int main(int argc, char **argv)
{
/* Variable Declarations */
AjPStr code = NULL;
AjPFile mfptr = NULL;
AjPFile wfptr = NULL;
AjPFile outf = NULL;
EmbPPropMolwt *mwdata;
EmbPPropAmino *aadata;
float *dhstat = NULL;
char code1;
AjPStr code3 = NULL;
ajint idx = 0;
ajuint i;
ajuint iend;
AjPStr propstr = NULL;
float charge;
char csign;
/* ACD File Processing */
embInit("inforesidue", argc, argv);
code = ajAcdGetString("code");
mfptr = ajAcdGetDatafile("aadata");
wfptr = ajAcdGetDatafile("mwdata");
outf = ajAcdGetOutfile("outfile");
aadata = embPropEaminoRead(mfptr);
mwdata = embPropEmolwtRead(wfptr);
if(!embReadAminoDataFloatC(DAYHOFF_FILE,&dhstat,(float)0.001))
ajFatal("Set the EMBOSS_DATA environment variable");
/* Application logic */
ajStrFmtUpper(&code);
iend = ajStrGetLen(code);
ajFmtPrintF(outf, "%-4s %-5s %-20s %6s %9s %-30s %s\n",
"Code", "Short", "Mnemonic",
"Charge", "MolWt",
"Properties", "Ambiguity");
for(i=0; i<iend; i++)
{
code1=ajStrGetCharPos(code,i);
if(ajResidueExistsChar(code1))
{
idx = ajBasecodeToInt(code1);
ajResidueToTriplet(code1, &code3);
ajStrFmtTitle(&code3);
if(!embPropGetProperties(aadata[idx], &propstr))
ajStrAssignC(&propstr, "(none)");
charge = embPropGetCharge(aadata[idx]);
if(charge > 0.0)
csign = '+';
else if(charge < 0.0)
csign = '-';
else
csign = ' ';
ajFmtPrintF(outf, "%-4c %-5S %-20S %3c%3.1f %9.4f %-30S %S\n",
code1, code3, ajResidueGetMnemonic(code1),
csign, fabs(charge),
embPropMolwtGetMolwt(mwdata[idx]),
propstr, ajResidueGetCodes(code1));
}
else
{
ajFmtPrintF(outf, "%-4c %-5s %-20s %6s %9s %-30s %s\n",
code1, ".", "invalid", ".", ".", ".", ".");
}
}
/* Memory management and exit */
ajStrDel(&code);
ajStrDel(&code3);
ajStrDel(&propstr);
ajFileClose(&outf);
ajFileClose(&mfptr);
ajFileClose(&wfptr);
ajFileClose(&outf);
embPropAminoDel(&aadata);
embPropMolwtDel(&mwdata);
AJFREE(dhstat);
embExit();
return 0;
}
int main(int argc, char **argv)
{
ajint begin, end;
AjPSeqall seqall;
AjPSeq seq;
EmbPShow ss;
AjPFile outfile;
AjPStr tablename;
ajint table;
AjPRange uppercase;
AjPRange highlight;
AjBool threeletter;
AjBool numberseq;
AjBool nameseq;
ajint width;
ajint length;
ajint margin;
AjBool description;
ajint offset;
AjBool html;
AjPStr descriptionline;
ajint orfminsize;
AjPTrn trnTable;
AjBool translation;
AjBool reverse;
AjBool cutlist;
AjBool flat;
EmbPMatMatch mm = NULL;
AjPStr *framelist;
AjBool frames[6]; /* frames to be translated 1 to 3, -1 to -3 */
/* stuff for tables and lists of enzymes and hits */
ajint default_mincuts = 1;
ajint default_maxcuts = 2000000000;
AjPTable hittable; /* enzyme hits */
/* stuff lifted from Alan's 'restrict.c' */
AjPStr enzymes = NULL;
ajint mincuts;
ajint maxcuts;
ajint sitelen;
AjBool single;
AjBool blunt;
AjBool sticky;
AjBool ambiguity;
AjBool plasmid;
AjBool commercial;
AjBool limit;
AjBool methyl;
AjPFile enzfile = NULL;
AjPFile equfile = NULL;
AjPFile methfile = NULL;
AjPTable retable = NULL;
ajint hits;
AjPList restrictlist = NULL;
embInit("remap", argc, argv);
seqall = ajAcdGetSeqall("sequence");
outfile = ajAcdGetOutfile("outfile");
tablename = ajAcdGetListSingle("table");
uppercase = ajAcdGetRange("uppercase");
highlight = ajAcdGetRange("highlight");
threeletter = ajAcdGetBoolean("threeletter");
numberseq = ajAcdGetBoolean("number");
width = ajAcdGetInt("width");
length = ajAcdGetInt("length");
margin = ajAcdGetInt("margin");
nameseq = ajAcdGetBoolean("name");
description = ajAcdGetBoolean("description");
offset = ajAcdGetInt("offset");
html = ajAcdGetBoolean("html");
orfminsize = ajAcdGetInt("orfminsize");
translation = ajAcdGetBoolean("translation");
reverse = ajAcdGetBoolean("reverse");
cutlist = ajAcdGetBoolean("cutlist");
flat = ajAcdGetBoolean("flatreformat");
