static void blastiodAxtOutput(FILE *f, struct axt *axt, int tSize, int qSize,
int lineSize, boolean isProt, boolean isTranslated)
/* Output base-by-base part of alignment in blast-like fashion. */
{
int tOff = axt->tStart;
int dt = (isTranslated ? 3 : 1);
int qOff = axt->qStart;
int lineStart, lineEnd, i;
int digits = calcDigitCount(axt, tSize, qSize);
struct axtScoreScheme *ss = NULL;
if (isProt)
ss = axtScoreSchemeProteinDefault();
for (lineStart = 0; lineStart < axt->symCount; lineStart = lineEnd)
{
lineEnd = lineStart + lineSize;
if (lineEnd > axt->symCount) lineEnd = axt->symCount;
fprintf(f, "Query: %-*d ", digits, plusStrandPos(qOff, qSize, axt->qStrand, FALSE));
for (i=lineStart; i<lineEnd; ++i)
{
char c = axt->qSym[i];
fputc(c, f);
if (c != '-')
++qOff;
}
fprintf(f, " %-d\n", plusStrandPos(qOff, qSize, axt->qStrand, TRUE));
fprintf(f, " %*s ", digits, " ");
for (i=lineStart; i<lineEnd; ++i)
{
char q, t, c;
q = axt->qSym[i];
t = axt->tSym[i];
if (isProt)
{
if (q == t)
c = q;
else if (ss->matrix[(int)q][(int)t] > 0)
c = '+';
else
c = ' ';
}
else
c = ((toupper(q) == toupper(t)) ? '|' : ' ');
fputc(c, f);
}
fprintf(f, "\n");
fprintf(f, "Sbjct: %-*d ", digits, plusStrandPos(tOff, tSize, axt->tStrand, FALSE));
for (i=lineStart; i<lineEnd; ++i)
{
char c = axt->tSym[i];
fputc(c, f);
if (c != '-')
tOff += dt;
}
fprintf(f, " %-d\n", plusStrandPos(tOff, tSize, axt->tStrand, TRUE));
fprintf(f, "\n");
}
}
static int countPositives(char *a, char *b, int size)
/* Count positive (not necessarily identical) protein matches. */
{
int count = 0;
int i;
struct axtScoreScheme *ss = axtScoreSchemeProteinDefault();
for (i=0; i<size; ++i)
{
if (ss->matrix[(int)a[i]][(int)b[i]] > 0)
++count;
}
return count;
}
void doOtherProteinAli(struct sqlConnection *conn,
char *localId, char *localName)
/* Put up page that shows alignment between this protein sequence
* and other species. */
{
char *otherTable = cartString(cart, hggOtherPepTable);
char *otherId = cartString(cart, hggOtherId);
char *localTable = genomeSetting("knownGenePep");
bioSeq *localSeq = getSeq(conn, localTable, localId);
bioSeq *otherSeq = getSeq(conn, otherTable, otherId);
if (localSeq != NULL && otherSeq != NULL)
{
struct axtScoreScheme *ss = axtScoreSchemeProteinDefault();
if (axtAffineSmallEnough(localSeq->size, otherSeq->size))
{
struct axt *axt = axtAffine(localSeq, otherSeq, ss);
hPrintf("<TT><PRE>");
if (axt != NULL)
{
printf("ID (including gaps) %3.1f%%, coverage (of both) %3.1f%%, score %d\n",
axtIdWithGaps(axt)*100,
axtCoverage(axt, localSeq->size, otherSeq->size)*100,
axt->score);
printf("Alignment between %s (top %s %daa) and\n",
localName, localSeq->name, localSeq->size);
printf("%s homolog (bottom %s %daa)\n",
otherTable, otherSeq->name, otherSeq->size);
