--- /dev/null
+
+/* copyright (c) 1996, 1997, 1998, 1999 William R. Pearson and the
+ U. of Virginia */
+
+/* $Name: fa_34_26_5 $ - $Id: faatran.c,v 1.6 2007/04/02 18:08:11 wrp Exp $ */
+
+/* aatran.c translates from nt to aa, 1 char codes */
+/* modified July 2, 1987 for all 6 frames */
+/* 23 Jan 1991 fixed bug for short sequences */
+
+/* this mapping is not alphabet independent */
+
+#define XTERNAL
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "upam.h"
+#include "uascii.h"
+
+/*
+1. The Standard Code (transl_table=1)
+
+By default all transl_table in GenBank flatfiles are equal to id 1, and this
+is not shown. When transl_table is not equal to id 1, it is shown as a
+qualifier on the CDS feature.
+
+*/
+static
+char *AA1="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
+/*
+ Starts = ---M---------------M---------------M----------------------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+2. The Vertebrate Mitochondrial Code (transl_table=2)
+*/
+static
+char *AA2 ="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG";
+/*
+ Starts = --------------------------------MMMM---------------M------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+3. The Yeast Mitochondrial Code (transl_table=3)
+*/
+static
+char *AA3 ="FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
+/*
+ Starts = -----------------------------------M----------------------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the
+Mycoplasma/Spiroplasma Code (transl_table=4)
+*/
+static
+char *AA4 ="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
+/*
+ Starts = --MM---------------M------------MMMM---------------M------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+5. The Invertebrate Mitochondrial Code (transl_table=5)
+*/
+static
+char *AA5 ="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG";
+/*
+ Starts = ---M----------------------------MMMM---------------M------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+6. The Ciliate, Dasycladacean and Hexamita Nuclear Code (transl_table=6)
+*/
+static
+char *AA6 ="FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
+/*
+ Starts = -----------------------------------M----------------------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+9. The Echinoderm Mitochondrial Code (transl_table=9)
+*/
+static
+char *AA7 ="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG";
+/*
+ Starts = -----------------------------------M----------------------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+10. The Euplotid Nuclear Code (transl_table=10)
+*/
+static
+char *AA10="FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
+/*
+ Starts = -----------------------------------M----------------------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+11. The Bacterial "Code" (transl_table=11)
+*/
+static
+char *AA11="FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
+/*
+ Starts = ---M---------------M------------MMMM---------------M------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+12. The Alternative Yeast Nuclear Code (transl_table=12)
+*/
+static
+char *AA12 ="FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
+/*
+ Starts = -------------------M---------------M----------------------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+13. The Ascidian Mitochondrial Code (transl_table=13)
+*/
+static
+char *AA13="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG";
+/*