framelist = ajAcdGetList("frame");
/* restriction enzyme stuff */
mincuts = ajAcdGetInt("mincuts");
maxcuts = ajAcdGetInt("maxcuts");
sitelen = ajAcdGetInt("sitelen");
single = ajAcdGetBoolean("single");
blunt = ajAcdGetBoolean("blunt");
sticky = ajAcdGetBoolean("sticky");
ambiguity = ajAcdGetBoolean("ambiguity");
plasmid = ajAcdGetBoolean("plasmid");
commercial = ajAcdGetBoolean("commercial");
limit = ajAcdGetBoolean("limit");
enzymes = ajAcdGetString("enzymes");
methfile = ajAcdGetDatafile("mfile");
methyl = ajAcdGetBoolean("methylation");
if(!blunt && !sticky)
ajFatal("Blunt/Sticky end cutters shouldn't both be disabled.");
/* get the number of the genetic code used */
ajStrToInt(tablename, &table);
trnTable = ajTrnNewI(table);
/* read the local file of enzymes names */
remap_read_file_of_enzyme_names(&enzymes);
/* get the frames to be translated */
remap_GetFrames(framelist, frames);
while(ajSeqallNext(seqall, &seq))
{
/* get begin and end positions */
begin = ajSeqGetBegin(seq)-1;
end = ajSeqGetEnd(seq)-1;
/* do the name and description */
if(nameseq)
{
if(html)
ajFmtPrintF(outfile, "<H2>%S</H2>\n",
ajSeqGetNameS(seq));
else
ajFmtPrintF(outfile, "%S\n", ajSeqGetNameS(seq));
}
if(description)
{
/*
** wrap the description line at the width of the sequence
** plus margin
*/
if(html)
ajFmtPrintF(outfile, "<H3>%S</H3>\n",
ajSeqGetDescS(seq));
else
{
descriptionline = ajStrNew();
ajStrAssignS(&descriptionline, ajSeqGetDescS(seq));
ajStrFmtWrap(&descriptionline, width+margin);
ajFmtPrintF(outfile, "%S\n", descriptionline);
ajStrDel(&descriptionline);
}
}
/* get the restriction cut sites */
/*
** most of this is lifted from the program 'restrict.c' by Alan
** Bleasby
*/
if(single)
maxcuts=mincuts=1;
retable = ajTablestrNew(EQUGUESS);
enzfile = ajDatafileNewInNameC(ENZDATA);
if(!enzfile)
ajFatal("Cannot locate enzyme file. Run REBASEEXTRACT");
if(limit)
{
equfile = ajDatafileNewInNameC(EQUDATA);
if(!equfile)
limit = ajFalse;
else
remap_read_equiv(&equfile, &retable, commercial);
}
ajFileSeek(enzfile, 0L, 0);
restrictlist = ajListNew();
/* search for hits, but don't use mincuts and maxcuts criteria yet */
hits = embPatRestrictMatch(seq, begin+1, end+1, enzfile, methfile,
enzymes, sitelen,plasmid, ambiguity,
default_mincuts, default_maxcuts, blunt,
sticky, commercial, methyl,
restrictlist);
ajDebug("Remap found %d hits\n", hits);
if(hits)
{
/* this bit is lifted from printHits */
embPatRestrictRestrict(restrictlist, hits, !limit,
ajFalse);
if(limit)
remap_RestrictPreferred(restrictlist,retable);
}
ajFileClose(&enzfile);
ajFileClose(&methfile);
/*
** Remove those violating the mincuts and maxcuts
** criteria, but save them in hittable for printing out later.
** Keep a count of how many hits each enzyme gets in hittable.
*/
hittable = ajTablestrNewCase(TABLEGUESS);
remap_RemoveMinMax(restrictlist, hittable, mincuts, maxcuts);
/* make the Show Object */
ss = embShowNew(seq, begin, end, width, length, margin, html, offset);
if(html)
ajFmtPrintF(outfile, "<PRE>");
/* create the format to display */
embShowAddBlank(ss);
embShowAddRE(ss, 1, restrictlist, plasmid, flat);
embShowAddSeq(ss, numberseq, threeletter, uppercase, highlight);
if(!numberseq)
embShowAddTicknum(ss);
embShowAddTicks(ss);
if(reverse)
{
embShowAddComp(ss, numberseq);
embShowAddRE(ss, -1, restrictlist, plasmid, flat);
}
if(translation)
{
if(reverse)
embShowAddBlank(ss);
if(frames[0])
embShowAddTran(ss, trnTable, 1, threeletter,
numberseq, NULL, orfminsize,
AJFALSE, AJFALSE, AJFALSE, AJFALSE);
if(frames[1])
embShowAddTran(ss, trnTable, 2, threeletter,
numberseq, NULL, orfminsize,
AJFALSE, AJFALSE, AJFALSE, AJFALSE);
if(frames[2])
embShowAddTran(ss, trnTable, 3, threeletter,
