4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/visiGene/hgVisiGene/printCaption.c src/hg/visiGene/hgVisiGene/printCaption.c index 0d7f8ea..3f9d678 100644 --- src/hg/visiGene/hgVisiGene/printCaption.c +++ src/hg/visiGene/hgVisiGene/printCaption.c @@ -1,954 +1,954 @@ /* printCaption - query database for info and print it out * in a caption. */ /* Copyright (C) 2013 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hash.h" #include "dystring.h" #include "jksql.h" #include "cart.h" #include "htmshell.h" #include "hdb.h" #include "visiGene.h" #include "hgVisiGene.h" #include "captionElement.h" #include "printCaption.h" struct probeAndColor /* Just a little structure to store probe and probeColor. */ { struct probeAndColor *next; int probe; /* Probe id. */ int probeColor; /* ProbeColor id. */ }; char *getKnownGeneUrl(struct sqlConnection *conn, int geneId) /* Given gene ID, try and find known gene on browser in same * species. */ { char query[256]; char tableName[256]; int taxon; char *url = NULL; char *genomeDb = NULL; /* Figure out taxon. */ sqlSafef(query, sizeof(query), "select taxon from gene where id = %d", geneId); taxon = sqlQuickNum(conn, query); genomeDb = hDbForTaxon(taxon); if (genomeDb != NULL) { /* Make sure known genes track exists - we may need * to tweak this at some point for model organisms. */ safef(tableName, sizeof(tableName), "%s.knownToVisiGene", genomeDb); if (!sqlTableExists(conn, tableName)) genomeDb = NULL; } /* If no db for that organism revert to human. */ if (genomeDb == NULL) genomeDb = hDefaultDb(); safef(tableName, sizeof(tableName), "%s.knownToVisiGene", genomeDb); if (sqlTableExists(conn, tableName)) { struct dyString *dy = dyStringNew(0); char *knownGene = NULL; if (sqlCountColumnsInTable(conn, tableName) == 3) { sqlDyStringPrintf(dy, "select name from %s.knownToVisiGene where geneId = %d", genomeDb, geneId); } else { struct slName *imageList, *image; sqlSafef(query, sizeof(query), "select imageProbe.image from probe,imageProbe " "where probe.gene=%d and imageProbe.probe=probe.id", geneId); imageList = sqlQuickList(conn, query); if (imageList != NULL) { sqlDyStringPrintf(dy, "select name from %s.knownToVisiGene ", genomeDb); dyStringAppend(dy, "where value in("); for (image = imageList; image != NULL; image = image->next) { sqlDyStringPrintf(dy, "'%s'", image->name); if (image->next != NULL) dyStringAppendC(dy, ','); } dyStringAppend(dy, ")"); slFreeList(&imageList); } } if (dy->stringSize > 0) { knownGene = sqlQuickString(conn, dy->string); if (knownGene != NULL) { char temp[1024]; safef(temp, sizeof temp, "../cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=none", genomeDb, knownGene); url = cloneString(temp); } } dyStringFree(&dy); } freez(&genomeDb); return url; } static struct slName *geneProbeList(struct sqlConnection *conn, int id) /* Get list of gene names with hyperlinks to probe info page. */ { struct slName *returnList = NULL; char query[256], **row; struct sqlResult *sr; struct dyString *dy = dyStringNew(0); struct probeAndColor *pcList = NULL, *pc; int probeCount = 0; /* Make up a list of all probes in this image. */ sqlSafef(query, sizeof(query), "select probe,probeColor from imageProbe where image=%d", id); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { AllocVar(pc); pc->probe = sqlUnsigned(row[0]); pc->probeColor = sqlUnsigned(row[1]); slAddHead(&pcList, pc); ++probeCount; } slReverse(&pcList); for (pc = pcList; pc != NULL; pc = pc->next) { int geneId; char *geneName; int probe = pc->probe; char *geneUrl = NULL; /* Get gene