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/inc/spDb.h src/hg/inc/spDb.h
index 45892b6..c919fad 100644
--- src/hg/inc/spDb.h
+++ src/hg/inc/spDb.h
@@ -1,244 +1,244 @@
/* Copyright (C) 2008 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. */
/* Routines to get data from relational version of
* SwissProt database. This database is generated
* from SwissProt flat files by the spToDb program.
*
* Most of the routines take the primary SwissProt accession
* as input, and will abort if this is not found in the database.
* Use spIsPrimaryAcc to check for existence first if you want
* to avoid this. The routines that return strings need them
* free'd when you are done, and the routines that return lists
* need them spFreeList'd when done unless you don't mind memory
* leaks. */
#ifndef SPDB_H
#define SPDB_H
#ifndef JKSQL_H
#include "jksql.h"
#endif
#define UNIPROT_DB_NAME "uniProt"
#define PROTEOME_DB_NAME "proteome"
typedef char SpAcc[20]; /* Enough space for accession and 0 terminator. */
struct spFeature
/* A swissProt feature - that is an annotation attatched to
* part of a protein. */
{
struct spFeature *next;
int start; /* Start coordinate (zero-based) */
int end; /* End coordinate (non-inclusive) */
int featureClass; /* ID of featureClass */
int featureType; /* ID of featureType */
char softEndBits;/* 1 for start <, 2 for start ?, 4 for end >, 8 for end ? */
};
#define spFeatureStartLess 1
#define spFeatureStartFuzzy 2
#define spFeatureEndGreater 4
#define spFeatureEndFuzzy 8
struct spCitation
/* A SwissProt citation of a reference. Generally
* you'll just grab the reference id out of this.
* If you love SwissProt RP and RC lines you might use
* the other fields. */
{
struct spCitation *next;
int id; /* Database (not SwissProt) ID */
SpAcc acc; /* SwissProt accession. */
int reference; /* ID in reference table. */
int rp; /* Id in rp table. */
};
boolean spIsPrimaryAcc(struct sqlConnection *conn, char *acc);
/* Return TRUE if this is a primary accession in database. */
char *spFindAcc(struct sqlConnection *conn, char *id);
/* Return primary accession given either display ID,
* primary accession, or secondary accession. Return
* NULL if not found. */
char *spAnyAccToId(struct sqlConnection *conn, char *acc);
char *spAccToId(struct sqlConnection *conn, char *acc);
/* Convert primary accession to SwissProt ID (which will
* often look something like HXA1_HUMAN. */
char *spIdToAcc(struct sqlConnection *conn, char *id);
/* Convert SwissProt ID (things like HXA1_HUMAN) to
* accession. Returns NULL if the conversion fails.
* (doesn't abort). */
char *spLookupPrimaryAccMaybe(struct sqlConnection *conn,
char *anyAcc); /* Primary or secondary accession. */
/* This will return the primary accession. It's ok to pass in
* either a primary or secondary accession. Return NULL if
* not found. */
char *spLookupPrimaryAcc(struct sqlConnection *conn,
char *anyAcc); /* Primary or secondary accession. */
/* This will return the primary accession. It's ok to pass in
* either a primary or secondary accession. ErrAbort if
* not found */
char *spDescription(struct sqlConnection *conn, char *acc);
/* Return protein description. FreeMem this when done. */
boolean spIsCurated(struct sqlConnection *conn, char *acc);
/* Return TRUE if it is a curated entry. */
int spAaSize(struct sqlConnection *conn, char *acc);
/* Return number of amino acids. */
int spMolWeight(struct sqlConnection *conn, char *acc);
/* Return molecular weight in daltons. */
char *spCreateDate(struct sqlConnection *conn, char *acc);
/* Return creation date in YYYY-MM-DD format. FreeMem
* this when done. */
char *spSeqDate(struct sqlConnection *conn, char *acc);
/* Return sequence last update date in YYYY-MM-DD format. FreeMem
* this when done. */
char *spAnnDate(struct sqlConnection *conn, char *acc);
/* Return annotation last update date in YYYY-MM-DD format. FreeMem
* this when done. */
char *spOrganelle(struct sqlConnection *conn, char *acc);
/* Return text description of organelle. FreeMem this when done.