numberseq, NULL, orfminsize,
AJFALSE, AJFALSE, AJFALSE, AJFALSE);
if(reverse)
{
embShowAddTicks(ss);
if(frames[5])
embShowAddTran(ss, trnTable, -3, threeletter,
numberseq, NULL, orfminsize,
AJFALSE, AJFALSE, AJFALSE, AJFALSE);
if(frames[4])
embShowAddTran(ss, trnTable, -2, threeletter,
numberseq, NULL, orfminsize,
AJFALSE, AJFALSE, AJFALSE, AJFALSE);
if(frames[3])
embShowAddTran(ss, trnTable, -1, threeletter,
numberseq, NULL, orfminsize,
AJFALSE, AJFALSE, AJFALSE, AJFALSE);
}
}
embShowPrint(outfile, ss);
/* display a list of the Enzymes that cut and don't cut */
if(cutlist)
{
remap_CutList(outfile, hittable,
limit, html, mincuts, maxcuts);
remap_NoCutList(outfile, hittable, html, enzymes, blunt,
sticky, sitelen, commercial, ambiguity,
limit, retable);
}
/* add a gratuitous newline at the end of the sequence */
ajFmtPrintF(outfile, "\n");
/* tidy up */
embShowDel(&ss);
while(ajListPop(restrictlist,(void **)&mm))
embMatMatchDel(&mm);
ajListFree(&restrictlist);
remap_DelTable(&hittable);
ajTablestrFree(&retable);
}
ajTrnDel(&trnTable);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajFileClose(&outfile);
ajStrDel(&tablename);
ajStrDel(&enzymes);
ajStrDelarray(&framelist);
ajRangeDel(&uppercase);
ajRangeDel(&highlight);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPSeq seq = NULL;
AjPReport outf = NULL;
AjPFile inf = NULL;
ajint begin;
ajint end;
AjPList l = NULL;
AjPStr strand = NULL;
AjPStr substr = NULL;
AjPStr line = NULL;
AjPStr name = NULL;
AjPStr acc = NULL;
AjPStr bf = NULL;
AjPStr menu;
AjPStr pattern = NULL;
AjPStr opattern = NULL;
AjPStr pname = NULL;
AjPStr key = NULL;
AjPStr value = NULL;
AjPTable atable = NULL;
AjPTable btable = NULL;
ajint mismatch;
ajint minlength;
ajint sum;
ajint v;
char cp;
const char *p;
embInit("tfscan", argc, argv);
seqall = ajAcdGetSeqall("sequence");
outf = ajAcdGetReport("outfile");
mismatch = ajAcdGetInt("mismatch");
minlength = ajAcdGetInt("minlength");
menu = ajAcdGetListSingle("menu");
pname = ajStrNew();
cp=ajStrGetCharFirst(menu);
if(cp=='F')
ajStrAssignC(&pname,"tffungi");
else if(cp=='I')
ajStrAssignC(&pname,"tfinsect");
else if(cp=='O')
ajStrAssignC(&pname,"tfother");
else if(cp=='P')
ajStrAssignC(&pname,"tfplant");
else if(cp=='V')
ajStrAssignC(&pname,"tfvertebrate");
else if(cp=='C')
inf = ajAcdGetDatafile("custom");
if(cp!='C')
{
inf = ajDatafileNewInNameS(pname);
if(!inf)
ajFatal("Either EMBOSS_DATA undefined or TFEXTRACT needs running");
}
name = ajStrNew();
acc = ajStrNew();
bf = ajStrNewC("");
substr = ajStrNew();
line = ajStrNew();
pattern = ajStrNewC("AA");
opattern = ajStrNew();
while(ajSeqallNext(seqall, &seq))
{
begin=ajSeqallGetseqBegin(seqall);
end=ajSeqallGetseqEnd(seqall);
ajStrAssignC(&name,ajSeqGetNameC(seq));
strand=ajSeqGetSeqCopyS(seq);
ajStrAssignSubC(&substr,ajStrGetPtr(strand),begin-1,end-1);
ajStrFmtUpper(&substr);
l=ajListNew();
atable = ajTablestrNew(1000);
btable = ajTablestrNew(1000);
sum=0;
while(ajReadlineTrim(inf,&line))
{
p = ajStrGetPtr(line);
if(!*p || *p=='#' || *p=='\n' || *p=='!')
continue;
ajFmtScanS(line,"%S%S%S",&pname,&pattern,&acc);
p += ajStrGetLen(pname);
while(*p && *p==' ')
++p;
p += ajStrGetLen(pattern);
while(*p && *p==' ')
++p;
p += ajStrGetLen(acc);
while(*p && *p==' ')
++p;
ajStrAssignS(&opattern,pattern);
ajStrAssignC(&bf,p); /* rest of line */
v = embPatVariablePattern(pattern,substr,pname,l,0,
mismatch,begin);
if(v)
{
key = ajStrNewS(pname);
value = ajStrNewS(acc);
ajTablePut(atable,(void *)key,(void *)value);
key = ajStrNewS(pname);
value = ajStrNewS(bf);
ajTablePut(btable,(void *)key,(void *)value);
}
sum += v;
}
if(sum)
tfscan_print_hits(&l,sum,outf,atable,seq,minlength,
btable);
ajFileSeek(inf,0L,0);
ajListFree(&l);
