',fd);
- else fputc(map_sym_10[seqca[i]],fd);
-
- if (i%50 == 49) fputc('\n',fd);
- }
- if ((i-1)%50!=49 || seqc1[i-1]==' ') fputc('\n',fd);
-#endif
- return;
- }
-
- memset(line[0],' ',MAXOUT);
- memset(line[1],' ',MAXOUT);
- memset(line[2],' ',MAXOUT);
-
- /* cl0 indicates whether a coordinate should be printed over the first
- sequence; cl1 indicates a coordinate for the second;
- */
-
- ic = 0; del0=del1=0;
- for (il=0; il<(nc+l_llen-1)/l_llen; il++) {
- loff=il*l_llen;
- lend=min(l_llen,nc-loff);
-
- ll0 = NO; ll1 = NO;
-
- memset(cline[0],' ',MAXOUT+1);
- memset(cline[1],' ',MAXOUT+1);
-
- ic_save = ic;
- for (i=0; i<lend; i++, ic++,ioff0++,ioff1++) {
- cl0 = cl1 = rl0 = rl1 = YES;
- if ((line[0][i]=seqc0[ic])=='-' || seqc0[ic]=='\\') {
- del0++; cl0=rl0=NO;
- }
- else if (seqc0[ic]=='/') {
- del0++; cl0=rl0=NO;
- }
- if ((line[2][i]=seqc1[ic])=='-' || seqc1[ic]=='\\') {
- del1++; cl1=rl1=NO;
- }
- else if (seqc1[ic]=='/') {
- del1++; cl1=rl1=NO;
- }
-
- if (seqc0[ic]==' ') {del0++; cl0=rl0=NO;}
- else ll0 = YES;
- if (seqc1[ic]==' ') {del1++; cl1=rl1=NO;}
- else ll1 = YES;
-
- qqoff = m_msg.sq0off - 1 + qoffset + (long)qlsgn*ioff00 +
- (long)qlsgn*qlfact*(ioff0-del0-ioff00);
- if (cl0 && qqoff%10 == 9) {
- sprintf(&clinep[0][i-qfxn],"%8ld",qqoff+1l);
- clinep[0][i+8-qfxn]=' ';
- rl0 = NO;
- }
- else if (cl0 && qqoff== -1) {
- sprintf(&clinep[0][i-qfxn],"%8ld",0l);
- clinep[0][i+8-qfxn]=' ';
- rl0 = NO;
- }
- else if (rl0 && (qqoff+1)%10 == 0) {
- sprintf(&clinep[0][i-qfxn],"%8ld",qqoff+1);
- clinep[0][i+8-qfxn]=' ';
- }
-
- /* the lloff coordinate of a residue is the sum of:
- m_msg.sq1off-1 - the user defined coordinate
- loffset - the offset into the library sequence
- llsgn*ioff10 - the offset into the beginning of the alignment
- (given in the "natural" coordinate system,
- except for tfasta3 which provides context)
- llsgn*llfact*(ioff1-del1-ioff10)
- - the position in the consensus aligment, -gaps
- */
-
- lloff = m_msg.sq1off-1 + loffset + aln->frame +
- (long)llsgn*aln->llmult*ioff10 +
- (long)llsgn*llfact*(ioff1-del1-ioff10);
-
- if (cl1 && lloff%10 == 9) {
- sprintf(&clinep[1][i-lfxn],"%8ld",lloff+1l);
- clinep[1][i+8-lfxn]=' ';
- rl1 = NO;
- }
- else if (cl1 && lloff== -1) {
- sprintf(&clinep[1][i],"%8ld",0l);
- clinep[1][i+8-lfxn]=' ';
- rl1 = NO;
- }
- else if (rl1 && (lloff+1)%10 == 0) {
- sprintf(&clinep[1][i-lfxn],"%8ld",lloff+1);
- clinep[1][i+8-lfxn]=' ';
- }
-
- line[1][i] = ' ';
- if (ioff0-del0 >= aln->amin0 && ioff0-del0 <= aln->amax0) {
- if (seqca[ic]==4) {line[1][i]=map_sym_p[4];}
- else if ((m_msg.markx&MX_ATYPE)==2) line[1][i]=line[2][i];
- else line[1][i] = map_sym_p[seqca[ic]];
- }
- else if ((m_msg.markx&MX_ATYPE)==2) line[1][i]=line[2][i];
- }
-
- if (m_msg.ann_flg) {
- for (ic=ic_save,i=0; i<lend; ic++,i++) {
- if (seqc0a[ic]!= ' ') clinep[0][i+7-qfxn] = seqc0a[ic];
- }
- }
-
- line[0][lend]=line[1][lend]=line[2][lend]=0;
- clinep[0][lend+7]=clinep[1][lend+7]=0;
-
- ll01 = ll0&&ll1;
- if ((m_msg.markx&MX_ATYPE)==2 && (!aln->showall || ll0)) ll1=0;
- fprintf(fd,"\n");
- if (ll0) fprintf(fd,"%s%s\n",blank,clinep[0]);
