987241ea99c99b93aea51bb63bdf579f927e9d2b kent Wed Oct 7 13:46:09 2015 -0700 Fixing copyright on some old essentially public domain files. diff --git src/inc/ens.h src/inc/ens.h index b48dfa4..6ef6875 100644 --- src/inc/ens.h +++ src/inc/ens.h @@ -1,168 +1,167 @@ -/***************************************************************************** - * Copyright (C) 2000 Jim Kent. This source code may be freely used * - * for personal, academic, and non-profit purposes. Commercial use * - * permitted only by explicit agreement with Jim Kent (jim_kent@pacbell.net) * - *****************************************************************************/ -/* ens.h - Interface to ensEMBL database. */ +/* ens.h - Interface to ensEMBL database. + * + * This file is copyright 2000 Jim Kent, but license is hereby + * granted for all use - public, private or commercial. */ + #ifndef ENS_H #define ENS_H #ifndef DNAUTIL_H #include "dnautil.h" #endif #ifndef DLIST_H #include "dlist.h" #endif #ifndef UNFIN_H #include "unfin.h" #endif struct ensAnalysis /* A category of a feature. */ { struct ensAnalysis *next; /* Next in list */ int id; /* Unique id for this feature type. */ char *db; /* Database used. */ char *dbVersion; /* Version of database. */ char *program; /* Program used. */ char *programVersion; /* Version of program. */ char *gffSource; /* Source field from GFF. */ char *gffFeature; /* Feature field from GFF. */ char *shortName; /* 15 letter summary. */ }; struct ensFeature /* An ensemble feature. */ { struct ensFeature *next; /* Next in list. */ struct contigTree *tContig; /* Name of target (genomic) sequence */ int tStart, tEnd; /* Position in genomic sequence. */ int score; /* Score (I don't know units) */ int orientation; /* +1 or -1. Strand relative to contig. */ int type; /* Index into analysis table describing type of feature. */ char *typeName; /* Subtype of type really. May be NULL. Not alloced here. */ int qStart, qEnd; /* Query (cDNA, protein, etc.) sequence position. */ char *qName; /* Query sequence name. */ }; struct ensExon /* An ensemble exon. Since multiple transcripts can * use the same exon, this is stored as a reference on * a dlList in the transcript and as an instance in the * slList in the gene. */ { struct ensExon *next; /* Next in list (in ensGene) */ char *id; /* Ensemble ID (not allocated here). */ struct contigTree *contig; /* Contig within clone this is in. (Not allocated here).*/ char phase; /* AKA Frame - codon position of 1st base. */ char endPhase; /* Codon position of last base. */ int orientation; /* +1 or -1. Strand relative to contig. */ int seqStart; /* Start position. */ int seqEnd; /* End position. */ }; struct ensTranscript /* A transcript (isoform) of a gene. */ { struct ensTranscript *next; /* Next in list. */ char *id; /* Ensemble ID. */ struct dlList *exonList; /* Ordered list of exon references. */ struct ensExon *startExon; /* Reference to first coding exon. */ struct ensExon *endExon; /* Reference to last coding exon. */ int startSeq, endSeq; /* Start, end of coding region. */ }; struct ensGene /* A gene. A collection of exons and how they * are put together. */ { struct ensGene *next; /* Next in list. */ char *id; /* Ensemble ID with many zeroes. */ struct ensTranscript *transcriptList; /* List of ways to transcribe and splice. */ struct hash *exonIdHash; /* Fast lookup of exons from exon ids. */ struct ensExon *exonList; /* Total exons in all transcripts. */ }; void ensGetAnalysisTable(struct ensAnalysis ***retTable, int *retCount); /* Returns analysis table (array of different things a feature can be). * No need to free this, it's managed by system. */ struct dnaSeq *ensDnaInBacRange(char *clone, int start, int end, enum dnaCase dnaCase); /* Get DNA for range of clone in browser coordinates, including NNNs between contigs. */ struct dnaSeq *ensDnaInBac(char *clone, enum dnaCase dnaCase); /* Get DNA for clone in browser coordinates, including NNNs between contigs. */ struct ensFeature *ensGetFeature(char *featureId); /* Get a single feature of the given ID. Returns NULL if no such feature. */ struct ensFeature *ensFeaturesInBac(char *clone); /* Get list of features associated with BAC clone. */ struct ensFeature *ensFeaturesInBacRange(char *clone, int start, int end); /* Get list of features associated a section of BAC clone. */ void ensFreeFeature(struct ensFeature **pFeature); /* Free up a single feature. */ void ensFreeFeatureList(struct ensFeature **pFeatureList); /* Free up a list of features. */ struct slName *ensGeneNamesInBac(char *bacName); /* Get list of all gene names in bac. */ struct ensGene *ensGetGene(char *geneName); /* Get named gene. This can also be viewed as a list of one genes. */ struct ensGene *ensGenesInBac(char *bacName); /* Get list of all genes in bac. */ struct ensGene *ensGenesInBacRange(char *bacName, int start, int end); /* Get list of genes in a section of a BAC clone. The start/end are * in browser coordinates. */ void ensFreeGene(struct ensGene **pGene); /* Free up a single gene. */ void ensFreeGeneList(struct ensGene **pGeneList); /* Free up a list of genes. */ void ensParseContig(char *combined, char retBac[32], int *retContig); /* Parse combined bac.contig into two separate values. */ int ensBrowserCoordinates(struct contigTree *contig, int x); /* Return x in browser coordinates. */ int ensSubmitCoordinates(struct contigTree *contig, int x); /* Return x in GenBank/EMBL submission coordinates. */ int ensBacBrowserLength(char *clone); /* Return size of clone in browser coordinate space. */ int ensBacSubmitLength(char *clone); /* Return size of clone in GenBank/EMBL submission coordinate space. */ struct contigTree *ensBacContigs(char *bacId); /* Return contigTree rooted at Bac. Do not free this or modify it, * the system takes care of it. */ struct contigTree *ensGetContig(char *contigId); /* Return contig associated with contigId. Do not free this, system * takes care of it. */ void ensTranscriptBounds(struct ensTranscript *trans, int *retStart, int *retEnd); /* Find beginning and end of transcript in browser coordinates. */ void ensGeneBounds(struct ensGene *gene, int *retStart, int *retEnd); /* Find beginning and end of gene in browser coordinates. */ #endif /* ENS_H */