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("</TR></TABLE>\n"); printf("<BR>\n"); slFreeList(&list); } /* Do modBase link. */ { printf("<B>ModBase Predicted Comparative 3D Structure on "); modBaseAnchor(spAcc); printf("%s", spAcc); printf("</A></B><BR>\n"); printf("<TABLE><TR>"); printf("<TD>"); modBaseAnchor(spAcc); - printf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s\"></A></TD>", spAcc); + printf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s\"></A></TD>", spAcc); printf("<TD>"); modBaseAnchor(spAcc); - printf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=x°ree=90\"></A></TD>", spAcc); + printf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s&axis=x°ree=90\"></A></TD>", spAcc); printf("<TD>"); modBaseAnchor(spAcc); - printf("\n<IMG SRC=\"https://modbase.compbio.ucsf.edu/modbase-cgi/image/modbase.jpg?database_id=%s&axis=y°ree=90\"></A></TD>", spAcc); + printf("\n<IMG SRC=\"http://salilab.org/modbaseimages/image/modbase.jpg?database_id=%s&axis=y°ree=90\"></A></TD>", spAcc); printf("</TR><TR>\n"); printf("<TD ALIGN=CENTER>Front</TD>"); printf("<TD ALIGN=CENTER>Top</TD>"); printf("<TD ALIGN=CENTER>Side</TD>"); printf("</TR></TABLE>\n"); printf("<I>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.</I><p>"); } printf("</td></tr></tbody></table><br>\n"); /* Gene Homology */ @@ -3237,43 +3237,43 @@ /* Close table */ printf("</tbody>\n"); printf("</table>\n"); printf("</td></tr></tbody>\n"); printf("</table>\n"); bedFree(&primer); hFreeConn(&conn); printTrackHtml(tdb); } void doWiki(char *track, struct trackDb *tdb, char *itemName) { - char strand[2]; + //char strand[2]; printf("<HEAD>%s", getCspMetaHeader()); if(startsWith("Make", itemName)) { - strand[0] = itemName[strlen(itemName)-1]; - strand[1] = 0; - printf("<META HTTP-EQUIV=\"REFRESH\" content=\"0; URL=http://lowelabwiki.soe.ucsc.edu/index.php/BED:%s:%s:%d-%d:%s\"</META>", database, seqName, winStart, winEnd, strand); + //strand[0] = itemName[strlen(itemName)-1]; + //strand[1] = 0; + /*printf("<META HTTP-EQUIV=\"REFRESH\" content=\"0; URL=http://lowelabwiki.soe.ucsc.edu/index.php/BED:%s:%s:%d-%d:%s\"</META>", database, seqName, winStart, winEnd, strand);*/ } else { - printf("<META HTTP-EQUIV=\"REFRESH\" content=\"0; URL=http://lowelabwiki.soe.ucsc.edu/index.php/BED:%s:%s:%s\"</META>", database, seqName, itemName); + /*printf("<META HTTP-EQUIV=\"REFRESH\" content=\"0; URL=http://lowelabwiki.soe.ucsc.edu/index.php/BED:%s:%s:%s\"</META>", database, seqName, itemName);*/ } printf("</HEAD>"); } 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("<B>Name:</B> %s\n", infoload->name); - // archdev-holmes no longer exists, but what should this be? - printf(" <A HREF=\"http://archdev-holmes.soe.ucsc.edu/cgi-bin/hgFrame?track=loweOrthologs&refseq=1&db=%s&name=%s\">List of Orthologs</A><BR>",database,infoload->name); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\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("<B>Name:</B> %s<BR>\n", infoload->name); printf("<B>Accession:</B> %s<A HREF=\"http://www.ncbi.nlm.nih.gov/nuccore/%s\" TARGET=_blank>", infoload->name, infoload->name); printf(" Link to NCBI Site</A> <BR>\n"); printf("<B>Description:</B> %s<BR>\n", infoload->fullname); printf("<B>E-value:</B> %0.0e", infoload->evalue); - #ifdef LISTUI - printf(" <A HREF=\"http://archdev-holmes.soe.ucsc.edu/cgi-bin/hgList?track=megablastInfo&order=evalue&db=%s\">Sort by E-value</A>",database); - #endif printf("<BR>\n"); printf("<B>Protein Identity:</B> %u%%\n", infoload->percentident); - #ifdef LISTUI - printf(" <A HREF=\"http://archdev-holmes.soe.ucsc.edu/cgi-bin/hgList?track=megablastInfo&order=percentident&db=%s\">Sort by Percent Identity</A>",database); - #endif printf("<BR>\n"); printf("<B>Position:</B> " "<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">", hgTracksPathAndSettings(), database, infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("%s:%d-%d</A><BR>\n", infoload->chrom, infoload->chromStart + 1, infoload->chromEnd); printf("<B>Strand:</B> %s<BR>\n", infoload->strand); printf("<B>Genomic size: </B> %d nt<BR>\n", (infoload->chromEnd - infoload->chromStart)); if (infoload->next != NULL) printf("<hr>\n"); } sqlFreeResult(&sr); hFreeConn(&conn); megablastInfoFree(&infoload); printTrackHtml(tdb); }