* This may return NULL if it's not an organelle. */
struct slName *spGeneToAccs(struct sqlConnection *conn,
char *gene, int taxon);
/* Get list of accessions associated with this gene. If
* taxon is zero then this will return all accessions, if
* taxon is non-zero then it will restrict it to a single
* organism with that taxon ID. */
struct slName *spGenes(struct sqlConnection *conn, char *acc);
/* Return list of genes associated with accession */
struct slName *spTaxons(struct sqlConnection *conn, char *acc);
/* Return list of taxons associated with accession */
struct slName *spBinomialNames(struct sqlConnection *conn, char *acc);
/* Return list of scientific names of organisms
* associated with accessoin */
int spTaxon(struct sqlConnection *conn, char *acc);
/* Return taxon of first organism associated with accession. */
int spBinomialToTaxon(struct sqlConnection *conn, char *name);
/* Return taxon associated with binomial (Mus musculus) name. */
int spCommonToTaxon(struct sqlConnection *conn, char *commonName);
/* Return taxon ID associated with common (mouse) name or
* binomial name. */
char *spTaxonToBinomial(struct sqlConnection *conn, int taxon);
/* Return Latin binomial name associated with taxon. */
char *spTaxonToCommon(struct sqlConnection *conn, int taxon);
/* Given NCBI common ID return first common name associated
* with it if possible, otherwise return scientific name. */
struct slName *spKeywords(struct sqlConnection *conn, char *acc);
/* Return list of keywords for accession. */
struct slName *spKeywordSearch(struct sqlConnection *conn, char *keyword,
int taxon);
/* Return list of accessions that use keyword. If taxon is non-zero
* then restrict accessions to given organism. */
struct slName *slComments(struct sqlConnection *conn,
char *acc, /* Primary accession. */
char *type); /* Comment type name, NULL for all comments. */
/* Get list of comments associated with accession.
* If optional type parameter is included it should be
* something in the commentType table. Some good types
* are: DISEASE, FUNCTION, "SUBCELLULAR LOCATION" etc. */
struct slName *slCommentTypes(struct sqlConnection *conn);
/* Get list of comment types in database. */
char *spCommentType(struct sqlConnection *conn, int typeId);
/* Look up text associated with typeId. freeMem result when done. */
char *spCommentVal(struct sqlConnection *conn, int valId);
/* Look up text associated with valId. freeMem result when done. */
struct slName *spExtDbAcc1List(struct sqlConnection *conn, char *acc,
char *db);
/* Get list of accessions from external database associated with this
* swissProt entity. The db parameter can be anything in the
* extDb table. Some common external databases are 'EMBL' 'PDB' 'Pfam'
* 'Interpro'. */
struct slName *spEmblAccs(struct sqlConnection *conn, char *acc);
/* Get list of EMBL/Genbank mRNAaccessions associated with this. */
struct slName *spPdbAccs(struct sqlConnection *conn, char *acc);
/* Get list of PDB associations associated with this. */
char *spAccFromEmbl(struct sqlConnection *conn, char *acc);
/* Get SwissProt accession associated with EMBL mRNA. */
struct spFeature *spFeatures(struct sqlConnection *conn, char *acc,
int classId, /* Feature class ID, 0 for all */
int typeId); /* Feature type ID, 0 for all */
/* Get feature list. slFreeList this when done. */
char *spFeatureTypeName(struct sqlConnection *conn, int featureType);
/* Return name associated with featureType */
int spFeatureTypeId(struct sqlConnection *conn, char *name);
/* Return feature type id associated with given name. */
char *spFeatureClassName(struct sqlConnection *conn, int featureClass);
/* Return name associated with featureClass. */
int spFeatureClassId(struct sqlConnection *conn, char *name);
/* Return feature class id associated with given name. */
struct spCitation *spCitations(struct sqlConnection *conn, char *acc);
/* Get list of citations to references associated with this
* accession. You can slFreeList this when done. */
char *spRefTitle(struct sqlConnection *conn, int refId);
/* Get title of reference. This can be NULL legitimately. */
struct slName *spRefAuthors(struct sqlConnection *conn, int refId);
/* Get list of authors associated with reference. */
char *spRefCite(struct sqlConnection *conn, int refId);
/* Get journal/page/etc of reference. */
char *spRefPubMed(struct sqlConnection *conn, int refId);
/* Get PubMed id. May be NULL legitimately. */
struct slName *spRefToAccs(struct sqlConnection *conn, int refId);
/* Get list of accessions associated with reference. */
char *oldSpDisplayId(char *newSpDisplayId);
/* Convert from new Swiss-Prot display ID to old display ID */
char *newSpDisplayId(char *oldSpDisplayId);
/* Convert from old Swiss-Prot display ID to new display ID */
char *uniProtFindPrimAcc(char *id);
/* Return primary accession given an alias. */
char *uniProtFindPrimAccFromGene(char *gene, char *db);
/* Return primary accession given gene name.
* NULL if not found. */
struct slName *spProteinEvidence(struct sqlConnection *conn, char *acc);
/* Get list of evidence that protein exists for accession. There will be at least one. */
#endif /* SPDB_H */