printf("\n");
axtPrintTraditional(axt, 60, ss, stdout);
axtFree(&axt);
}
else
{
printf("%s and %s don't align\n", localSeq->name, otherSeq->name);
}
hPrintf("</PRE></TT>");
}
else
{
printf("Sorry, %s (%d amino acids) and %s (%d amino acids) are too big to align",
localSeq->name, localSeq->size, otherSeq->name, otherSeq->size);
}
}
else
{
warn("Couldn't get sequences, database out of sync?");
}
}
void freen(char *out)
/* Test some hair-brained thing. */
{
char *a = "CVMVFTVSCSKMSSIVDRDDSSIFDGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELG"
"SMLPGNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPTFLSNEEFTQLMLEAL"
"DGFFLAIMTDGSIIYVSESVTSLLEHLPSDLVDQSIFNFIPEGEHSEVYKILSTHLLESD"
"SLTPEYLKSKNQLEFCCHMLRGTIDPKEPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQ"
"RTHRPSYEDRVCFVATVRLATPQFIKEMCTVEEPNEEFTSRHSLEWKFLFLDHRAPPIIG"
"YLPFEVLGTSGYDYYHVDDLENLAKCHEHLMQYGKGKSCYYRFLTKGQQWIWLQTHYYIT"
"YHQWNSRPEFIVCTHTVVSYAEVRAERRRELGIEESLPETAADKSQDSGSDNRINTVSLK"
"EALERFDHSPTPSASSRSSRKSSHTAVSDPSSTPTKIPTDTSTPPRQHLPAHEKMTQRRS"
"SFSSQSINSQSVGPSLTQPAMSQAANLPIPQGMSQFQFSAQLGAMQHLKDQLEQRTRMIE"
"ANIHRQQEELRKIQEQLQMVHGQGLQMFLQQSNPGLNFGSVQLSSGNSNIQQLTPVNMQG"
"QVVPANQVQSGHISTGQHMIQQQTLQSTSTQQSQQSVMSGHSQQTSLPSQTPSTLTAPLY"
"NTMVISQPAAGSMVQIPSSMPQNSTQSATVTTFTQDRQIRFSQGQQLVTKLVTAPVACGA"
"VMVPSTMLMGQVVTAYPTFATQQQQAQTLSVTQQQQQQQQQPPQQQQQQQQSSQEQQLPS"
"VQQPAQAQLGQPPQQFLQTSRLLHGNPSTQLILSAAFPLQQSTFPPSHHQQHQPQQQQQL"
"PRHRTDSLTDPSKVQPQ";
char *b = "CVMVFTVSCSKMSSIVDRDDSSIFDGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELG"
"SMLPGNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPTFLSNEEFTQLMLEAL"
"DGFFLAIMTDGSIIYVSESVTSLLEHLPSDLVDQSIFNFIPEGEHSEVYKILSTHLLESD"
"SLTPEYLKSKNQLEFCCHMLRGTIDPKEPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQ"
"RTHRPSYEDRVCFVATVRLATPQFIKEMCTVEEPNEEFTSRHSLEWKFLFLDHRAPPIIG"
"xQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ"
"YHQWNSRPEFIVCTHTVVSYAEVRAERRRELGIEESLPETAADKSQDSGSDNRINTVSLK"
"EALERFDHSPTPSASSRSSRKSSHTAVSDPSSTPTKIPTDTSTPPRQHLPAHEKMTQRRS"
"SFSSQSINSQSVGPSLTQPAMSQAANLPIPQGMSQFQFSAQLGAMQHLKDQLEQRTRMIE"
"ANIHRQQEELRKIQEQLQMVHGQGLQMFLQQSNPGLNFGSVQLSSGNSNIQQLTPVNMQG"
"QVVPANQVQSGHISTGQHMIQQQTLQSTSTQQSQQSVMSGHSQQTSLPSQTPSTLTAPLY"
"NTMVISQPAAGSMVQIPSSMPQNSTQSATVTTFTQDRQIRFSQGQQLVTKLVTAPVACGA"
"VMVPSTMLMGQVVTAYPTFATQQQQAQTLSVTQQQQQQQQQPPQQQQQQQQSSQEQQLPS"
"VQQPAQAQLGQPPQQFLQTSRLLHGNPSTQLILSAAFPLQQSTFPPSHHQQHQPQQQQQL"
"PRHRTDSLTDPSKVQPQ";
char *c = "CVMVFTVSCSKMSSIVDRDDSSIFDGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELG"
"xMLPGNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPTFLSNEEFTQLMLEAL"
"xxFFLAIMTDGSIIYVSESVTSLLEHLPSDLVDQSIFNFIPEGEHSEVYKILSTHLLESD"
"xxxPEYLKSKNQLEFCCHMLRGTIDPKEPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQ"