ajTablestrFree(&atable);
ajTablestrFree(&btable);
ajStrDel(&strand);
}
ajStrDel(&line);
ajStrDel(&name);
ajStrDel(&acc);
ajStrDel(&pname);
ajStrDel(&opattern);
ajStrDel(&bf);
ajStrDel(&pattern);
ajStrDel(&substr);
ajSeqDel(&seq);
ajFileClose(&inf);
ajReportClose(outf);
ajReportDel(&outf);
ajSeqallDel(&seqall);
ajSeqDel(&seq);
ajStrDel(&menu);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPSeq seq;
AjPGraph graph = 0;
AjPFile outf = NULL;
AjPFile file = NULL;
AjPStr buffer = NULL;
float twist[4][4][4];
float roll[4][4][4];
float tilt[4][4][4];
float rbend;
float rcurve;
float bendscale;
float curvescale;
float twistsum = (float) 0.0;
float pi = (float) 3.14159;
float pifac = (pi/(float) 180.0);
float pi2 = pi/(float) 2.0;
ajint *iseq = NULL;
float *x;
float *y;
float *xave;
float *yave;
float *curve;
float *bend;
const char *ptr;
ajint i;
ajint ii;
ajint k;
ajint j;
char residue[2];
float maxbend;
float minbend;
float bendfactor;
float maxcurve;
float mincurve;
float curvefactor;
float fxp;
float fyp;
float yincr;
float yy1;
ajint ixlen;
ajint iylen;
ajint ixoff;
ajint iyoff;
float ystart;
float defheight;
float currentheight;
ajint count;
ajint portrait = 0;
ajint title = 0;
ajint numres;
ajint ibeg;
ajint iend;
ajint ilen;
AjPStr sstr = NULL;
ajint ipos;
float dx;
float dy;
float rxsum;
float rysum;
float yp1;
float yp2;
double td;
embInit("banana", argc, argv);
seq = ajAcdGetSeq("sequence");
file = ajAcdGetDatafile("anglesfile");
outf = ajAcdGetOutfile("outfile");
graph = ajAcdGetGraph("graph");
numres = ajAcdGetInt("residuesperline");
ibeg = ajSeqGetBegin(seq);
iend = ajSeqGetEnd(seq);
ajStrAssignSubS(&sstr, ajSeqGetSeqS(seq), ibeg-1, iend-1);
ilen = ajStrGetLen(sstr);
AJCNEW0(iseq,ilen+1);
AJCNEW0(x,ilen+1);
AJCNEW0(y,ilen+1);
AJCNEW0(xave,ilen+1);
AJCNEW0(yave,ilen+1);
AJCNEW0(curve,ilen+1);
AJCNEW0(bend,ilen+1);
ptr= ajStrGetPtr(sstr);
for(ii=0;ii<ilen;ii++)
{
if(*ptr=='A' || *ptr=='a')
iseq[ii+1] = 0;
else if(*ptr=='T' || *ptr=='t')
iseq[ii+1] = 1;
else if(*ptr=='G' || *ptr=='g')
iseq[ii+1] = 2;
else if(*ptr=='C' || *ptr=='c')
iseq[ii+1] = 3;
else
ajErr("%c is not an ATCG hence not valid",*ptr);
ptr++;
}
if(!file)
ajErr("Banana failed to open angle file");
ajReadline(file,&buffer); /* 3 junk lines */
ajReadline(file,&buffer);
ajReadline(file,&buffer);
for(k=0;k<4;k++)
for(ii=0;ii<4;ii++)
{
if(ajReadline(file,&buffer))
{
sscanf(ajStrGetPtr(buffer),"%f,%f,%f,%f",
&twist[ii][0][k],&twist[ii][1][k],&twist[ii][2][k],
&twist[ii][3][k]);
}
else
ajErr("Error reading angle file");
for(j=0;j<4;j++)
twist[ii][j][k] *= pifac;
}
for(k=0;k<4;k++)
for(ii=0;ii<4;ii++)
if(ajReadline(file,&buffer))
{
sscanf(ajStrGetPtr(buffer),"%f,%f,%f,%f",&roll[ii][0][k],
&roll[ii][1][k],&roll[ii][2][k],&roll[ii][3][k]);
}
else
ajErr("Error reading angle file");
for(k=0;k<4;k++)
for(ii=0;ii<4;ii++)
if(ajReadline(file,&buffer))
sscanf(ajStrGetPtr(buffer),"%f,%f,%f,%f",&tilt[ii][0][k],
&tilt[ii][1][k],&tilt[ii][2][k],&tilt[ii][3][k]);
else
ajErr("Error reading angle file");
if(ajReadline(file,&buffer))
sscanf(ajStrGetPtr(buffer),"%f,%f,%f,%f",&rbend,&rcurve,
&bendscale,&curvescale);
else
ajErr("Error reading angle file");
ajFileClose(&file);
ajStrDel(&buffer);
for(ii=1;ii<ilen-1;ii++)
{
twistsum += twist[iseq[ii]][iseq[ii+1]][iseq[ii+2]];
dx = (roll[iseq[ii]][iseq[ii+1]][iseq[ii+2]]*sinfban(twistsum)) +
(tilt[iseq[ii]][iseq[ii+1]][iseq[ii+2]]*sinfban(twistsum-pi2));
dy = roll[iseq[ii]][iseq[ii+1]][iseq[ii+2]]*cosfban(twistsum) +
tilt[iseq[ii]][iseq[ii+1]][iseq[ii+2]]*cosfban(twistsum-pi2);
x[ii+1] = x[ii]+dx;
y[ii+1] = y[ii]+dy;
}
for(ii=6;ii<ilen-6;ii++)
{
rxsum = 0.0;
rysum = 0.0;
for(k=-4;k<=4;k++)
{
rxsum+=x[ii+k];
rysum+=y[ii+k];
}
rxsum+=(x[ii+5]*(float)0.5);
