00001 /***************************************************************************** 00002 * Copyright (C) 2000 Jim Kent. This source code may be freely used * 00003 * for personal, academic, and non-profit purposes. Commercial use * 00004 * permitted only by explicit agreement with Jim Kent (jim_kent@pacbell.net) * 00005 *****************************************************************************/ 00006 /* hgdb - Stuff to access human genome database. */ 00007 #ifndef HGDB_H 00008 #define HGDB_H 00009 00010 char *hgdbRootDir(); 00011 /* Return root directory of human genome database. */ 00012 00013 struct dnaSeq *hgdbRnaSeq(char *accession); 00014 /* Return mRNA or EST sequence from an accession number. */ 00015 00016 struct fof *hgdbRnaFof(); 00017 /* Return index for RNA sequences. */ 00018 00019 struct dnaSeq *hgdbShortSeq(char *accession); 00020 /* Return mRNA, EST, BACend or STS sequence based on 00021 * accession number. */ 00022 00023 struct fof *hgdbShortFof(); 00024 /* Return index for short sequences. */ 00025 00026 struct dnaSeq *hgdbFinishedSeq(char *accession); 00027 /* Return finished BAC sequence. */ 00028 00029 struct dnaSeq *hgdbUnfinishedSeq(char *accession); 00030 /* Return unfinished BAC sequence. May be in 00031 * several contigs (dnaSeq returned may be a list.) */ 00032 00033 struct dnaSeq *hgdbGetSeq(char *accession); 00034 /* Return sequence from any source. */ 00035 00036 char *hgdbKeyText(char *accession); 00037 /* Get key-value lines about accession number. */ 00038 00039 struct fof *hgdbKeyFof(); 00040 /* Return index for key-values indexed by accession. */ 00041 00042 boolean hgdbSmallKey(char *accession, char *key, char *valBuf, int valBufSize); 00043 /* Get value of small key. Returns FALSE if key doesn't exist. */ 00044 00045 #endif /* HGDB_H */ 00046
1.5.2