- if (ll0) fprintf(fd,afmt,name0,line[0]);
- if (ll01) fprintf(fd,afmt,name01,line[1]);
- if (ll1) fprintf(fd,afmt,name1,line[2]);
- if (ll1) fprintf(fd,"%s%s\n",blank,clinep[1]);
- }
-}
-
-static float gscale= -1.0;
-
-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 mlen, int markx)
-{
- int i, gstart, gstop, gend;
- int llen;
- char line[MAXOUT+1];
- char afmt[16], afmtf[64];
-
- if (nml > 6) {
- sprintf(afmt,"%%-%ds",nml);
- }
- else {
- strncpy(afmt,"%-6s",sizeof(afmt));
- }
- strncpy(afmtf,afmt,sizeof(afmtf));
- strncat(afmtf," %4ld-%4ld: %5.1f%%:%s:\n",sizeof(afmtf));
-
- llen = mlen - 10;
- memset(line,' ',llen);
-
- line[llen-1]='\0';
- if (gscale < 0.0) {
- gscale = (float)llen/(float)n0;
- if ((markx&MX_ATYPE) == 7 )
- fprintf(fd,afmtf,name0,sq0off,sq0off+n0-1,100.0,line);
- }
-
- gstart = (int)(gscale*(float)min0+0.5);
- gstop = (int)(gscale*(float)max0+0.5);
- gend = gstop+(int)(gscale*(float)(n1-max1));
-
- if (gstop >= llen) gstop = llen-1;
- if (gend >= llen) gend = llen-1;
- for (i=0; i<gstart; i++) line[i]=' ';
- for (; i<gstop; i++) line[i]='-';
- for (; i<llen; i++) line[i]=' ';
-
- line[gend]=':';
- line[llen]='\0';
-
- if (markx & MX_AMAP) {
- if ((markx & MX_ATYPE)==7) { /* markx==4 - no alignment */
- strncpy(afmtf,afmt,sizeof(afmtf));
- strncat(afmtf," %4ld-%4ld:%4d %5.1f%%:%s\n",sizeof(afmtf));
- fprintf(fd,afmtf,name1,min0+sq0off,max0+sq0off-1,score,percent,line);
- }
- else {
- afmtf[0]='>';
- strncpy(&afmtf[1],afmt,sizeof(afmtf)-1);
- strncat(afmtf," %4ld-%4ld:%s\n",sizeof(afmtf));
- fprintf(fd,afmtf, name1,min0+sq0off,max0+sq0off-1,line);
- }
- }
-}
-
-void
-aancpy(char *to, char *from, int count, struct pstruct pst)
-{
- char *tp, *sq;
- int nsq;
-
- if (pst.ext_sq_set) {
- nsq = pst.nsqx;
- sq = pst.sqx;
- }
- else {
- nsq = pst.nsq;
- sq = pst.sq;
- }
-
- tp=to;
- while (count-- && *from) {
- if (*from <= nsq) *tp++ = sq[*(from++)];
- else *tp++ = *from++;
- }
- *tp='\0';
-}
-
-void
-r_memcpy(dest,src,cnt)
- char *dest, *src;
- int cnt;
-{
- while (cnt--) *dest++ = *src++;
-}
-
-void
-l_memcpy(dest,src,cnt)
- char *dest, *src;
- int cnt;
-{
- dest = dest+cnt;
- src = src+cnt;
- while (cnt--) *--dest = *--src;
-}
-
-/* this routine now indexs from 1 (rather than 0) because sq starts
- with a 0 */
-
-#define MAXSQ 50 /* must be same as upam.h */
-
-void cal_coord(int n0, int n1, long sq0off, long loffset,
- struct a_struct *aln)
-{
- long qoffset;
- int llsgn, qlsgn, qfx0, qfxn, lfx0, lfxn;
-
- if (aln->qlrev == 1) {
- qoffset = sq0off -1 + n0;
- qlsgn = -1;
- qfx0 = 0;
- qfxn = 1;
- }
- else {
- qoffset = sq0off - 1;
- qlsgn = 1;
- qfx0 = 1;
- qfxn = 0;
- }
-
- if (aln->llrev == 1) {
- loffset += n1;
- llsgn = -1;
- lfx0 = 0;
- lfxn = 1;
- }
- else {
- llsgn = 1;
- lfx0 = 1;
- lfxn = 0;
- }
- aln->d_start0 = qoffset+qlsgn*aln->amin0+qfx0;
- aln->d_stop0 = qoffset+qlsgn*aln->amax0+qfxn;
- aln->d_start1 = loffset+llsgn*aln->amin1*aln->llmult+lfx0+aln->frame;
- aln->d_stop1 = loffset+llsgn*aln->amax1*aln->llmult+lfxn+aln->frame;
-}
git://source.jalview.org / jabaws.git / blobdiff