ID and name. */ sqlSafef(query, sizeof(query), "select gene from probe where id = %d", probe); geneId = sqlQuickNum(conn, query); geneName = vgGeneNameFromId(conn, geneId); /* Get url for known genes page if any. */ geneUrl = getKnownGeneUrl(conn, geneId); /* Print gene name, surrounded by hyperlink to known genes * page if possible. */ dyStringClear(dy); if (geneUrl != NULL) dyStringPrintf(dy, "<A HREF=\"%s\" target=_parent>", geneUrl); dyStringPrintf(dy, "%s", geneName); if (geneUrl != NULL) dyStringAppend(dy, "</A>"); freez(&geneName); /* Add color if there's more than one probe for this image. */ if (probeCount > 1) { char *color; sqlSafef(query, sizeof(query), "select probeColor.name from probeColor " "where probeColor.id = %d" , pc->probeColor); color = sqlQuickString(conn, query); if (color != NULL) dyStringPrintf(dy, " (%s)", color); freez(&color); } /* Add to return list. */ slNameAddTail(&returnList, dy->string); } slFreeList(&pcList); slReverse(&returnList); return returnList; } static struct slName *getProbeList(struct sqlConnection *conn, int id) /* Get list of probes with hyperlinks to probe info page. */ { struct slName *returnList = NULL; char query[256]; char *sidUrl = cartSidUrlString(cart); struct dyString *dy = dyStringNew(0); struct slInt *probeList = NULL, *probe; int submissionSource = 0; /* Make up a list of all probes in this image. */ sqlSafef(query, sizeof(query), "select probe from imageProbe where image=%d", id); probeList = sqlQuickNumList(conn, query); sqlSafef(query, sizeof(query), "select submissionSet.submissionSource from image, submissionSet" " where image.submissionSet = submissionSet.id and image.id=%d", id); submissionSource = sqlQuickNum(conn, query); for (probe = probeList; probe != NULL; probe = probe->next) { char *type; /* Create hyperlink to probe page around gene name. */ dyStringClear(dy); dyStringPrintf(dy, "<A HREF=\"%s?%s&%s=%d&%s=%d\" target=_parent>", hgVisiGeneCgiName(), sidUrl, hgpDoProbe, probe->val, hgpSs, submissionSource); sqlSafef(query, sizeof(query), "select probeType.name from probeType,probe where probe.id = %d " "and probe.probeType = probeType.id", probe->val); type = sqlQuickString(conn, query); dyStringPrintf(dy, "%s", naForEmpty(type)); if (sameWord(type, "antibody")) { char *abName; sqlSafef(query, sizeof(query), "select antibody.name from probe,antibody " "where probe.id = %d and probe.antibody = antibody.id" , probe->val); abName = sqlQuickString(conn, query); if (abName != NULL) { dyStringPrintf(dy, " %s", abName); freeMem(abName); } } else if (sameWord(type, "RNA")) { sqlSafef(query, sizeof(query), "select length(seq) from probe where id=%d", probe->val); if (sqlQuickNum(conn, query) > 0) dyStringPrintf(dy, " sequenced"); else { sqlSafef(query, sizeof(query), "select length(fPrimer) from probe where id=%d", probe->val); if (sqlQuickNum(conn, query) > 0) dyStringPrintf(dy, " from primers"); } } else if (sameWord(type, "BAC")) { char *name; sqlSafef(query, sizeof(query), "select bac.name from probe,bac " "where probe.id = %d and probe.bac = bac.id" , probe->val); name = sqlQuickString(conn, query); if (name != NULL) { dyStringPrintf(dy, " %s", name); freeMem(name); } } dyStringPrintf(dy, "</A>"); freez(&type); /* Add to return list. */ slNameAddTail(&returnList, dy->string); } slFreeList(&probeList); slReverse(&returnList); return returnList; } #ifdef UNUSED static char *genomeDbForImage(struct sqlConnection *conn, int imageId) /* Return the genome database to associate with image or NULL if none. */ { char *db; char *scientificName = visiGeneOrganism(conn, imageId); struct sqlConnection *cConn = hConnectCentral(); char query[256]; sqlSafef(query, sizeof(query), "select defaultDb.name from defaultDb,dbDb where " "defaultDb.genome = dbDb.organism and " "dbDb.active = 1 and " "dbDb.scientificName = '%s'" , scientificName); db = sqlQuickString(cConn, query); hDisconnectCentral(&cConn); return db; } #endif /* UNUSED */ struct slName *vgImageFileGenes(struct sqlConnection *conn, int imageFile) /* Return alphabetical list of all genes associated with image file. */ { struct hash *uniqHash = hashNew(0); struct slInt *imageList, *image; struct slName *geneList = NULL, *gene; imageList = visiGeneImagesForFile(conn, imageFile); for (image = imageList; image != NULL; image = image->next) { struct slName *oneList, *next; oneList = visiGeneGeneName(conn, image->val); for (gene = oneList; gene != NULL; gene = next) { next = gene->next; if (hashLookup(uniqHash, gene->name)) freeMem(gene); else { hashAdd(uniqHash, gene->name, NULL); slAddHead(&geneList, gene); } } } slFreeList(&imageList); hashFree(&uniqHash); slSort(&geneList, slNameCmp); return geneList; } struct slName *vgImageFileGenotypes(struct sqlConnection *conn, int imageFile) /* Return unique alphabetical list of all genotypes associated with image file. */ { struct hash *uniqHash = hashNew(0); struct slInt *imageList, *image; struct slName *genoList=NULL,*genotype=NULL; imageList = visiGeneImagesForFile(conn, imageFile); for (image = imageList; image != NULL; image = image->next) { struct slName *oneList, *next; oneList = visiGeneGenotypes(conn, image->val); for (genotype = oneList; genotype != NULL; genotype = next) { next = genotype->next; if (hashLookup(uniqHash, genotype->name)) freeMem(genotype); else { hashAdd(uniqHash, genotype->name, NULL); slAddHead(&genoList, genotype); } } } slFreeList(&imageList); hashFree(&uniqHash); slSort(&genoList, slNameCmp); return genoList; } struct slName *vgImageFileOrganisms(struct sqlConnection *conn, int imageFile) /* Return unique alphabetical list of all organisms associated with image file. */ { struct hash *uniqHash = hashNew(0); struct slInt *imageList, *image; struct slName *orgList=NULL; imageList = visiGeneImagesForFile(conn, imageFile); for (image = imageList; image != NULL; image = image->next) { char *organism = visiGeneOrganism(conn, image->val); char *org = cloneString(shortOrgName(organism)); freeMem(organism); if (hashLookup(uniqHash, org)) freeMem(org); else { hashAdd(uniqHash, org, NULL); slNameAddHead(&orgList, org); } } slFreeList(&imageList); hashFree(&uniqHash); slSort(&orgList, slNameCmp); return orgList; } void smallCaption(struct sqlConnection *conn, int imageId) /* Write out small format caption. */ { struct slName *geneList, *gene; struct slName *genotypeList, *genotype; struct slName *orgList, *org; int imageFile = visiGeneImageFile(conn, imageId); boolean mutant = FALSE; char *sep = ""; genotypeList = vgImageFileGenotypes(conn, imageFile); for (genotype = genotypeList; genotype != NULL; genotype = genotype->next) { if (!sameString(genotype->name,"wild type")) mutant = TRUE; } slFreeList(&genotypeList); if (mutant) printf("Mutant "); orgList = vgImageFileOrganisms(conn, imageFile); for (org = orgList; org != NULL; org = org->next) { printf("%s%s", sep, org->name); sep = " "; } slFreeList(&orgList); geneList = vgImageFileGenes(conn, imageFile); for (gene = geneList; gene != NULL; gene = gene->next) { printf(" %s", gene->name); } slFreeList(&geneList); } static struct slName *expTissuesForProbeInImage(struct