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 /* flydna.h - routines for accessing fly genome and cDNA sequences. */ 00007 00008 #ifndef FLYDNA_H 00009 #define FLYDNA_H 00010 00011 void flyLoadNt4Genome(struct nt4Seq ***retNt4Seq, int *retNt4Count); 00012 /* Load up entire packed fly genome into memory. */ 00013 00014 void flyFreeNt4Genome(struct nt4Seq ***pNt4Seq); 00015 /* Free up packed fly genome. */ 00016 00017 void flyChromNames(char ***retNames, int *retNameCount); 00018 /* Get list of fly chromosome names. */ 00019 00020 boolean flyCdnaSeq(char *name, struct dnaSeq **retDna, struct wormCdnaInfo *retInfo); 00021 /* Get a single fly cDNA sequence. Optionally (if retInfo is non-null) get additional 00022 * info about the sequence. */ 00023 00024 char *flyFeaturesDir(); 00025 /* Return the features directory. (Includes trailing slash.) */ 00026 00027 FILE *flyOpenGoodAli(); 00028 /* Opens good alignment file and reads signature. 00029 * (You can then cdaLoadOne() it.) */ 00030 00031 #endif /* FLYDNA_H */ 00032
1.5.2