void webPrintDoubleCell(double val)
/* Print right-justified cell in our colors with two digits to right of decimal. */
{
webPrintLinkCellRightStart();
printf("%4.2f", val);
webPrintLinkCellEnd();
}
void webPrintIntCell(int val)
/* Print right-justified int cell in our colors. */
{
webPrintLinkCellRightStart();
printf("%d", val);
webPrintLinkCellEnd();
}
static void showTableDataRows(struct fieldedTable *table, int pageSize, int maxLenField,
struct hash *tagOutputWrappers, void *wrapperContext)
/* Render data rows into HTML */
{
int count = 0;
struct fieldedRow *row;
boolean isNum[table->fieldCount];
int i;
for (i=0; i<table->fieldCount; ++i)
isNum[i] = fieldedTableColumnIsNumeric(table, i);
for (row = table->rowList; row != NULL; row = row->next)
{
if (++count > pageSize)
break;
printf("<TR>\n");
int fieldIx = 0;
for (fieldIx=0; fieldIx<table->fieldCount; ++fieldIx)
{
char shortVal[maxLenField+1];
char *longVal = emptyForNull(row->row[fieldIx]);
char *val = longVal;
int valLen = strlen(val);
if (maxLenField > 0 && maxLenField < valLen)
{
if (valLen > maxLenField)
{
memcpy(shortVal, val, maxLenField-3);
shortVal[maxLenField-3] = 0;
strcat(shortVal, "...");
val = shortVal;
}
}
if (isNum[fieldIx])
webPrintLinkCellRightStart();
else
webPrintLinkCellStart();
boolean printed = FALSE;
if (tagOutputWrappers != NULL && !isEmpty(val))
{
char *field = table->fields[fieldIx];
webTableOutputWrapperType *printer = hashFindVal(tagOutputWrappers, field);
if (printer != NULL)
{
printer(table, row, field, longVal, val, wrapperContext);
printed = TRUE;
}
}
if (!printed)
printf("%s", val);
webPrintLinkCellEnd();
}
printf("</TR>\n");
}
}
static void prAlign(struct sqlConnection *conn, char *pslTbl, struct psl *psl)
/* print an alignment */
{
// genomic location
webPrintLinkCellStart();
printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">%s:%d-%d</A>",
hgTracksPathAndSettings(), database, psl->tName, psl->tStart+1, psl->tEnd,
psl->tName, psl->tStart+1, psl->tEnd);
webPrintLinkCellEnd();
// genomic span
webPrintLinkCellRightStart();
printf("%d", psl->tEnd-psl->tStart);
webPrintLinkCellEnd();
// strand
webPrintLinkCell(psl->strand);
// mRNA location, linked to aligment viewer
webPrintLinkCellStart();
char other[128];
safef(other, sizeof(other), "%d&aliTable=%s", psl->tStart, pslTbl);
hgcAnchorSomewhere("htcCdnaAli", psl->qName, other, psl->tName);
printf("%s:%d-%d</A>", psl->qName, psl->qStart+1, psl->qEnd);
webPrintLinkCellEnd();
// identity
webPrintLinkCellRightStart();
printf("%.2f%%", 100.0 * pslIdent(psl));
webPrintLinkCellEnd();
// fraction aligned
webPrintLinkCellRightStart();
int aligned = psl->match + psl->misMatch + psl->repMatch;
printf("%.2f%%", 100.0*aligned/((float)psl->qSize));
webPrintLinkCellEnd();
}
static void prRefSeqSim(struct cloneInfo *ci, struct geneSim *gs)
/* print similarity information for a given RefSeq */
{
webPrintLinkTableNewRow();
// RefSeq acc and link
webPrintLinkCellStart();
printf("<a href=\"");
printEntrezNucleotideUrl(stdout, gs->gene->name);
printf("\" TARGET=_blank>%s</a>", gs->gene->name);
webPrintLinkCellEnd();
// link to browser
webPrintLinkCellStart();
printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\" target=_blank>%s:%d-%d</A>",
hgTracksPathAndSettings(), database,
gs->gene->chrom, gs->gene->txStart+1, gs->gene->txEnd,
gs->gene->chrom, gs->gene->txStart+1, gs->gene->txEnd);
webPrintLinkCellEnd();
