305cf5b58959929ced4acf3293ebd035bb35ff43 galt Mon Aug 20 14:08:40 2018 -0700 Cleanup requested by Lowe Lab. diff --git src/hg/hgc/lowelab.c src/hg/hgc/lowelab.c index 1707f4e..b503203 100644 --- src/hg/hgc/lowelab.c +++ src/hg/hgc/lowelab.c @@ -842,37 +842,37 @@ } printf("\n"); printf("
\n"); slFreeList(&list); } /* Do modBase link. */ { printf("ModBase Predicted Comparative 3D Structure on "); modBaseAnchor(spAcc); printf("%s", spAcc); printf("
\n"); printf(""); printf("", spAcc); + printf("\n", spAcc); printf("", spAcc); + printf("\n", spAcc); printf("", spAcc); + printf("\n", spAcc); printf("\n"); printf(""); printf(""); printf(""); printf("
"); modBaseAnchor(spAcc); - printf("\n"); modBaseAnchor(spAcc); - printf("\n"); modBaseAnchor(spAcc); - printf("\n
FrontTopSide
\n"); printf("The pictures above may be empty if there is no " "ModBase structure for the protein. The ModBase structure " "frequently covers just a fragment of the protein. You may " "be asked to log onto ModBase the first time you click on the " "pictures. It is simplest after logging in to just click on " "the picture again to get to the specific info on that model.

"); } printf("
\n"); /* Gene Homology */ @@ -3237,43 +3237,43 @@ /* Close table */ printf("\n"); printf("\n"); printf("\n"); printf("\n"); bedFree(&primer); hFreeConn(&conn); printTrackHtml(tdb); } void doWiki(char *track, struct trackDb *tdb, char *itemName) { - char strand[2]; + //char strand[2]; printf("%s", getCspMetaHeader()); if(startsWith("Make", itemName)) { - strand[0] = itemName[strlen(itemName)-1]; - strand[1] = 0; - printf("", database, seqName, winStart, winEnd, strand); + //strand[0] = itemName[strlen(itemName)-1]; + //strand[1] = 0; + /*printf("", database, seqName, winStart, winEnd, strand);*/ } else { - printf("", database, seqName, itemName); + /*printf("", database, seqName, itemName);*/ } printf(""); } void doRNAHybridization(struct trackDb *tdb, char *itemName) { struct sqlConnection *conn = hAllocConn(database); char query[512]; struct sqlResult *sr; char **row; struct rnaHybridization *rnaHyb; char rnaHybridizationTable[] = "rnaHybridization"; char tRNATable[] = "tRNAs"; char jgiTable[] = "jgiGene"; @@ -3439,32 +3439,30 @@ bedSize = atoi(words[1]); if (bedSize < 3) bedSize = 3; genericHeader(tdb,itemName); dupe = cloneString(tdb->type); wordCount = chopLine(dupe, words); rowOffset = hOffsetPastBin(database,seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = bedLoadN(row+rowOffset, bedSize); printf("Name: %s\n", infoload->name); - // archdev-holmes no longer exists, but what should this be? - printf(" List of Orthologs
",database,infoload->name); printf("Position: " "", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d
\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("Strand: %s
\n", infoload->strand); printf("Genomic size: %d nt
\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("

\n"); } sqlFreeResult(&sr); hFreeConn(&conn); printTrackHtml(tdb); } @@ -3551,38 +3549,32 @@ genericHeader(tdb,itemName); rowOffset = hOffsetPastBin(database,seqName, tdb->table); sqlSafef(query, sizeof query, "select * from %s where name = '%s' and chrom = '%s' and chromStart = %d and chromEnd = '%d';", tdb->table, itemName,seqName,start, end); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { infoload = megablastInfoLoad(row+rowOffset); printf("Name: %s
\n", infoload->name); printf("Accession: %s", infoload->name, infoload->name); printf(" Link to NCBI Site
\n"); printf("Description: %s
\n", infoload->fullname); printf("E-value: %0.0e", infoload->evalue); - #ifdef LISTUI - printf(" Sort by E-value",database); - #endif printf("
\n"); printf("Protein Identity: %u%%\n", infoload->percentident); - #ifdef LISTUI - printf(" Sort by Percent Identity",database); - #endif printf("
\n"); printf("Position: " "", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d
\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("Strand: %s
\n", infoload->strand); printf("Genomic size: %d nt
\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("
\n"); } sqlFreeResult(&sr); hFreeConn(&conn); megablastInfoFree(&infoload); printTrackHtml(tdb); }