rysum+=(y[ii+5]*(float)0.5);
rxsum+=(x[ii-5]*(float)0.5);
rysum+=(y[ii-5]*(float)0.5);
xave[ii] = rxsum*(float)0.1;
yave[ii] = rysum*(float)0.1;
}
for(i=(ajint)rbend+1;i<=ilen-(ajint)rbend-1;i++)
{
td = sqrt(((x[i+(ajint)rbend]-x[i-(ajint)rbend])*
(x[i+(ajint)rbend]-x[i-(ajint)rbend])) +
((y[i+(ajint)rbend]-y[i-(ajint)rbend])*
(y[i+(ajint)rbend]-y[i-(ajint)rbend])));
bend[i] = (float) td;
bend[i]*=bendscale;
}
for(i=(ajint)rcurve+6;i<=ilen-(ajint)rcurve-6;i++)
{
td = sqrt(((xave[i+(ajint)rcurve]-
xave[i-(ajint)rcurve])*(xave[i+(ajint)rcurve]-
xave[i-(ajint)rcurve]))+
((yave[i+(ajint)rcurve]-yave[i-(ajint)rcurve])*
(yave[i+(ajint)rcurve]-yave[i-(ajint)rcurve])));
curve[i] = (float) td;
}
if(outf)
{
ajFmtPrintF(outf,"Base Bend Curve\n");
ptr = ajStrGetPtr(sstr);
for(ii=1;ii<=ilen;ii++)
{
ajFmtPrintF(outf,"%c %6.1f %6.1f\n",
*ptr, bend[ii], curve[ii]);
ptr++;
}
ajFileClose(&outf);
}
if(graph)
{
maxbend = minbend = 0.0;
maxcurve = mincurve = 0.0;
for(ii=1;ii<=ilen;ii++)
{
if(bend[ii] > maxbend)
maxbend = bend[ii];
if(bend[ii] < minbend)
minbend = bend[ii];
if(curve[ii] > maxcurve)
maxcurve = curve[ii];
if(curve[ii] < mincurve)
mincurve = curve[ii];
}
ystart = 75.0;
ajGraphAppendTitleS(graph, ajSeqGetUsaS(seq));
ajGraphicsSetPagesize(960, 768);
ajGraphOpenWin(graph,(float)-1.0, (float)numres+(float)10.0,
(float)0.0, ystart+(float)5.0);
ajGraphicsGetParamsPage(&fxp,&fyp,&ixlen,&iylen,&ixoff,&iyoff);
if(portrait)
{
ixlen = 768;
iylen = 960;
}
else
{
ixlen = 960;
iylen = 768;
}
ajGraphicsGetCharsize(&defheight,¤theight);
if(!currentheight)
{
defheight = currentheight = (float) 4.440072;
currentheight = defheight *
((float)ixlen/ ((float)(numres)*(currentheight+(float)1.0)))
/currentheight;
}
ajGraphicsSetCharscale(((float)ixlen/((float)(numres)*
(currentheight+(float)1.0)))/
currentheight);
ajGraphicsGetCharsize(&defheight,¤theight);
yincr = (currentheight + (float)3.0)*(float)0.3;
if(!title)
yy1 = ystart;
else
yy1 = ystart-(float)5.0;
count = 1;
residue[1]='\0';
bendfactor = (3*yincr)/maxbend;
curvefactor = (3*yincr)/maxcurve;
ptr = ajStrGetPtr(sstr);
yy1 = yy1-(yincr*((float)5.0));
for(ii=1;ii<=ilen;ii++)
{
if(count > numres)
{
yy1 = yy1-(yincr*((float)5.0));
if(yy1<1.0)
{
if(!title)
yy1=ystart;
else
yy1 = ystart-(float)5.0;
yy1 = yy1-(yincr*((float)5.0));
ajGraphNewpage(graph,AJFALSE);
}
count = 1;
}
residue[0] = *ptr;
ajGraphicsDrawposTextAtend((float)(count)+(float)2.0,yy1,residue);
if(ii>1 && ii < ilen)
{
yp1 = yy1+yincr + (bend[ii]*bendfactor);
yp2 = yy1+yincr + (bend[ii+1]*bendfactor);
ajGraphicsDrawposLine((float)count+(float)1.5,yp1,
(float)(count)+(float)2.5,yp2);
}
ipos = ilen-(ajint)rcurve-7;
if(ipos < 0)
ipos = 0;
if(ii>rcurve+5 && ii<ipos)
{
yp1 = yy1+yincr + (curve[ii]*curvefactor);
yp2 = yy1+yincr + (curve[ii+1]*curvefactor);
ajGraphicsDrawposLine((float)count+(float)1.7,yp1,
(float)(count)+(float)2.3,yp2);
}
ajGraphicsDrawposLine((float)count+(float)1.5,yy1+yincr,
(float)(count)+(float)2.5,yy1+yincr);
count++;
ptr++;
}
ajGraphicsClose();
}
AJFREE(iseq);
AJFREE(x);
AJFREE(y);
AJFREE(xave);
AJFREE(yave);
AJFREE(curve);
AJFREE(bend);
ajStrDel(&sstr);
ajSeqDel(&seq);
ajFileClose(&file);
ajFileClose(&outf);
ajGraphxyDel(&graph);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPSeq seq = NULL;
AjPFile angles = NULL;
AjPFile energies = NULL;
AjPFile result = NULL;
AjPTable angletable = NULL;
AjPTable energytable = NULL;
AjPStr nucs = NULL;
const AjPStr valstr = NULL;
const char * dinuc = NULL;
ajint len;
ajint begin;
ajint end;
ajint i;
float val;
float anglesum = 0.0;
float energysum = 0.0;
float twists = 0.0;
float basesperturn = 0.0;
float energyperbase = 0.0;
embInit ("btwisted", argc, argv);
seq = ajAcdGetSeq ("sequence");