+ Starts = -----------------------------------M----------------------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+14. The Flatworm Mitochondrial Code (transl_table=14)
+*/
+static
+char *AA14 ="FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG";
+/*
+ Starts = -----------------------------------M----------------------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+
+15. Blepharisma Nuclear Code (transl_table=15)
+*/
+static
+char *AA15="FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
+/*
+ Starts = -----------------------------------M----------------------------
+ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+*/
+
+static
+char *AA16 ="FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
+/*
+ id 16 ,
+ name "Chlorophycean Mitochondrial" ,
+ sncbieaa "-----------------------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+*/
+
+static
+char *AA21 ="FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG";
+/*
+ name "Trematode Mitochondrial" ,
+ id 21 ,
+ sncbieaa "-----------------------------------M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+*/
+
+static
+char *AA22 ="FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
+/*
+ name "Scenedesmus obliquus Mitochondrial" ,
+ id 22 ,
+ sncbieaa "-----------------------------------M----------------------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+*/
+
+static
+char *AA23 ="FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG";
+/*
+ name "Thraustochytrium Mitochondrial" ,
+ id 23 ,
+ sncbieaa "--------------------------------M--M---------------M------------"
+ -- Base1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+ -- Base2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+ -- Base3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+*/
+
+
+static char aacmap[64]={
+ 'K','N','K','N','T','T','T','T','R','S','R','S','I','I','M','I',
+ 'Q','H','Q','H','P','P','P','P','R','R','R','R','L','L','L','L',
+ 'E','D','E','D','A','A','A','A','G','G','G','G','V','V','V','V',
+ '*','Y','*','Y','S','S','S','S','*','C','W','C','L','F','L','F'
+};
+
+static int aamap[64]; /* integer aa values */
+static int aamapr[64]; /* reverse sequence map */
+
+/* tnt is used only by aatran.c. It must be consistent with lascii and
+the nt alphabet. It uses 3,3 because T and U are considered separately
+*/
+static int tnt[]={0,0,1,2,3,3,0,1,0,0,1,2,0,0,0,1,0,0,
+ 0,1,2,3,3,0,1,0,0,1,2,0,0,0,1,0,0};
+
+static int debug_set;
+
+int
+aatran(const unsigned char *ntseq, unsigned char *aaseq, int maxs, int frame)
+{
+ int iaa, im, nna, i;
+ register int *nnp;
+ const unsigned char *nts0;
+ register int *aamp;
+ register unsigned char *aap;
+
+ iaa=nna=(maxs-(frame<3?frame:frame-3))/3;
+ if (nna <= 3 ) {
+ aaseq[0]=EOSEQ;
+ return 0;
+ }
+
+ nnp = tnt;
+
+ if (frame < 3) {
+ aamp = aamap;
+ nts0 = &ntseq[frame];
+ aap = aaseq;
+ while (nna--) {
+ im = nnp[*nts0++]<<4;
+ im += nnp[*nts0++]<<2;
+ im += nnp[*nts0++];
+ *aap++ = aamp[im];
+
+ /* this check is included because of a bug in tfasty
+ which occurs only during the alignment process */
+
+#ifdef DEBUG
+ if (debug_set && aamp[im] > MAXUC) {
+ fprintf(stderr,"faatran: %d %d %d %d %d?%d\n",
+ *(nts0-3),*(nts0-2),*(nts0-1), im, aamp[im],aamap[im]);
+
+ /* this allows recovery, but should not be done frequently */
+ for (i=0; i<64; i++) {
+ aamap[i]=aascii[aacmap[i]];
+ aamapr[i]=aascii[aacmap[(~i)&63]];
+ }
+ *(aap-1) = aamp[im];
+ }
+#endif
+ }
+ }
+ else {
+ aamp = aamapr;
+ nts0 = &ntseq[maxs-(frame-3)];