sqlConnection *conn, int imageId, int probeId) /* Get list of tissue where we have expression info in gene. * Put + or - depending on expression level. */ { struct dyString *dy = dyStringNew(0); struct slName *tissueList = NULL, *tissue; char query[512], **row; struct sqlResult *sr; sqlSafef(query, sizeof(query), "select bodyPart.name,expressionLevel.level,expressionPattern.description " "from expressionLevel join bodyPart join imageProbe " "left join expressionPattern on expressionLevel.expressionPattern = expressionPattern.id " "where imageProbe.image = %d " "and imageProbe.probe = %d " "and imageProbe.id = expressionLevel.imageProbe " "and expressionLevel.bodyPart = bodyPart.id " "order by bodyPart.name" , imageId, probeId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { double level = atof(row[1]); char *pattern = row[2]; if (pattern) tolowers(pattern); dyStringClear(dy); dyStringAppend(dy, row[0]); if (level == 1.0) dyStringAppend(dy, "(+)"); else if (level == 0.0) dyStringAppend(dy, "(-)"); else dyStringPrintf(dy, "(%.2f)",level); if (pattern && !sameWord(pattern,"Not Applicable") && !sameWord(pattern,"Not Specified")) dyStringPrintf(dy, " %s",pattern); tissue = slNameNew(dy->string); slAddHead(&tissueList, tissue); } sqlFreeResult(&sr); slReverse(&tissueList); dyStringFree(&dy); return tissueList; } struct expInfo /* Info on expression in various tissues for a particular gene. */ { struct expInfo *next; /* Next in list. */ int probeId; /* Id in probe table. */ int geneId; /* Id in gene table. */ char *geneName; /* Name of gene. */ struct slName *tissueList; /* List of tissues where gene expressed */ }; #ifdef UNUSED static void expInfoFree(struct expInfo **pExp) /* Free up memory associated with expInfo. */ { struct expInfo *exp = *pExp; if (exp != NULL) { freeMem(exp->geneName); slFreeList(&exp->tissueList); freez(pExp); } } static void expInfoFreeList(struct expInfo **pList) /* Free a list of dynamically allocated expInfo's */ { struct expInfo *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; expInfoFree(&el); } *pList = NULL; } #endif /* UNUSED */ static struct expInfo *expInfoForImage(struct sqlConnection *conn, int imageId) /* Return list of expression info for a given pane. */ { struct expInfo *expList = NULL, *exp; char query[512], **row; struct sqlResult *sr; /* Get list of probes associated with image, and start building * expList around it. */ sqlSafef(query, sizeof(query), "select imageProbe.probe,probe.gene from imageProbe,probe " "where imageProbe.image = %d " "and imageProbe.probe = probe.id", imageId); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { AllocVar(exp); exp->probeId = sqlUnsigned(row[0]); exp->geneId = sqlUnsigned(row[1]); slAddHead(&expList, exp); } sqlFreeResult(&sr); slReverse(&expList); /* Finish filling in expInfo and return. */ for (exp = expList; exp != NULL; exp = exp->next) { exp->geneName = vgGeneNameFromId(conn, exp->geneId); exp->tissueList = expTissuesForProbeInImage(conn, imageId, exp->probeId); } return expList; } static void addExpressionInfo(struct sqlConnection *conn, int imageId, struct captionElement **pCeList) /* Add information about expression to caption element list. * Since the pane can contain multiple genes each with * separate caption information this is more complex than * the other caption elements. We'll make one captionElement * for each gene that we have expression info on. */ { int geneWithDataCount = 0, expCount = 0; struct expInfo *exp, *expList = expInfoForImage(conn, imageId); struct captionElement *ce; /* Figure out how much data we really have. */ for (exp = expList; exp != NULL; exp = exp->next) { if (exp->tissueList != NULL) ++geneWithDataCount; ++expCount; } /* If no data just add n/a */ if (geneWithDataCount == 0) { ce = captionElementNew(imageId, "Expression", cloneString("n/a")); slAddHead(pCeList, ce); } else { for (exp = expList; exp != NULL; exp = exp->next) { if (exp->tissueList != NULL) { char label[256]; if (expCount == 1) safef(label, sizeof(label), "Expression"); else safef(label, sizeof(label), "Expression of %s", exp->geneName); ce = captionElementNew(imageId, label, makeCommaSpacedList(exp->tissueList)); slAddHead(pCeList, ce); } } } } static struct slName *wrapUrlList(struct slName *labelList, struct slName *idList, char *url) /* Return list that substitutes id into url and wraps * url as a hyperlink around label. */ { struct slName *list = NULL, *label, *id; struct dyString *dy = dyStringNew(0); for (id = idList, label = labelList; id != NULL && label != NULL; id = id->next, label = label->next) { dyStringClear(dy); dyStringAppend(dy, "<A HREF=\""); dyStringPrintf(dy, url, id->name); dyStringAppend(dy, "\" target=_blank>"); dyStringAppend(dy, label->name); dyStringAppend(dy, "</A>"); slNameAddHead(&list, dy->string); } slReverse(&list); return list; } static char *getSimplifiedAllele(char *geneName, char *allele) /* If allele is of form geneName<varient> then return just * varient. Else return allele. Do a freeMem on result when * done. */ { int len = strlen(geneName); if (startsWith(geneName, allele) && allele[len] == '<') { char *s = allele + len + 1; char *e = strrchr(s, '>'); if (e == NULL) e = s + strlen(s); return cloneStringZ(s, e - s); } else return cloneString(allele); } char *visiGeneHypertextGenotype(struct sqlConnection *conn, int id) /* Return genotype of organism if any in nifty hypertext format. */ { int genotypeId; struct slName *geneIdList, *geneId; char query[256]; struct dyString *html; /* Look up genotype ID. */ sqlSafef(query, sizeof(query), "select specimen.genotype from image,specimen " "where image.id=%d and image.specimen = specimen.id", id); genotypeId = sqlQuickNum(conn, query); if (genotypeId == 0) return NULL; /* Get list of genes involved. */ sqlSafef(query, sizeof(query), "select distinct allele.gene from genotypeAllele,allele " "where genotypeAllele.genotype=%d " "and genotypeAllele.allele = allele.id" , genotypeId); geneIdList = sqlQuickList(conn, query); if (geneIdList == NULL) return cloneString("wild type"); /* Loop through each gene adding information to html. */ html = dyStringNew(0); for (geneId = geneIdList; geneId != NULL; geneId = geneId->next) { char *geneName; struct slName *alleleList, *allele; int alleleCount; boolean needsSlash = FALSE; /* Get gene name. */ sqlSafef(query, sizeof(query), "select name from gene where id='%s'", geneId->name); geneName = sqlQuickString(conn, query); if (geneName == NULL) internalErr(); /* Process each allele of gene. */ sqlSafef(query, sizeof(query), "select allele.name from genotypeAllele,allele " "where genotypeAllele.genotype=%d " "and genotypeAllele.allele = allele.id " "and allele.gene=%s" , genotypeId, geneId->name); alleleList = sqlQuickList(conn, query); alleleCount = slCount(alleleList); for (allele = alleleList; allele != NULL; allele = allele->next) { char *simplifiedAllele = getSimplifiedAllele(geneName, allele->name); int repCount = 1, rep; if (alleleCount == 1) repCount = 2; for (rep = 0; rep < repCount; ++rep) { if (needsSlash) dyStringAppendC(html, '/'); else needsSlash = TRUE; dyStringAppend(html, geneName); dyStringPrintf(html, "<SUP>%s</SUP>", simplifiedAllele); } freeMem(simplifiedAllele); } if (geneId->next != NULL) dyStringAppendC(html, ' '); slFreeList(&alleleList); freeMem(geneName); } slFreeList(&geneIdList); return dyStringCannibalize(&html); } static struct captionElement *makePaneCaptionElements( struct sqlConnection *conn, struct slInt *imageList) /* Make list of all caption elements */ { struct slInt *image; struct captionElement *ceList = NULL, *ce; for (image = imageList; image != NULL; image = image->next) { int paneId = image->val; struct slName *geneList = geneProbeList(conn, paneId); struct slName *genbankRawList = visiGeneGenbank(conn, paneId); struct slName *genbankUrlList = wrapUrlList(genbankRawList, genbankRawList, "https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?" "cmd=Search&db=Nucleotide&term=%s&doptcmdl=GenBank&tool=genome.ucsc.edu"); struct slName *probeList = getProbeList(conn, paneId); ce = captionElementNew(paneId, "Gene", makeCommaSpacedList(geneList)); ce->hasHtml = TRUE; slAddHead(&ceList, ce); ce = captionElementNew(paneId, "Probe", makeCommaSpacedList(probeList)); ce->hasHtml = TRUE; slAddHead(&ceList, ce); ce = captionElementNew(paneId, "GenBank", makeCommaSpacedList(genbankUrlList)); slAddHead(&ceList, ce); ce->hasHtml = TRUE; ce = captionElementNew(paneId, "Organism", visiGeneOrganism(conn, paneId)); slAddHead(&ceList, ce); ce = captionElementNew(paneId, "Sex", naForNull(visiGeneSex(conn, paneId))); slAddHead(&ceList, ce); ce = captionElementNew(paneId, "Strain", naForNull(visiGeneStrain(conn, paneId))); slAddHead(&ceList, ce); ce = captionElementNew(paneId, "Genotype", naForNull(visiGeneHypertextGenotype(conn, paneId))); ce->hasHtml = TRUE; slAddHead(&ceList, ce); ce = captionElementNew(paneId, "Stage", visiGeneStage(conn, paneId, TRUE)); slAddHead(&ceList, ce); ce = captionElementNew(paneId, "Body Part", naForNull(visiGeneBodyPart(conn, paneId))); slAddHead(&ceList, ce); addExpressionInfo(conn, paneId, &ceList); ce = captionElementNew(paneId, "Section Type", naForNull(visiGeneSliceType(conn, paneId))); slAddHead(&ceList, ce); ce = captionElementNew(paneId, "Permeablization", naForNull(visiGenePermeablization(conn, paneId))); } slReverse(&ceList); return ceList; } static int nonTagStrlen(char *s) /* Count up string length excluding everything between '<' and '>' * Since this is a non-critical function just for layout purposes * it is simple, not dealing with corner cases like characters in * quotes. */ { char c; int count = 0; boolean inTag = FALSE; while ((c = *s++) != 0) { if (inTag) { if (c == '>') inTag = FALSE; } else { if (c == '<') inTag = TRUE; else count += 1; } } return count; } static void printCaptionElements(struct sqlConnection *conn, struct captionElement *captionElements, struct slInt *imageList) /* Print out caption elements - common elements first and then * pane-specific ones. */ { struct captionBundle *bundleList, *bundle; struct slRef *ref; struct captionElement *ce; int bundleCount; int maxCharsInLine = 70; bundleList = captionElementBundle(captionElements, imageList); bundleCount = slCount(bundleList); for (bundle = bundleList; bundle != NULL; bundle = bundle->next) { int charsInLine = 0, charsInEl; if (bundleCount > 1) printf("<HR>\n"); if (bundle->image != 0) { char *label = visiGenePaneLabel(conn, bundle->image); if (label != NULL) printf("<B>Pane %s</B><BR>\n", label); } else if (bundleCount > 1) { printf("<B>All Panes</B><BR>\n"); } for (ref = bundle->elements; ref != NULL; ref = ref->next) { ce = ref->val; charsInEl = strlen(ce->type) + 2; if (ce->hasHtml) charsInEl += nonTagStrlen(ce->value); else charsInEl += strlen(ce->value); if (charsInLine != 0) { if (charsInLine + charsInEl > maxCharsInLine ) { printf("<BR>\n"); charsInLine = 0; } else if (charsInLine != 0) printf(" "); } printf("<B>%s:</B> ", ce->type); if (ce->hasHtml) printf("%s", ce->value); else htmTextOut(stdout, ce->value); charsInLine += charsInEl; } if (charsInLine != 0) printf("<BR>\n"); } if (bundleCount > 1) printf("<HR>\n"); } static int visiGeneForwardedImageFile(struct sqlConnection *conn, int imageFile) /* Given imageFile ID, return ID of imageFile with better * caption info. If no such better info, just return zero. */ { char query[256]; sqlSafef(query, sizeof(query), "select toIf from imageFileFwd where fromIf = %d " , imageFile); return sqlQuickNum(conn, query); } static int vgForwardedImage(struct sqlConnection *conn, int image) /* Return id of image with better caption information if available. * Otherwise return zero. We are working in image ids instead of * imageFile ids only because much of the software works off image ids. */ { int imageFile = visiGeneImageFile(conn, image); int forwardedImage = 0; int forwardedImageFile = visiGeneForwardedImageFile(conn, imageFile); if (forwardedImageFile) { char query[256]; sqlSafef(query, sizeof(query), "select id from image where imageFile=%d", forwardedImageFile); forwardedImage = sqlQuickNum(conn, query); } return forwardedImage; } static void showSource(struct sqlConnection *conn, int id) /* Put up source info for id if available. */ { char *itemUrl = visiGeneItemUrl(conn, id); if (itemUrl != NULL) { printf("<B>source:</B> "); char *source = visiGeneSubmissionSource(conn, id); if (sameString(itemUrl,"")) printf("%s ", source); else { printf("<A HREF=\""); printf(itemUrl, visiGeneSubmitId(conn, id)); printf("\" target=_blank>%s</A> ", source); } } } static void showAcknowledgement(struct sqlConnection *conn, int id) /* Print acknowledgement info if any. */ { char *acknowledgement = visiGeneAcknowledgement(conn, id); if (acknowledgement != NULL) printf("<B>Acknowledgements:</B> %s<BR>\n", acknowledgement); } void fullCaption(struct sqlConnection *conn, int id) /* Print information about image. */ { char *publication, *copyright; char *caption = NULL; int imageFile = -1; struct slInt *imageList; int oldId = 0; struct captionElement *captionElements; int forwardedId = vgForwardedImage(conn, id); if (forwardedId) { oldId = id; id = forwardedId; } caption = visiGeneCaption(conn, id); imageFile = visiGeneImageFile(conn, id); showSource(conn, oldId); showSource(conn, id); publication = visiGenePublication(conn,id); if (publication != NULL) { char *pubUrl = visiGenePubUrl(conn,id); printf("<B>Reference:</B> "); if (pubUrl != NULL && pubUrl[0] != 0) printf("<A HREF=\"%s\" target=_blank>%s</A>", pubUrl, publication); else { printf("%s", naForEmpty(publication)); } printf("<BR>\n"); } printf("<B>Year:</B> %d ", visiGeneYear(conn,id)); printf("<B>Contributors:</B> %s<BR>\n", naForNull(visiGeneContributors(conn,id))); if (caption != NULL) { printf("<B>Notes:</B> %s<BR>\n", caption); freez(&caption); } imageList = visiGeneImagesForFile(conn, imageFile); captionElements = makePaneCaptionElements(conn, imageList); printCaptionElements(conn, captionElements, imageList); copyright = visiGeneCopyright(conn, id); if (copyright != NULL) printf("<B>Copyright:</B> %s<BR>\n", copyright); showAcknowledgement(conn, oldId); showAcknowledgement(conn, id); printf("<BR>\n"); }