angles = ajAcdGetDatafile("angledata");
energies = ajAcdGetDatafile("energydata");
result = ajAcdGetOutfile ("outfile");
nucs = ajStrNew();
angletable = btwisted_getdinucdata(angles);
energytable = btwisted_getdinucdata(energies);
ajFileClose(&angles);
ajFileClose(&energies);
begin = ajSeqGetBegin(seq);
end = ajSeqGetEnd(seq);
len = end-begin+1;
dinuc = ajSeqGetSeqC(seq);
for(i=begin-1; i<end-1; ++i)
{
ajStrAssignSubC(&nucs,dinuc,i,i+1);
if(!(valstr = ajTableFetchS(angletable, nucs)))
ajFatal("Incomplete table");
ajStrToFloat(valstr,&val);
anglesum += val;
if(!(valstr = ajTableFetchS(energytable, nucs)))
ajFatal("Incomplete table");
ajStrToFloat(valstr,&val);
energysum += val;
}
twists = anglesum / (float)360.0 ;
basesperturn = (float) len * (float)360.0 /anglesum;
energyperbase = energysum/(float) (len-1);
ajFmtPrintF(result, "# Output from BTWISTED\n");
ajFmtPrintF(result, "# Twisting calculated from %d to %d of %s\n",
begin, end, ajSeqGetNameC(seq));
ajFmtPrintF(result,"Total twist (degrees): %.1f\n", anglesum);
ajFmtPrintF(result,"Total turns : %.2f\n", twists);
ajFmtPrintF(result,"Average bases per turn: %.2f\n", basesperturn);
ajFmtPrintF(result,"Total stacking energy : %.2f\n", energysum);
ajFmtPrintF(result,"Average stacking energy per dinucleotide: %.2f\n",
energyperbase);
ajTablestrFree(&angletable);
ajTablestrFree(&energytable);
ajStrDel(&nucs);
ajFileClose(&result);
ajSeqDel(&seq);
embExit ();
return 0;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPSeq seq = NULL;
AjPStr seqcmp = NULL;
AjPStr enzymes = NULL;
AjPFile outf = NULL;
ajint begin;
ajint end;
ajint min;
ajint max;
ajint sitelen;
AjBool alpha;
AjBool single;
AjBool blunt;
AjBool ambiguity;
AjBool sticky;
AjBool plasmid;
AjBool threeprime;
AjBool commercial;
AjBool html;
AjBool limit;
AjBool frags;
AjBool methyl;
AjPFile dfile;
AjPFile enzfile = NULL;
AjPFile equfile = NULL;
AjPFile methfile = NULL;
AjPStr name = NULL;
AjPTable table = NULL;
ajint hits;
AjPList l = NULL;
embInit("restover", argc, argv);
seqall = ajAcdGetSeqall("sequence");
seqcmp = ajAcdGetString("seqcomp");
ajStrFmtUpper(&seqcmp);
outf = ajAcdGetOutfile("outfile");
/*
** Some of these are not needed but I left them in case someone wants to
** use them some time ...
*/
enzymes = ajStrNewC("all");
min = ajAcdGetInt("min");
max = ajAcdGetInt("max");
sitelen = 2;
threeprime = ajAcdGetBoolean("threeprime");
blunt = ajAcdGetBoolean("blunt");
sticky = ajAcdGetBoolean("sticky");
single = ajAcdGetBoolean("single");
html = ajAcdGetBoolean("html");
alpha = ajAcdGetBoolean("alphabetic");
ambiguity = ajAcdGetBoolean("ambiguity");
plasmid = ajAcdGetBoolean("plasmid");
commercial = ajAcdGetBoolean("commercial");
limit = ajAcdGetBoolean("limit");
frags = ajAcdGetBoolean("fragments");
methyl = ajAcdGetBoolean("methylation");
dfile = ajAcdGetDatafile("datafile");
methfile = ajAcdGetDatafile("mfile");
if(single)
max = min = 1;
table = ajTablestrNew(EQUGUESS);
l = ajListNew();
if(threeprime)
ajStrReverse(&seqcmp);
/* read the local file of enzymes names */
restover_read_file_of_enzyme_names(&enzymes);
if(!dfile)
{
enzfile = ajDatafileNewInNameC(ENZDATA);
if(!enzfile)
ajFatal("Cannot locate enzyme file. Run REBASEEXTRACT");
}
else
{
enzfile = dfile;
}
if(limit)
{
equfile = ajDatafileNewInNameC(EQUDATA);
if(!equfile)
limit=ajFalse;
else
{
restover_read_equiv(equfile,table);
ajFileClose(&equfile);
}
}
while(ajSeqallNext(seqall, &seq))
{
begin = ajSeqallGetseqBegin(seqall);
end = ajSeqallGetseqEnd(seqall);
ajFileSeek(enzfile,0L,0);
ajSeqFmtUpper(seq);
hits = embPatRestrictMatch(seq,begin,end,enzfile,methfile,enzymes,
sitelen,plasmid,ambiguity,min,max,blunt,
sticky,commercial,methyl,l);
ajDebug("hits:%d listlen:%u\n", hits, ajListGetLength(l));