+ aap = aaseq;
+ while (nna--) {
+ im = nnp[*--nts0]<<4;
+ im += nnp[*--nts0]<<2;
+ im += nnp[*--nts0];
+ *aap++ = aamp[im];
+ /* this check is included because of a bug in tfasty
+ which occurs only during the alignment process */
+
+#ifdef DEBUG
+ if (debug_set && aamp[im] > MAXUC) {
+ fprintf(stderr,"faatran: %d %d %d %d %d?%d\n",
+ *(nts0-3),*(nts0-2),*(nts0-1), im, aamp[im],aamap[im]);
+
+ /* this allows recovery, but should not be done frequently */
+ for (i=0; i<64; i++) {
+ aamap[i]=aascii[aacmap[i]];
+ aamapr[i]=aascii[aacmap[(~i)&63]];
+ }
+ *(aap-1) = aamp[im];
+ }
+#endif
+ }
+ }
+ aaseq[iaa]=EOSEQ;
+ return iaa;
+}
+
+/* slower version that masks out NNN,XXX */
+
+/* - A C G T U R Y M W S K D H V B N X */
+static int snt[]={0,0,1,2,3,3,0,1,0,0,4,4,4,4,4,4,4,4};
+
+int
+saatran(const unsigned char *ntseq,
+ unsigned char *aaseq, int maxs, int frame)
+{
+ int iaa, im, it, nna, xflag;
+ register int *nnp;
+ const unsigned char *nts0;
+ register int *aamp;
+ register unsigned char *aap;
+
+ iaa=nna=(maxs-(frame<3?frame:frame-3))/3;
+ if (nna <= 3 ) {
+ aaseq[0]=EOSEQ;
+ return 0;
+ }
+
+ nnp = snt;
+ if (frame < 3) {
+ aamp = aamap;
+ nts0 = &ntseq[frame];
+ aap = aaseq;
+ while (nna--) {
+ xflag = 0;
+ if ((it=nnp[*nts0++])<4) {im = it<<4;}
+ else {xflag = 1; im=0;}
+ if ((it=nnp[*nts0++])<4) {im += it<<2;}
+ else xflag = 1;
+ if ((it=nnp[*nts0++])<4) {im += it;}
+ else xflag = 1;
+ if (xflag) *aap++ = aascii['X'];
+ else *aap++ = aamp[im];
+ }
+ }
+ else {
+ aamp = aamapr;
+ nts0 = &ntseq[maxs-(frame-3)];
+ aap = aaseq;
+ while (nna--) {
+ xflag = 0;
+ if ((it=nnp[*--nts0]) < 4) im = it<<4;
+ else {xflag = 1; im=0;}
+ if ((it=nnp[*--nts0]) < 4) im += it<<2;
+ else xflag = 1;
+ if ((it=nnp[*--nts0]) < 4) im += it;
+ else xflag = 1;
+ if (xflag) *aap++ = aascii['X'];
+ else *aap++ = aamp[im];
+ }
+ }
+ aaseq[iaa]=EOSEQ;
+ return iaa;
+}
+
+void
+aainit(int tr_type, int debug)
+{
+ int i,j;
+ char *aasmap;
+ int imap[4]={3,1,0,2}, i0, i1, i2, ii;
+
+ debug_set = debug;
+
+ aasmap = AA1;
+ if (tr_type > 0) {
+ /* need to put in a new translation table */
+ switch (tr_type) {
+ case 1: aasmap = AA1; break;
+ case 2: aasmap = AA2; break;
+ case 3: aasmap = AA3; break;
+ case 4: aasmap = AA4; break;
+ case 5: aasmap = AA5; break;
+ case 6: aasmap = AA6; break;
+ case 7: aasmap = AA7; break;
+ case 10: aasmap = AA10; break;
+ case 11: aasmap = AA11; break;
+ case 12: aasmap = AA12; break;
+ case 13: aasmap = AA13; break;
+ case 14: aasmap = AA14; break;
+ case 15: aasmap = AA15; break;
+ case 16: aasmap = AA16; break;
+ case 21: aasmap = AA21; break;
+ case 22: aasmap = AA22; break;
+ case 23: aasmap = AA23; break;
+
+ default: aasmap = AA1; break;
+ }
+
+ if (debug) fprintf(stderr," codon table: %d\n new old\n",tr_type);
+ for (i0 = 0; i0 < 4; i0++)
+ for (i1 = 0; i1 < 4; i1++)
+ for (i2 = 0; i2 < 4; i2++) {
+ ii = (imap[i0]<<4) + (imap[i1]<<2) + imap[i2];
+ if (debug && aacmap[ii] != *aasmap)
+ fprintf(stderr," %c%c%c: %c - %c\n",
+ nt[imap[i0]+1],nt[imap[i1]+1],nt[imap[i2]+1],
+ *aasmap,aacmap[ii]);
+ aacmap[ii]= *aasmap++;
+ }
+
+ /*
+ for (i=0; i<64; i++) {
+ fprintf(stderr,"'%c',",aacmap[i]);
+ if ((i%16)==15) fputc('\n',stderr);
+ }
+ fputc('\n',stderr);
+ */
+ }
+ for (i=0; i<64; i++) {
+ aamap[i]=aascii[aacmap[i]];
+ aamapr[i]=aascii[aacmap[(~i)&63]];
+ }
+}
+
+void
+aagetmap(char *to, int n)
+{
+ int i;
+ for (i=0; i<n; i++) to[i] = aacmap[i];
+}
git://source.jalview.org / jabaws.git / blobdiff