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 /* unfin - things to help handle unfinished (fragmented) DNA sequences). */ 00007 #ifndef UNFIN_H 00008 #define UNFIN_H 00009 00010 enum {contigPad = 800,}; 00011 /* How may N's between contigs. */ 00012 00013 struct contigTree 00014 /* A hierarchical structure of contigs. A forest of these is 00015 * maintained by the system. (No need to free these.) */ 00016 { 00017 struct contigTree *next; /* Sibling. */ 00018 struct contigTree *children; /* Sub-contigs. */ 00019 struct contigTree *parent; /* Parent of contig. */ 00020 char *id; /* Ensemble ID. (Not allocated here.) */ 00021 int submitLength; /* Number of bases in submission. */ 00022 int submitOffset; /* Offset relative to parent in genBank submission. */ 00023 int orientation; /* +1 or -1. Strand relative to parent.*/ 00024 int corder; /* Order of contig in genBank submission. */ 00025 int browserOffset; /* Offset relative to parent for browser, ordered by ensemble, with 00026 * ensContigPad N's between each contig. */ 00027 int browserLength; /* Size including padding. */ 00028 }; 00029 00030 #endif /* UNFIN_H */ 00031
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