if(hits)
{
name = ajStrNewC(ajSeqGetNameC(seq));
restover_printHits(seq, seqcmp, outf,l,name,hits,begin,end,
min,max,plasmid,
sitelen,limit,table,alpha,frags,
html);
ajStrDel(&name);
}
ajListFree(&l);
}
ajListFree(&l);
ajSeqDel(&seq);
ajFileClose(&outf);
ajFileClose(&dfile);
ajFileClose(&enzfile);
ajFileClose(&equfile);
ajFileClose(&methfile);
ajSeqallDel(&seqall);
ajStrDel(&seqcmp);
ajStrDel(&enzymes);
ajStrDel(&name);
ajTablestrFree(&table);
embExit();
return 0;
}
int main(ajint argc, char **argv)
{
/* Variable declarations */
AjPFile inf_edam = NULL; /* Name of EDAM data (input) file */
AjPFile acdoutf = NULL; /* Name of ACD (output) file */
AjPList acdinlist = NULL; /* List of ACD file names (input) */
AjPFile acdinf = NULL; /* Name of ACD (input) file */
AjPStr acdname = NULL; /* Name of current acd file */
AjPDirout acdoutdir = NULL; /* Directory for ACD files (output) */
AjPFile inf_ktype = NULL; /* Name of knowntypes.standard file */
PEdam edam = NULL; /* EDAM relations data */
PKtype ktype = NULL; /* Data from knowntype.standard */
/* Read data from acd. */
embInitP("acdrelations",argc,argv,"MYEMBOSS");
/* ACD data handling */
inf_edam = ajAcdGetDatafile("infileedam");
inf_ktype = ajAcdGetInfile("infiletype");
acdinlist = ajAcdGetDirlist("indir");
acdoutdir = ajAcdGetOutdir("outdir");
/* Read data file */
edam = ajEdamNew();
ktype = ajKtypeNew();
acdrelations_readdatfile(inf_edam, &edam);
acdrelations_readtypefile(inf_ktype, &ktype);
/* Main application loop. Process each ACD file in turn. */
while(ajListPop(acdinlist,(void **)&acdname))
{
if(!(acdinf = ajFileNewInNameS(acdname)))
ajFatal("Cannot open input ACD file %S\n", acdname);
ajFilenameTrimPath(&acdname);
if(!(acdoutf = ajFileNewOutNameDirS(acdname, acdoutdir)))
ajFatal("Cannot open output ACD file %S\n", acdname);
acdrelations_procacdfile(acdinf, acdoutf, edam, ktype);
ajFileClose(&acdinf);
ajFileClose(&acdoutf);
}
/* Clean up and exit */
ajFileClose(&inf_edam);
ajFileClose(&inf_ktype);
ajListFree(&acdinlist);
ajDiroutDel(&acdoutdir);
ajEdamDel(&edam);
ajExit();
return 0;
}
int main(ajint argc, char **argv)
{
AjPFile datafile;
AjPFile outf = NULL;
AjPSeqall seqall;
AjPSeq ajseq = NULL;
ajuint i;
ajint verb;
ajint window;
ajint pt;
ajint which;
ajint weighted;
ajint t = 0;
ajint tc = 0;
ajint mode;
ajint min_seg;
const AjPStr seqdes;
float min_P;
struct hept_pref *h;
embInit("newcoils",argc,argv);
window = ajAcdGetInt("window");
weighted = ajAcdGetInt("weighted");
verb = ajAcdGetInt("verb");
mode = ajAcdGetInt("mode");
min_P = ajAcdGetFloat("minp");
min_seg = ajAcdGetInt("minseg");
outf = ajAcdGetOutfile("outfile");
datafile = ajAcdGetDatafile("datafile");
seqall = ajAcdGetSeqall("sequence");
ajseq = ajSeqNew();
h = newcoils_read_matrix(datafile);
if(verb)
{
for(i=0; i<strlen(NCAAs); ++i)
if(NCAAs[i] != '_')
{
pt = (int)(NCAAs[i]-'A');
ajFmtPrintF(outf,"AA %c %4.2f %4.2f %4.2f %4.2f %4.2f %4.2f "
"%4.2f\n",NCAAs[i],h->m[pt][0],h->m[pt][1],
h->m[pt][2],h->m[pt][3],h->m[pt][4],
h->m[pt][5],h->m[pt][6]);
}
for(i=0; i<(ajuint)h->n; ++i)
ajFmtPrintF(outf,"Window %4d %1d %f %f %f %f %f\n",h->f[i].win,
h->f[i].w,h->f[i].m_cc,h->f[i].sd_cc,h->f[i].m_g,
h->f[i].sd_g,h->f[i].sc);
}
/* See if there is a file for the chosen window length/weight scheme */
which = -1;
for(i=0; i<(ajuint)h->n; ++i)
{
if((h->f[i].win == window) && (h->f[i].w == weighted))
{ /* match */
if(verb)
ajFmtPrintF(outf,"Found fitting data for win %4d w %d\n",
window,weighted);
which = i;
}
}
while(ajSeqallNext(seqall, &ajseq))
{
seqdes = ajSeqGetDescS(ajseq);
newcoils_pred_coils(outf,ajSeqGetSeqC(ajseq),ajSeqGetNameC(ajseq),
seqdes,h,window,
which,weighted,mode,min_P,&t,&tc,min_seg);
}
