e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/inc/visiGene.h src/hg/inc/visiGene.h index 34def84..b629b43 100644 --- src/hg/inc/visiGene.h +++ src/hg/inc/visiGene.h @@ -1,160 +1,163 @@ /* visiGene.h - Interface to visiGene database. * The id that almost every routine uses is the image.id * field. */ +/* Copyright (C) 2006 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #ifndef VISIGENE_H #define VISIGENE_H int visiGeneImageFile(struct sqlConnection *conn, int id); /* Return image file ID associated with image ID. A file * con contain multiple images. */ struct slInt *visiGeneImagesForFile(struct sqlConnection *conn, int imageFile); /* Given image file ID, return list of all associated image IDs. */ char *visiGenePaneLabel(struct sqlConnection *conn, int id); /* Return label for pane of this image in file if any, NULL if none. * FreeMem this when done. */ boolean visiGeneImageSize(struct sqlConnection *conn, int id, int *imageWidth, int *imageHeight); /* Get width and height of image with given id. * Return FALSE with warning if not found. */ char *visiGeneFullSizePath(struct sqlConnection *conn, int id); /* Fill in path for full image visiGene of given id. FreeMem * this when done */ char *visiGeneThumbSizePath(struct sqlConnection *conn, int id); /* Fill in path for thumbnail image (~200x200) visiGene of given id. * FreeMem when done. */ char *visiGeneOrganism(struct sqlConnection *conn, int id); /* Return binomial scientific name of organism associated with given image. * FreeMem this when done. */ char *visiGeneStage(struct sqlConnection *conn, int id, boolean doLong); /* Return string describing growth stage of organism. The description * will be 5 or 6 characters wide if doLong is false, and about * 20 characters wide if it is true. FreeMem this when done. */ struct slName *visiGeneGeneName(struct sqlConnection *conn, int id); /* Return list of gene names - HUGO if possible, RefSeq/GenBank, etc if not. * slNameFreeList this when done. */ struct slName *visiGeneRefSeq(struct sqlConnection *conn, int id); /* Return list of RefSeq accessions or n/a if none available. * slNameFreeList this when done. */ struct slName *visiGeneGenbank(struct sqlConnection *conn, int id); /* Return list of Genbank accessions or n/a if none available. * slNameFreeList this when done. */ struct slName *visiGeneUniProt(struct sqlConnection *conn, int id); /* Return list of UniProt accessions or n/a if none available. * slNameFreeList this when done. */ char *visiGeneSubmitId(struct sqlConnection *conn, int id); /* Return submitId for image. (Internal id for data set) * FreeMem this when done. */ char *visiGeneBodyPart(struct sqlConnection *conn, int id); /* Return body part if any. FreeMem this when done. */ char *visiGeneSex(struct sqlConnection *conn, int id); /* Return sex if known. FreeMem this when done. */ char *visiGeneStrain(struct sqlConnection *conn, int id); /* Return strain of organism if any. FreeMem this when done. */ struct slName *visiGeneGenotypes(struct sqlConnection *conn, int id); /* Return list of genotypes. A genotype is either "wild type" * or gene:allele. slFreeList this when done. */ char *visiGeneSliceType(struct sqlConnection *conn, int id); /* Return slice type if any. FreeMem this when done. */ char *visiGeneFixation(struct sqlConnection *conn, int id); /* Return fixation conditions if any. FreeMem this when done.*/ char *visiGeneEmbedding(struct sqlConnection *conn, int id); /* Return fixation conditions if any. FreeMem this when done.*/ char *visiGenePermeablization(struct sqlConnection *conn, int id); /* Return permeablization conditions if any. FreeMem this when done.*/ char *visiGeneCaption(struct sqlConnection *conn, int id); /* Return free text caption if any. FreeMem this when done. */ char *visiGeneContributors(struct sqlConnection *conn, int id); /* Return comma-separated list of contributors in format Kent W.H, Wu F.Y. * FreeMem this when done. */ int visiGeneYear(struct sqlConnection *conn, int id); /* Return year of publication. */ char *visiGenePublication(struct sqlConnection *conn, int id); /* Return name of publication associated with image if any. * FreeMem this when done. */ char *visiGenePubUrl(struct sqlConnection *conn, int id); /* Return url of publication associated with image if any. * FreeMem this when done. */ char *visiGeneSetUrl(struct sqlConnection *conn, int id); /* Return contributor url associated with image set if any. * FreeMem this when done. */ char *visiGeneItemUrl(struct sqlConnection *conn, int id); /* Return contributor url associated with this image. * Substitute in submitId for %s before using. May be null. * FreeMem when done. */ char *visiGeneAbUrl(struct sqlConnection *conn, int id); /* Return contributor antibody url. * Substitute in submitId for %s before using. May be null. * FreeMem when done. */ char *visiGeneAcknowledgement(struct sqlConnection *conn, int id); /* Return acknowledgement if any, NULL if none. * FreeMem this when done. */ char *visiGeneSubmissionSource(struct sqlConnection *conn, int id); /* Return name of submission source. */ char *visiGeneCopyright(struct sqlConnection *conn, int id); /* Return copyright statement if any, NULL if none. * FreeMem this when done. */ enum visiGeneSearchType { vgsNone = 0, vgsExact = 1, vgsPrefix = 2, vgsLike = 3, }; struct slInt *visiGeneSelectNamed(struct sqlConnection *conn, char *name, enum visiGeneSearchType how); /* Return ids of images that have probes involving gene that match name. */ struct slInt *visiGeneSelectRefSeq(struct sqlConnection *conn, char *acc); /* Return ids of images that have probes involving refSeq mRNA seq. */ struct slInt *visiGeneSelectLocusLink(struct sqlConnection *conn, char *id); /* Return ids of images that have probes involving locusLink (entrez gene) * id. */ struct slInt *visiGeneSelectGenbank(struct sqlConnection *conn, char *acc); /* Return ids of images that have probes involving genbank accessioned * sequence */ struct slInt *visiGeneSelectUniProt(struct sqlConnection *conn, char *acc); /* Return ids of images that have probes involving UniProt accessioned * sequence. */ char *vgGeneNameFromId(struct sqlConnection *conn, int geneId); /* Return gene name associated with gene ID - HUGO if possible, * RefSeq/GenBank, etc if not. You can freeMem this when done. */ #endif /* VISIGENE_H */