"xxxxPSYEDRVCFVATVRLATPQFIKEMCTVEEPNEEFTSRHSLEWKFLFLDHRAPPIIG"
"xxxxxVLGTSGYDYYHVDDLENLAKCHEHLMQYGKGKSCYYRFLTKGQQWIWLQTHYYIT"
"xxxxxxRPEFIVCTHTVVSYAEVRAERRRELGIEESLPETAADKSQDSGSDNRINTVSLK"
"xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
"xxxxxxxxSQSVGPSLTQPAMSQAANLPIPQGMSQFQFSAQLGAMQHLKDQLEQRTRMIE"
"xxxxxxxxxLRKIQEQLQMVHGQGLQMFLQQSNPGLNFGSVQLSSGNSNIQQLTPVNMQG"
"xxxxxxxxxxGHISTGQHMIQQQTLQSTSTQQSQQSVMSGHSQQTSLPSQTPSTLTAPLY"
"xxxxxxxxxxxSMVQIPSSMPQNSTQSATVTTFTQDRQIRFSQGQQLVTKLVTAPVACGA"
"xxxxxxxxxxxxVTAYPTFATQQQQAQTLSVTQQQQQQQQQPPQQQQQQQQSSQEQQLPS"
"xxxxxxxxxxxxxQQFLQTSRLLHGNPSTQLILSAAFPLQQSTFPPSHHQQHQPQQQQQL"
"PRHRTDSLTDPSKVQPQ";
char *d = "CVMVFTVSCSKMSSIVDRDDSSIFDGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELG"
"SMLPGNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPTFLSNEEFTQLMLEAL"
"DGFFLAIMTDGSIIYVSESVTSLLEHLPSDLVDQSIFNFIPEGEHSEVYKILSTHLLESD"
"SLTPEYLKSKNQLEFCCHMLRGTIDPKEPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQ"
"RTHRPSYEDRVCFVATVRLATPQFIKEMCTVEEPNEEFTSRHSLEWKFLFLDHRAPPIIG"
"XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX"
"YHQWNSRPEFIVCTHTVVSYAEVRAERRRELGIEESLPETAADKSQDSGSDNRINTVSLK"
"EALERFDHSPTPSASSRSSRKSSHTAVSDPSSTPTKIPTDTSTPPRQHLPAHEKMTQRRS"
"SFSSQSINSQSVGPSLTQPAMSQAANLPIPQGMSQFQFSAQLGAMQHLKDQLEQRTRMIE"
"ANIHRQQEELRKIQEQLQMVHGQGLQMFLQQSNPGLNFGSVQLSSGNSNIQQLTPVNMQG"
"QVVPANQVQSGHISTGQHMIQQQTLQSTSTQQSQQSVMSGHSQQTSLPSQTPSTLTAPLY"
"NTMVISQPAAGSMVQIPSSMPQNSTQSATVTTFTQDRQIRFSQGQQLVTKLVTAPVACGA"
"VMVPSTMLMGQVVTAYPTFATQQQQAQTLSVTQQQQQQQQQPPQQQQQQQQSSQEQQLPS"
"VQQPAQAQLGQPPQQFLQTSRLLHGNPSTQLILSAAFPLQQSTFPPSHHQQHQPQQQQQL"
"PRHRTDSLTDPSKVQPQ";
char *e = "CVMVFTVSCSKMSSIVDRDDSSIFDGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELG"
"XXXXXXXXXXXXXXXXXXXXXXXXXHKETTAQSDASEIRQDWKPTFLSNEEFTQLMLEAL"
"XXXXXXXXXXXXXXXXXXXXXXXXEHLPSDLVDQSIFNFIPEGEHSEVYKILSTHLLESD"
"XXXXXXXXXXXXXXXXXXXXXXXIDPKEPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQ"
"XXXXXXXXXXXXXXXXXXXXXXQFIKEMCTVEEPNEEFTSRHSLEWKFLFLDHRAPPIIG"
"XXXXXVXXXXXXXXXXXXXXXNLAKCHEHLMQYGKGKSCYYRFLTKGQQWIWLQTHYYIT"
"XXXXXXXXXXXXXXXXXXXXAEVRAERRRELGIEESLPETAADKSQDSGSDNRINTVSLK"
"XXXXXXXXXXXXXXXXXXXRKSSHTAVSDPSSTPTKIPTDTSTPPRQHLPAHEKMTQRRS"
"XXXXXXXXXXXXXXXXXXPAMSQAANLPIPQGMSQFQFSAQLGAMQHLKDQLEQRTRMIE"
"XXXXXXXXXXXXXXXXXQMVHGQGLQMFLQQSNPGLNFGSVQLSSGNSNIQQLTPVNMQG"
"XXXXXXXXXXXXXXXXQHMIQQQTLQSTSTQQSQQSVMSGHSQQTSLPSQTPSTLTAPLY"
"XXXXXXXXXXXXXXXIPSSMPQNSTQSATVTTFTQDRQIRFSQGQQLVTKLVTAPVACGA"
"XXXXXXXXXXXXXXAYPTFATQQQQAQTLSVTQQQQQQQQQPPQQQQQQQQSSQEQQLPS"
"XXXXXXXXXXXXXQQFLQTSRLLHGNPSTQLILSAAFPLQQSTFPPSHHQQHQPQQQQQL"
"PRHRTDSLTDPSKVQPQ";
a = cloneString(a);
// tolowers(a);
b = cloneString(b);
// tolowers(b);
xenAlignAffine(a, strlen(a), b, strlen(b), axtScoreSchemeProteinDefault(), stdout, FALSE);
}