if (outf)
ajFileClose(&outf);
ajSeqDel(&ajseq);
embExit();
return 0;
}
int main(int argc, char **argv)
{
AjPSeqall seqall;
AjPSeq a;
AjPStr substr;
AjPStr rname;
ajint be;
ajint en;
ajint len;
AjBool unfavoured;
AjBool overlap;
AjBool allpartials;
AjPStr menu;
AjPStr rag;
ajint n = 0;
ajint r = 0;
AjPFile outf = NULL;
AjPReport report = NULL;
AjPFeattable TabRpt = NULL;
AjPStr tmpStr = NULL;
AjPList l;
AjPList pa;
AjPFile mfptr = NULL;
AjBool nterm = ajFalse;
AjBool cterm = ajFalse;
AjBool dorag = ajFalse;
ajint ncomp;
ajint npart;
EmbPPropMolwt *mwdata = NULL;
AjBool mono;
embInit("digest", argc, argv);
seqall = ajAcdGetSeqall("seqall");
menu = ajAcdGetListSingle("menu");
dorag = ajAcdGetBoolean("ragging");
rag = ajAcdGetListSingle("termini");
unfavoured = ajAcdGetBoolean("unfavoured");
overlap = ajAcdGetBoolean("overlap");
allpartials = ajAcdGetBoolean("allpartials");
report = ajAcdGetReport("outfile");
mfptr = ajAcdGetDatafile("mwdata");
mono = ajAcdGetBoolean("mono");
/* obsolete. Can be uncommented in acd file and here to reuse */
/* outf = ajAcdGetOutfile("originalfile"); */
ajStrToInt(menu, &n);
--n;
ajStrToInt(rag, &r);
if(r==2 || r==4)
nterm = ajTrue;
if(r==3 || r==4)
cterm = ajTrue;
mwdata = embPropEmolwtRead(mfptr);
while(ajSeqallNext(seqall, &a))
{
substr = ajStrNew();
be = ajSeqGetBegin(a);
en = ajSeqGetEnd(a);
ajStrAssignSubC(&substr,ajSeqGetSeqC(a),be-1,en-1);
ajStrFmtUpper(&substr);
len = en-be+1;
l = ajListNew();
pa = ajListNew();
rname = ajStrNew();
TabRpt = ajFeattableNewSeq(a);
embPropCalcFragments(ajStrGetPtr(substr),n,&l,&pa,
unfavoured,overlap,
allpartials,&ncomp,&npart,&rname,
nterm, cterm, dorag, mwdata, mono);
if(outf)
ajFmtPrintF(outf,"DIGEST of %s from %d to %d Molwt=%10.3f\n\n",
ajSeqGetNameC(a),be,en,
embPropCalcMolwt(ajSeqGetSeqC(a),0,len-1,mwdata,mono));
if(!ncomp)
{
if(outf)
ajFmtPrintF(outf,
"Is not proteolytically digested using %s\n",
ajStrGetPtr(rname));
}
else
{
if(outf)
{
ajFmtPrintF(outf,"Complete digestion with %s "
"yields %d fragments:\n",
ajStrGetPtr(rname),ncomp);
digest_print_hits(l,outf,be,ajStrGetPtr(substr));
}
ajFmtPrintS(&tmpStr,
"Complete digestion with %S yields %d fragments",
rname,ncomp);
ajReportSetHeaderS(report, tmpStr);
digest_report_hits(TabRpt,l,be, ajStrGetPtr(substr));
ajReportWrite(report, TabRpt, a);
ajFeattableClear(TabRpt);
}
if(overlap && !allpartials && npart)
{
if(outf)
{
ajFmtPrintF(outf,
"\n\nPartial digest with %s yields %d extras.\n",
ajStrGetPtr(rname),npart);
ajFmtPrintF(outf,"Only overlapping partials shown:\n");
digest_print_hits(pa,outf,be,ajStrGetPtr(substr));
}
ajFmtPrintS(&tmpStr,
"\n\nPartial digest with %S yields %d extras.\n",
rname,npart);
ajFmtPrintAppS(&tmpStr,"Only overlapping partials shown:\n");
ajReportSetHeaderS(report, tmpStr);
digest_report_hits(TabRpt, pa,be,ajStrGetPtr(substr));
ajReportWrite(report, TabRpt, a);
ajFeattableClear(TabRpt);
}
if(allpartials && npart)
{
if(outf)
{
ajFmtPrintF(outf,
"\n\nPartial digest with %s yields %d extras.\n",
ajStrGetPtr(rname),npart);
ajFmtPrintF(outf,"All partials shown:\n");
digest_print_hits(pa,outf,be,ajStrGetPtr(substr));
}
ajFmtPrintS(&tmpStr,
"\n\nPartial digest with %S yields %d extras.\n",
rname,npart);
ajFmtPrintAppS(&tmpStr,"All partials shown:\n");
ajReportSetHeaderS(report, tmpStr);
digest_report_hits(TabRpt, pa,be, ajStrGetPtr(substr));
ajReportWrite(report, TabRpt, a);
ajFeattableClear(TabRpt);
}
}
embPropMolwtDel(&mwdata);
ajReportDel(&report);
ajFeattableDel(&TabRpt);
ajSeqDel(&a);
ajSeqallDel(&seqall);
ajStrDel(&rname);
ajStrDel(&substr);
ajListFree(&pa);
ajListFree(&l);
ajStrDel(&menu);
ajStrDel(&rag);
if(outf)
ajFileClose(&outf);
ajFileClose(&mfptr);
ajStrDel(&tmpStr);
embExit();
return 0;
}