// similarity
webPrintLinkCellRightStart();
printf("%0.2f%%", 100.0*gs->sim);
webPrintLinkCellEnd();
}
void showCdsEvidence(char *geneName, struct trackDb *tdb, char *evTable)
/* Print out stuff from cdsEvidence table. */
{
struct sqlConnection *conn = hAllocConn(database);
double bestScore = 0;
if (sqlTableExists(conn, evTable))
{
webNewSection("CDS Prediction Information");
char query[512];
sqlSafef(query, sizeof(query),
"select count(*) from %s where name='%s'", evTable, geneName);
if (sqlQuickNum(conn, query) > 0)
{
sqlSafef(query, sizeof(query),
"select * from %s where name='%s' order by score desc", evTable, geneName);
struct sqlResult *sr = sqlGetResult(conn, query);
char **row;
webPrintLinkTableStart();
webPrintLabelCell("ORF<BR>size");
webPrintLabelCell("start in<BR>transcript");
webPrintLabelCell("end in<BR>transcript");
webPrintLabelCell("source");
webPrintLabelCell("accession");
webPrintLabelCell("ad-hoc<BR>score");
webPrintLabelCell("start<BR>codon");
webPrintLabelCell("end<BR>codon");
webPrintLabelCell("piece<BR>count");
webPrintLabelCell("piece list");
webPrintLabelCell("frame");
webPrintLinkTableNewRow();
while ((row = sqlNextRow(sr)) != NULL)
{
struct cdsEvidence *ev = cdsEvidenceLoad(row);
webPrintIntCell(ev->end - ev->start);
int i;
webPrintIntCell(ev->start+1);
webPrintIntCell(ev->end);
webPrintLinkCell(ev->source);
webPrintLinkCell(ev->accession);
webPrintLinkCellRightStart();
printf("%3.2f", ev->score);
bestScore = max(ev->score, bestScore);
webPrintLinkCellEnd();
webPrintLinkCell(ev->startComplete ? "yes" : "no");
webPrintLinkCell(ev->endComplete ? "yes" : "no");
webPrintIntCell(ev->cdsCount);
webPrintLinkCellRightStart();
for (i=0; i<ev->cdsCount; ++i)
{
int start = ev->cdsStarts[i];
int end = start + ev->cdsSizes[i];
printf("%d-%d ", start+1, end);
}
webPrintLinkCellEnd();
webPrintLinkCellRightStart();
for (i=0; i<ev->cdsCount; ++i)
{
if (i>0) printf(",");
printf("%d", ev->cdsStarts[i]%3 + 1);
}
webPrintLinkCellEnd();
webPrintLinkTableNewRow();
}
sqlFreeResult(&sr);
webPrintLinkTableEnd();
printf("This table shows CDS predictions for this transcript from a number of "
"sources including alignments against UniProtKB proteins, alignments against Genbank "
"mRNAs with CDS regions annotated by the sequence submitter, and "
"Victor Solovyev's bestorf program. Each prediction is assigned an ad-hoc score "
"score is based on several factors including the quality of "
"any associated alignments, the quality of the source, and the length of the "
"prediction. For RefSeq transcripts with annotated CDSs the ad-hoc score "
"is over a million unless there are severe problems mapping the mRNA to the "
"genome. In other cases the score generally ranges from 0 to 50,000. "
"The highest scoring prediction in this table is used to define the CDS "
"boundaries for this transcript.<P>If no score is 2000 or more, the transcript "
"is considered non-coding. In cases where the CDS is subject to "
"nonsense-mediated decay the CDS is removed. The CDS is also removed "
"from transcripts when evidence points to it being in an artifact of an "
"incompletely processed transcript. Specifically if the CDS is entirely "
"enclosed in the 3' UTR or an intron of a refSeq or other high quality "
"transcript, the CDS is removed.");
}
else
{
printf("no significant CDS prediction found, likely %s is noncoding",
geneName);
}
}
hFreeConn(&conn);
}
